#!/bin/tcsh
#
# 
#
#####################################################################
# work out what cell cycle/ arrest/cell size regulation/ annotations should be made for long and short cells
# what should the cell cycle phenotype be  and how related to cell size regulation FYPO:0000059 abnormal mitotic cell cycle progression

# all elongated should be some dot of inviable after spore germination (should everything?)
# after updated check lists against advanced query (add to to do list)
# remover some cells don't germinate, even for WT….
# ask JAcky for general conditions
# add cytoskeletal and HU stuff
# check all PERL has echo...
# checks required
# Jacky approve
# check that the description and the substation match
# check that the number of terms in the perl is correct
# check that penetrance and specificity included whenever possible
# check all ***** removed
# check all annotation_extension removed
# remove degrees sign in raw date (number 5)
# query inviable after spore germination, multiple cell divisions, abnormal morphology (CELL PHENOTYPE)has_output microcolony_formation (would want it to be annotated to this, is it?)
# other lines to fix
# SPAC1006.03c
# SPAC15E1.04
# long low penetrance….should these have a population phenotype that specifies "occasionally long"
# check that population of germinated spores/ is a chile of vegetative population (and the same for cell phenotype)

#####################################################################
# PMID:23697806
# conditions 
# PECO:0000005 standard temperature 25-32
# PECO:0000004 high temperature  (over 32)
# pentrance 
# high FYPO_EXT:0000001 
# low  FYPO_EXT:0000003

# expressivity 
# high FYPO_EXT:0000001 
# low  FYPO_EXT:0000003

#####################################################################

# 1.
# VIABLE WT cells at 25-32- poor germination
# broad classifier: WT
# cell phenotype
# FYPO:0002177 viable vegetative cell with normal cell morphology  (high penetrance)
# FYPO:0000582 decreased rate of spore germination (NOT ADDED after discussion with Jacky as not quantified)
# population phenotype
# FYPO:0002195 normal morphology viable vegetative cell population

echo "1." 
perl -pi -e 's/VIABLE WT cells at 25-32- poor germination/FYPO:0002177,PECO:0000005,has_penetrance(FYPO_EXT:0000001)| FYPO:0002195,PECO:0000005/g' tab_phenotype.csv


# 2.
# VIABLE WT cells at 32 cells slightly misshapen at 25
# broad classifier: misshapen weak viable
# https://sourceforge.net/p/pombase/fission-yeast-phenotype/825/
# cell phenotype
# FYPO:0001510 viable vegetative cell, abnormal cell shape, normal cell size (low expressivity) (high penetrance)
# poplulation phenotype
# FYPO:0002198 viable vegetative cell population with abnormal cell shape

echo  "2."
perl -pi -e 's/VIABLE WT cells at 32 cells slightly misshapen at 25/FYPO:0001510,PECO:0000005,has_expressivity(FYPO_EXT:0000003),has_penetrance(FYPO_EXT:0000001)| FYPO:0002198,PECO:0000005/g' tab_phenotype.csv

# 3.
# VIABLE WT cells at 25-32- some dead cells (1)
# broad classifier: WT
# https://sourceforge.net/p/pombase/fission-yeast-phenotype/824/
# cell phenotype
# FYPO:0002177 viable cell with normal cell morphology (high penetrance)
# poplulation phenotype
# FYPO:0002195 normal morphology viable vegetative cell population

echo "3." 
perl -pi -e 's/VIABLE WT cells at 25-32- some dead cells/FYPO:0002177,PECO:0000005,has_penetrance(FYPO_EXT:0000001)| FYPO:0002195,PECO:0000005/g' tab_phenotype.csv

# 4.
# VIABLE WT cells at 25-32- dead cells causes wavy edges to colony
# broad classifier: WT
# https://sourceforge.net/p/pombase/fission-yeast-phenotype/824/
# cell phenotype
# FYPO:0002177 viable cell with normal cell morphology (high penetrance)
# FYPO:0001489 inviable vegetative cell (low penetrance)
# poplulation phenotype
# FYPO wavy edged colony? (bnormal colony morphology
# FYPO NEW? mixed population of viable normal morphology cells and some dead cells

echo "3." 
perl -pi -e 's/VIABLE WT cells at 25-32- dead cells causes wavy edges to colony/FYPO:0002177,PECO:0000005,has_penetrance(FYPO_EXT:0000001)| FYPO:0001489,PECO:0000005,has_penetrance(FYPO_EXT:0000003)| FYPO:********,PECO:0000005/g' tab_phenotype.csv

# query about wavy colony edges

# 5.
# VIABLE WT cells at 25,32, many dead cells at 36°C (1)
# remove degrees sign first

# 6.
# VIABLE WT cells at 25-32" piled up" colony morphology 
# broad classifier WT
# https://sourceforge.net/p/pombase/fission-yeast-phenotype/824/
# https://sourceforge.net/p/pombase/fission-yeast-phenotype/826/ (piled up colony morphology)
# cell phenotype
# FYPO:0002177 viable vegetative cell with normal cell morphology (high penetrance)
# poplulation phenotype
# FYPO:0002195 normal morphology viable vegetative cell population FYPO:0002195 
# (cell***??????not colony)
# FYPO*NEW new piled up colony morphology
echo "6."
perl -pi -e 's/VIABLE WT cells at 25-32\" piled up\" colony morphology/FYPO:0002177,PECO:0000005| FYPO:*******,PECO:0000005| FYPO:0002195,PECO:0000005/g' tab_phenotype.csv
# *****CHECK SUBST*****

# 7
# VIABLE WT cells at 25,32, poor growth at 36 (leaving out the poor growth, after discussion with Jacky)
# broad classifier WT
# https://sourceforge.net/p/pombase/fission-yeast-phenotype/824/
# cell phenotype
# FYPO:0002177 viable vegetative cell with normal cell morphology (high penetrance)
# poplulation phenotype
# FYPO:0002195 normal morphology viable vegetative cell population (824)

echo "7."
perl -pi -e 's/VIABLE WT cells at 25-32- poor growth at 36/FYPO:0002177,PECO:0000005,has_penetrance(FYPO_EXT:0000001)| FYPO:0002195,PECO:0000005/g' tab_phenotype.csv


# 8
# VIABLE WT cells at 25,32, possibly poor germination
# broad classifier WT
# https://sourceforge.net/p/pombase/fission-yeast-phenotype/824/
# cell phenotype
# FYPO:0002177 viable cell with normal cell morphology (high penetrance)
# after discussion with JAcky, ignoring possibly poor germination
# poplulation phenotype
# FYPO:0002195 normal morphology viable vegetative cell population (824)
echo "8."
perl -pi -e 's/VIABLE WT cells at 25-32- possibly poor germination/FYPO:0002177,PECO:0000005| FYPO:0002195,PECO:0000005/g' tab_phenotype.csv


# 9
# VIABLE WT cells at 25,32, longer at 36
# ctu1 WT
# trm10 long high penetrance
# asked Jacky DIFFERENT
# cell phenotype
# FYPO:0002177 viable vegetative cell with normal cell morphology (high penetrance) (standard temperature)
# poplulation phenotype
# FYPO:0002195 normal morphology viable vegetative cell population  (standard temperature)


echo "9."
perl -pi -e 's/VIABLE WT cells at 25,32, longer at 36/FYPO:0002177,PECO:0000005,has_penetrance(FYPO_EXT:0000003)| FYPO:0002195,PECO:0000005/g' tab_phenotype.csv




# 10 asked jacky about phenotype at 36 (add this)
# VIABLE WT cells with some long cells at 25-32- long cells at 36
# https://sourceforge.net/p/pombase/fission-yeast-phenotype/858/
# long low penetrance
# cell phenotype
# FYPO:0000059 abnormal mitotic cell cycle progression (low penetrance, standard temp)
# FYPO:0001492 elongated viable vegetative cell (low penetrance, standard temp)
# population phenotype
# FYPO:0002178 viable mixed population including long cells  (standard temp)
echo "10."
perl -pi -e 's/VIABLE WT cells with some long cells at 25-32- long cells at 36/FYPO:0000059,PECO:0000005,has_penetrance(FYPO_EXT:0000003)| FYPO:0001492,PECO:0000005,has_penetrance(FYPO_EXT:0000003)| FYPO:0002178,PECO:0000005/g' tab_phenotype.csv

# 11
# VIABLE WT cells at 25,32, initially slightly misshapen 
# misshapen weak viable
# cell phenotype
# FYPO:0001510 viable vegetative cell, abnormal cell shape, normal cell size (low expressivity)
# population phenotype
# FYPO:0002198 viable vegetative cell population with abnormal cell shape (should this move down to normal size?)
echo "11."
perl -pi -e 's/VIABLE WT cells at 25-32- initially slightly misshapen/FYPO:0001510,PECO:0000005,has_expressivity(FYPO_EXT:0000003)| FYPO:0002198,PECO:0000005/g' tab_phenotype.csv

# how to capture "initially misshapen"

# 12
# VIABLE WT cells at 32- cells slightly misshapen at 25 (1)
# misshapen weak viable
# cell phenotype
# FYPO:0001510 viable vegetative cell, abnormal cell shape, normal cell size (low expressivity************)
# population phenotype
# FYPO:0002198 viable vegetative cell population with abnormal cell shape (should this move down to normal size?)
echo "12."
perl -pi -e 's/VIABLE WT cells at 32- cells slightly misshapen at 25/FYPO:0001510,PECO:0000005,has_expressivity(FYPO_EXT:0000003)| FYPO:0002198,PECO:0000005/g' tab_phenotype.csv


# 13.
# VIABLE WT cells at 32- cells slightly misshapen at 25 (10)
# misshapen weak viable
# cell phenotype
# FYPO:0001510 viable vegetative cell, abnormal cell shape, normal cell size (low expressivity)
# population phenotype
# FYPO:0002198 viable vegetative cell population with abnormal cell shape (should this move down to normal size?)

echo "13."
perl -pi -e 's/VIABLE WT cells at 32- cells slightly misshapen at 25/FYPO:0001510,PECO:0000005,has_expressivity(FYPO_EXT:0000003)| FYPO:0002198,PECO:0000005/g' tab_phenotype.csv

# 14.
# VIABLE WT cells at 25-32- slightly misshapen at 36 (1)
# misshapen weak viable
# cell phenotype
# FYPO:0002177 viable cell with normal cell morphology  (standard temp) (****CALL VEGETATIVE?)
# FYPO:0001510 viable vegetative cell, abnormal cell shape, normal cell size (low expressivity) (high temp)
# population phenotype
# FYPO:0002195 normal morphology viable vegetative cell population (standard temp)
# FYPO:0002198 viable vegetative cell population with abnormal cell shape (high temp) (low expressivity) (***SHOULD WE ADD normal size to this term????)

echo "14."
perl -pi -e 's/VIABLE WT cells at 25-32- slightly misshapen at 36/FYPO:0002177,PECO:0000005| FYPO:0001510,PECO:0000004,has_expressivity(FYPO_EXT:0000003)| FYPO:0002195,PECO:0000005| FYPO:0002198,PECO:0000004,has_expressivity(FYPO_EXT:0000003)/g' tab_phenotype.csv

# 15.
# VIABLE WT cells at 25,32, initially cells look stubby 
# broad classifier stubby
# cell phenotype
# FYPO:0002177 viable cell with normal cell morphology  (standard temp) (high penetrance) (****CALL VEGETATIVE?)
# poplulation phenotype
# FYPO:0002195 normal morphology viable vegetative cell population (standard temp)

# not quite sure how to do this one…asking Jacky *************

# 16.
# VIABLE WT cells at 25,32, initially stubby cells
# stubby

# see above

# 17.
# VIABLE WT cells at 25,32, cells misshapen, long, septated at 36
# broad classifier: long high penetrance
# https://sourceforge.net/p/pombase/fission-yeast-phenotype/824/
# cell phenotype
# FYPO:0001492 elongated viable vegetative cell (high penetrance? high temp)
# FYPO:0002177 viable cell with normal cell morphology (high penetrance, standard temperature)
# poplulation phenotype
# FYPO:0002195 normal morphology viable vegetative cell population (standard temperature)
# FYPO:0002149 elongated inviable vegetative cell population (high temperature)
# FYPO:0000059 abnormal mitotic cell cycle progression (high temperature)
echo "17."
perl -pi -e 's/VIABLE WT cells at 25-32- cells misshapen- long- septated at 36/FYPO:0002177,PECO:0000005,has_penetrance(FYPO_EXT:0000001)| FYPO:0001492,PECO:000004,has_penetrance(FYPO_EXT:0000001)| FYPO:0002195,PECO:0000005| FYPO:0002149,PECO:000004,has_penetrance(FYPO_EXT:0000001)| FYPO:0000059,PECO:000004/g' tab_phenotype.csv


# 18.
# VIABLE long cells at 25-32- cells longer at 36
# long high penetrance
# cell phenotype
# https://sourceforge.net/p/pombase/fission-yeast-phenotype/867/
# FYPO:0000059 abnormal mitotic cell cycle progression (high penetrance, standard temp)
# FYPO:0001492 elongated viable vegetative cell (high penetrance, standard temp)
# FYPO:0000059 abnormal mitotic cell cycle progression (high penetrance, high expressivity, high temp)
# FYPO:0001492 elongated viable vegetative cell (high penetrance, high expressivity  hightemp)
# population phenotype
# FYPO:0002233 viable elongated vegetative cell population   (standard temp) (867)
# FYPO:0002233 viable elongated vegetative cell population   (high temp high expressivity) (867)
echo "18."
perl -pi -e 's/VIABLE long cells at 25-32- cells longer at 36/FYPO:0000059,PECO:0000005,has_penetrance(FYPO_EXT:0000003)| FYPO:0001492,PECO:0000005,has_penetrance(FYPO_EXT:0000003)| FYPO:0000059,PECO:0000004,has_penetrance(FYPO_EXT:0000003),has_expressivity(FYPO_EXT:0000003)| FYPO:0001492,PECO:0000004,has_penetrance(FYPO_EXT:0000003),has_expressivity(FYPO_EXT:0000003)| FYPO:0002233,PECO:0000005| FYPO:0002233,PECO:0000004,has_expressivity(FYPO_EXT:0000003)/g' tab_phenotype.csv

# 19
# VIABLE WT cells at 25-32- cells slightly curved at 36
# https://sourceforge.net/p/pombase/fission-yeast-phenotype/839/
# https://sourceforge.net/p/pombase/fission-yeast-phenotype/824/
# broad classifier: curved
# cell phenotype
# FYPO:0002177 viable vegetative cell with normal morphology (standard temp, high penetrance,) 
# FYPO:0002112 curved viable cell  (high penetrance, low expressivity, high temperature)
# population phenotype
# FYPO:0002216 viable curved vegetative cell population (high temp) (low expressivity) 
# FYPO:0002195 normal morphology viable vegetative cell population (standard temp)  (824)
echo "19."
perl -pi -e 's/VIABLE WT cells at 25-32- cells slightly curved at 36/FYPO:0002177,PECO:0000005,has_penetrance(FYPO_EXT:0000001)| FYPO:0002112,PECO:0000004,has_penetrance(FYPO_EXT:0000001),has_expressivity(FYPO_EXT:0000003)| FYPO:0002216,PECO:0000004,has_expressivity(FYPO_EXT:0000003)| FYPO:0002195,PECO:0000005/g' tab_phenotype.csv

# 20. see 19
# VIABLE WT cells at 25,32, cells more curved at 36
# broad classifier: curved
echo "20."
perl -pi -e 's/VIABLE WT cells at 25-32- cells more curved at 36/FYPO:0002177,PECO:0000005,has_penetrance(FYPO_EXT:0000001)| FYPO:0002112,PECO:0000004,has_penetrance(FYPO_EXT:0000001),has_expressivity(FYPO_EXT:0000003)| FYPO:0002195,PECO:0000004,has_expressivity(FYPO_EXT:0000003)| FYPO:0002195,PECO:0000005/g' tab_phenotype.csv


# 21.
# VIABLE WT cells at 25,32, occasionally slightly curved (1)
# https://sourceforge.net/p/pombase/fission-yeast-phenotype/872/
# broad classifier curved
# cell phenotype
# FYPO:0002177 viable vegetative cell with normal morphology (standard temp, high penetrance,) 
# FYPO:0002112 curved viable cell  (low penetrance, low expressivity, standard temp)
# population phenotype
# FYPO:***** viable mixed population including curved cells (872)

echo "21."
perl -pi -e 's/VIABLE WT cells at 25-32- occasionally slightly curved/FYPO:0002177,PECO:0000005,has_penetrance(FYPO_EXT:0000001)| FYPO:0002112,PECO:0000005,has_penetrance(FYPO_EXT:0000001),has_expressivity(FYPO_EXT:0000003)| FYPO:*******,PECO:0000005/g' tab_phenotype.csv


# 22.
# VIABLE WT cells at 25,32, small colonies curved misshapen cells, often septated at 36
# haven't mentioned septated because these are viable
# curved
# cell phenotype
# FYPO:0002177 viable vegetative cell with normal morphology (standard temp, high penetrance,) 
# FYPO:0002112 curved viable cell  (high temp) (***high penetracne?)
# population phenotype
# FYPO:0002195 normal morphology viable vegetative cell population (standard temp)
# FYPO:0002216 viable curved vegetative cell population (high temp)

echo "22."
perl -pi -e 's/VIABLE WT cells at 25-32- small colonies curved misshapen cells- often septated at 36/FYPO:0002177,PECO:0000005,has_penetrance(FYPO_EXT:0000001)| FYPO:0002112,PECO:0000004,has_penetrance(FYPO_EXT:0000001)| FYPO:0002195,PECO:0000005| FYPO:0002216,PECO:0000004/g' tab_phenotype.csv


# 23.
# VIABLE WT cells at 25,32, cells curved at 36 (1)
# broad classifier: curved
# cell phenotype
# FYPO:0002177 viable vegetative cell with normal morphology (standard temp, high penetrance,) 
# FYPO:0002112 curved viable cell  (high temp) (***high penetracne?)
# population phenotype
# FYPO:0002195 normal morphology viable vegetative cell population (standard temp)
# FYPO:0002216 viable curved vegetative cell population (high temp)

echo "23."
perl -pi -e 's/VIABLE WT cells at 25-32- cells curved at 36/FYPO:0002177,PECO:0000005,has_penetrance(FYPO_EXT:0000001)| FYPO:0002112,PECO:0000004,has_penetrance(FYPO_EXT:0000001)| FYPO:0002195,PECO:0000005| FYPO:0002216,PECO:0000004/g' tab_phenotype.csv

# 24.
# VIABLE WT cells at 32, microcolonies skittle cells at 25
# broad classifier: skittle
# https://sourceforge.net/p/pombase/fission-yeast-phenotype/870/
# cell phenotype
# FYPO:0002110 viable bottle-shaped vegetative cell (standard temperature)
# FYPO:0001315 normal cell morphology during vegetative growth (high temp)
# population phenotype
# FYPO:***870 viable vegetative cell population with skittle shaped cells (standard temperature)
# FYPO:0002195 normal morphology viable vegetative cell population  (high temp)

echo "24."
perl -pi -e 's/VIABLE WT cells at 32- microcolonies skittle cells at 25/FYPO:0002110,PECO:0000005,has_penetrance(FYPO_EXT:0000001)| FYPO:0001315,PECO:0000004,has_penetrance(FYPO_EXT:0000001)| FYPO:NTR,PECO:0000005| FYPO:0002195,PECO:0000004/g' tab_phenotype.csv

# 25.
# VIABLE WT cells at 25,32, small colonies slightly misshapen cells at 36 
# broad classifier: misshapen viable
# cell phenotype
# FYPO:0001315 normal cell morphology during vegetative growth (standard temp)
# FYPO:0001510 viable vegetative cell with abnormal cell shape, normal cell size (high temp) (low expressivity)
# population phenotype
# FYPO:0002195 normal morphology viable vegetative cell population  (standard temp)
# FYPO:0002198 viable vegetative cell population with abnormal cell shape  (825/) (**normal size ?) (high temp)

echo "25."
perl -pi -e 's/VIABLE WT cells at 25-32- small colonies slightly misshapen cells at 36/FYPO:0001315,PECO:0000005| FYPO:0001510,PECO:0000004,has_expressivity(FYPO_EXT:0000003)| FYPO:0002195,PECO:0000005| FYPO:0002198,PECO:0000004/g' tab_phenotype.csv


# 26.
# VIABLE WT cells at 25,32, slightly long at 36 (1)
# broad classifier: long high penetrance
# cell phenotype
# FYPO:0002177 viable vegetative cell with normal morphology  (standard temp)
# FYPO:0001492 elongated viable vegetative cell (high penetrance) (high temp) (low expressivity)
# FYPO:0000059 abnormal mitotic cell cycle progression (high temperature)
# population phenotype
# FYPO:0002195 normal morphology viable vegetative cell population  (standard temp)
# FYPO:0002233 population of elongated viable vegetative cells   (high temp) (low expressivity)

echo "26."
perl -pi -e 's/VIABLE WT cells at 25-32- slightly long at 36/FYPO:0002177,PECO:0000005,has_penetrance(FYPO_EXT:0000001)| FYPO:0001492,PECO:0000004,has_penetrance(FYPO_EXT:0000001), FYPO:0000059,PECO:0000004| FYPO:0002195,PECO:0000005| FYPO:0002233,PECO:0000004,has_expressivity(FYPO_EXT:0000003)/g' tab_phenotype.csv

# 27.
# VIABLE WT cells at 25,32, cells stubby  at 36 (1)
# broad classifier: stubby
# cell phenotype
# FYPO:0002177 viable vegetative cell with normal morphology (standard temp, high penetrance,) 
# FYPO:0002106 viable stubby vegetative cell  (high temp) (***high penetracne?)
# population phenotype
# FYPO:0002195 normal morphology viable vegetative cell population (standard temp)
# FYPO:0002201 viable stubby vegetative cell population (high temp)

echo "27."
perl -pi -e 's/VIABLE WT cells at 25-32- cells stubby at 36/FYPO:0002177,PECO:0000005,has_penetrance(FYPO_EXT:0000001)| FYPO:0002106,PECO:0000004,has_penetrance(FYPO_EXT:0000001)| FYPO:0002195,PECO:0000005| FYPO:0002201,PECO:0000004/g' tab_phenotype.csv

# 28. (ask jacky, what expressivity)
# VIABLE long cells at 32, WT cells at 25 
# long high penetrance
# FYPO:0002177 viable vegetative cell with normal morphology (standard temp, high penetrance,) 
# FYPO:0001492 viable elongated vegetative cell  (high temp) (high penetracne)
# FYPO:0000059 abnormal mitotic cell cycle progression (high temperature)
# population phenotype
# FYPO:0002195 normal morphology viable vegetative cell population (standard temp)
# FYPO:0002233 population of elongated viable vegetative cells  (high temp)

echo "28."
perl -pi -e 's/VIABLE long cells at 32, WT cells at 25/FYPO:0002177,PECO:0000005,has_penetrance(FYPO_EXT:0000001)| FYPO:0001492,PECO:0000004,has_penetrance(FYPO_EXT:0000001)| FYPO:0000059,PECO:0000004| FYPO:0002195,PECO:0000005| FYPO:0002233,PECO:0000004/g' tab_phenotype.csv



# 29.
# VIABLE very small colonies rounded cells at 25,32, lysis after 48h
# rounded

# 30.
# VIABLE slightly curved cells at 25,32, many misshapen cells on exit from stationary phase
# curved

# 31.
# VIABLE slightly misshapen cells at 25,32, cells more misshapen, occasionally slightly curved at 36
# misshapen weak viable


# 32.
# VIABLE slightly misshapen cells at 32, small colonies rounded cells at 25 (1)
# rounded

# 33.
# ESSENTIAL microcolonies long cells at 25,32, curved misshapen cells at 36 (1)
# long high penetrance

# 34.
# VIABLE slightly misshapen cells at 25,32, some colonies misshapen cells and lysis at 36
# misshapen weak viable
# broad classifier: misshapen weak viable
# cell phenotype
# FYPO:0002106 viable stubby vegetative cell (high penetrance, low expressivity, standard temp) 
# FYPO:0002106 viable stubby vegetative cell (low penetrance, low expressivity, high temp) 
# FYPO:0000647 cell lysis (low penetrance, high temp) 
# population phenotype
# FYPO:0002201 viable stubby vegetative cell population (low expressivity, standard temp)

echo "34."
perl -pi -e 's/VIABLE slightly misshapen cells at 25-32- some colonies misshapen cells and lysis at 36/FYPO:0002106,PECO:0000005,has_penetrance(FYPO_EXT:0000001),has_expressivity(FYPO_EXT:0000003)| FYPO:0002106,PECO:0000004,has_penetrance(FYPO_EXT:0000003),has_expressivity(FYPO_EXT:0000003)| FYPO:0000647,PECO:0000004,has_penetrance(FYPO_EXT:0000003)| FYPO:0002201,PECO:0000005,has_expressivity(FYPO_EXT:0000003)/g' tab_phenotype.csv


# 35.
# VIABLE slightly misshapen cells at 32- very small colonies slightly misshapen cells at 25 (1)
# broad classifier: misshapen weak viable
# cell phenotype
# FYPO:0002106 viable stubby vegetative cell (high penetrance, low expressivity) 
# population phenotype
# FYPO:0002201 viable stubby vegetative cell population (high penetrance, low expressivity)

echo "35."
perl -pi -e s'/VIABLE slightly misshapen cells at 32- very small colonies slightly misshapen cells at 25/FYPO:0002106,PECO:0000005| FYPO:0002201,PECO:0000005,has_penetrance(FYPO_EXT:0000001),has_expressivity(FYPO_EXT:0000003)/g' tab_phenotype.csv

# 36.
# VIABLE small colonies stubby cells at 25,32 cells grow better at 25
# broad classifier: stubby
# cell phenotype
# FYPO:0002106 viable stubby vegetative cell  (standard temp) (***high penetrance?)
# population phenotype
# FYPO:0002201 viable stubby vegetative cell population (standard temp)
echo "36."
perl -pi -e 's/VIABLE WT cells at 25-32 cells grow better at 25/FYPO:0002106,PECO:0000005,has_penetrance(FYPO_EXT:0000001)| FYPO:0002201,PECO:0000005/g' tab_phenotype.csv


# 37.
# VIABLE long cells at 25,32, cells longer mostly inviable at 36  (1)
# long high penetrance
# FYPO:0001492 viable elongated vegetative cell  (standard temp) (high penetracne)
# FYPO:0001490 inviable elongated vegetative cell  (high temp) (high penetracne)
# FYPO:0000059 abnormal mitotic cell cycle progression (standard temperature)
# population phenotype
# FYPO:0002233 population of elongated viable vegetative cells  (standard temp)
echo "37."
perl -pi -e 's/VIABLE long cells at 25-32- cells longer mostly inviable at 36/FYPO:0001492,PECO:0000005,has_penetrance(FYPO_EXT:0000001)| FYPO:0000059,PECO:0000005| FYPO:0001490,PECO:0000004,has_penetrance(FYPO_EXT:0000001)| FYPO:0002233,PECO:0000004/g' tab_phenotype.csv


# 38.
# VIABLE slightly stubby cells at 25,32, cells more stubby at 36
# stubby

# 39.
# VIABLE slightly misshapen cells at 25,32, cells initially misshapen from germination  (1) 
# misshapen weak viable

# 40.
# ESSENTIAL microcolonies skittle cells at 25,32 ,larger colonies at 25
# skittle

# 41.
# VIABLE slightly misshapen cells at 32, cells more WT at 25 (1)
# misshapen essential

# 42.
# VIABLE slightly misshapen cells at 25,32, cells long misshapen at 36
# misshapen viable

# 43.
# VIABLE small colonies long cells at 25,32, occasionally aberrantly septated with misplaced septum
# long high penetrance
# FYPO:0001492 viable elongated vegetative cell  (standard temp) (high penetracne)
# FYPO:0000059 abnormal mitotic cell cycle progression (standard temperature)
# population phenotype
# FYPO:0002233 population of elongated viable vegetative cells  (standard temp)
# FYPO:0000339 mislocalized septum (low penetracne)

echo "43."
perl -pi -e 's/VIABLE small colonies long cells at 25-32- occasionally aberrantly septated with misplaced septum/FYPO:0001492,PECO:0000005,has_penetrance(FYPO_EXT:0000001)| FYPO:0000059,PECO:0000005| FYPO:0002233,PECO:0000004| FYPO:0000339,PECO:0000004/g' tab_phenotype.csv

# 44. 
# VIABLE very small colonies long cells at 25,32, possibly suppressors
# long high penetrance
# ask jacky

# 45.
# VIABLE slightly misshapen cells at 25,32, ESSENTIAL long misshapen cells at 36 (1) 
# misshapen viable

# 46.
# VIABLE long cells at 32, cells slightly long at 25 (1)
# long high penetrance
# cell phenotype
# FYPO:0001492 viable elongated vegetative cell  (standard temp) (high penetracne)
# FYPO:0000059 abnormal mitotic cell cycle progression (standard temperature)
# population phenotype
# FYPO:0002233 population of elongated viable vegetative cells  (standard temp)
echo "46."
perl -pi -e 's/VIABLE long cells at 32- cells slightly long at 25/FYPO:0001492,PECO:0000005,has_penetrance(FYPO_EXT:0000001)| FYPO:0000059,PECO:0000005| FYPO:0002233,PECO:0000004/g' tab_phenotype.csv

# 47.
# VIABLE slightly misshapen cells at 25,32, cells long septated misshapen at 36 (1)
# long high penetrance
# cell phenotype
# FYPO:0001492 viable elongated vegetative cell  (high temp) (high penetracne)
# FYPO:0000059 abnormal mitotic cell cycle progression (high temperature)
# FYPO:0001510 viable vegetative cell, abnormal cell shape, normal cell size  (standard temp) (low expressivity)
# population phenotype
# FYPO:0002233 population of elongated viable vegetative cells  (high temp)
# FYPO:0002198 viable vegetative cell population with abnormal cell shape (standard_temp) (low expressivity)
echo "47."
perl -pi -e 's/VIABLE slightly misshapen cells at 25-32- cells long septated misshapen at 36/FYPO:0001492,PECO:0000004,has_penetrance(FYPO_EXT:0000001)| FYPO:0001510,PECO:0000005,has_expressivity(FYPO_EXT:0000003)| FYPO:0000059,PECO:0000004| FYPO:0002233,PECO:0000004| FYPO:0002198,PECO:0000005/g' tab_phenotype.csv


# 48.
# VIABLE small colonies long cells at 25,32, lots of dead cells (1)
# long high penetrance
# cell phenotype
# FYPO:0001492 viable elongated vegetative cell  (standard temp) (high penetracne)
# FYPO:0001490 inviable elongated vegetative cell (standard temp) (low penetracne)
# FYPO:0000059 abnormal mitotic cell cycle progression (high temperature)
# FYPO:0000059 abnormal mitotic cell cycle progression (standard temperature)
# population phenotype
# FYPO:0002233 population of elongated viable vegetative cells  (standard temp)
echo "48."
perl -pi -e 's/VIABLE small colonies long cells at 25-32- lots of dead cells/FYPO:0001492,PECO:0000005,has_penetrance(FYPO_EXT:0000001)| FYPO:0000059,PECO:0000004| FYPO:0000059,PECO:0000005| FYPO:0001490,PECO:0000005| FYPO:0002233,PECO:0000005/g' tab_phenotype.csv

# check this with jacky


# 49. 
# VIABLE slightly misshapen cells at 25,32, branched misshapen cells at 36 (1)
# misshapen viable

# 50. 
# VIABLE slightly misshapen cells at 32, possibly supressors, lots of dead cells (1)
# misshapen weak viable

# 51.
# VIABLE slightly long cells at 32, small colonies long cells at 25 (1)
# long high penetrance
# cell phenotype
# FYPO:0001492 viable elongated vegetative cell  (standard temp) (high penetracne)
# FYPO:0001492 viable elongated vegetative cell  (high temp) (high penetracne) (low expessivity)
# FYPO:0000059 abnormal mitotic cell cycle progression (high temperature)
# FYPO:0000059 abnormal mitotic cell cycle progression (standard temperature)
# population phenotype
# FYPO:0002233 population of elongated viable vegetative cells  (standard temp)
perl -pi -e 's/VIABLE slightly long cells at 32- small colonies long cells at 25/FYPO:0001492,PECO:0000005,has_penetrance(FYPO_EXT:0000001)| FYPO:0001492,PECO:0000004,has_expressivity(FYPO_EXT:0000003)| FYPO:0000059,PECO:0000004| FYPO:0000059,PECO:0000005| FYPO:0002233,PECO:0000005/g' tab_phenotype.csv


# 52.
# VIABLE small colonies stubby cells at 25,32, lots of dead cells
# stubby

# 53. 
# ESSENTIAL swollen spores at 25,32 some germinated spores at 25
# general classifier in paper: misshapen essential changed to spores
# cell phenotype
# swollen spores (standard temp)
# swollen spores (low temp)
# germinated spores (low temp)
# population phenotype
# population of swollen spores (standard temp)







# 54.
# ESSENTIAL microcolonies long cells at 25,32, grows better at 25
# long high penetrance
# NTR increased cell population growth at low temperature (have normal and decreased)
# FYPO:0000059 abnormal mitotic cell cycle progression 


# 55. 
# VIABLE long cells at 32, cells not long but often curved at 25 (1)
# long high penetrance
# cell phenotype
# FYPO:0001492 viable elongated vegetative cell  (standard temp) (high penetracne)

# FYPO:0002112 viable curved vegetative cell (low temp)
# population phenotype
# FYPO:0002233 population of elongated viable vegetative cells  (standard temp)
# FYPO:0000059 abnormal mitotic cell cycle progression (standard temperature)

perl -pi -e 's/VIABLE long cells at 32- cells not long but often curved at 25/FYPO:0001492,PECO:0000005,has_penetrance(FYPO_EXT:0000001)| FYPO:0000059,PECO:0000005| FYPO:0002112,PECO:000000*| FYPO:0002233,PECO:0000005/g' tab_phenotype.csv


# 56.
# VIABLE slightly misshapen cells at 25,32, rounded cells at 36
# rounded 

# 57.
# VIABLE slightly misshapen cells at 32, more septated cells at 25 (1)
# misshapen weak viable

# 58.
# VIABLE small colonies long cells at 25,32 many longer cells possibly diploidising (1)
# long high penetrance
# FYPO:0000059 abnormal mitotic cell cycle progression 

# 59.
# VIABLE small colonies WT cells at 25,32, some larger colonies after 2 days at 32 possibly suppressors 
# WT

# 60.
# VIABLE slightly misshapen cells at 25,32,  cells misshapen at 36
# misshapen viable

# 61. DONE BUT SUBSTRING SO NEEDS TO BE NEAR BOTTOM (substring of lots)
# VIABLE WT cells at 25-32
# broad classifier WT
# https://sourceforge.net/p/pombase/fission-yeast-phenotype/824/
# cell phenotype
# FYPO:0002177 viable vegetative cell with normal cell morphology (high penetrance)
# poplulation phenotype
# FYPO:0002195 normal morphology viable vegetative cell population 

echo "61."
perl -pi -e 's/VIABLE WT cells at 25-32/FYPO:0002177,PECO:0000005,has_penetrance(FYPO_EXT:0000003)| FYPO:0002195,PECO:0000005/g' tab_phenotype.csv


# 62. 
# ESSENTIAL microcolonies misshapen cells at 25-32
# broad classifier: misshapen essential
# https://sourceforge.net/p/pombase/fission-yeast-phenotype/831/
# cell phenotype
# FYPO:0002148 inviable after spore germination, multiple cell divisions, abnormal morphology (high_penetrance)
# population phenotype 
# FYPO:0002226 inviable microcolony, abnormal cell shape, normal cell size
echo "62."
perl -pi -e 's/ESSENTIAL microcolonies misshapen cells at 25-32/FYPO:0002148,PECO:0000005,has_penetrance(FYPO_EXT:0000001)| FYPO:0002226,PECO:0000005/g' tab_phenotype.csv


# 64.
# broad classifier: long high penetrance  
# ESSENTIAL germinated spores long at 25-32 (51)
# https://sourceforge.net/p/pombase/fission-yeast-phenotype/834/
# cell phenotype
# FYPO:0000314 inviable after spore germination with elongated germ tube (HIGH PENTRANCE)  
# FYPO:0000059 abnormal mitotic cell cycle progression (standard temperature)
# population phenotype
# FYPO:0002211 inviable vegetative cell population after spore germination, elongated germ tubes 
echo "63b."
perl -pi -e 's/ESSENTIAL germinated spores long at 25-32/FYPO:0000314,PECO:0000005,has_penetrance(FYPO_EXT:0000001)| FYPO:0000059,PECO:0000005| FYPO:0002211,PECO:0000005/g' tab_phenotype.csv

# 65.  
# ESSENTIAL microcolonies small cells at 25-32
# https://sourceforge.net/p/pombase/fission-yeast-phenotype/779
# cell phenotype
# FYPO:0000951 small inviable vegetative cell (High penetrance) 
# population phenotype
# FYPO:0002186  inviable microcolony, small cells 
echo "64."
perl -pi -e 's/ESSENTIAL microcolonies small cells at 25-32/FYPO:0000951,PECO:0000005,has_penetrance(FYPO_EXT:0000001)| FYPO:0002186,PECO:0000005/g' tab_phenotype.csv

# 66. 
# ESSENTIAL microcolonies rounded cells at 25-32 (29)
# broad classifier: rounded 
# https://sourceforge.net/p/pombase/fission-yeast-phenotype/780/
# cell phenotype
# FYPO:0002187 inviable normal volume spheroid vegetative cell   (high penetrance)  (780)
# population phenotype
# FYPO:0002188 inviable microcolony, normal volume spheroid cells 
echo "66."
perl -pi -e 's/ESSENTIAL microcolonies rounded cells at 25-32/FYPO:0002187,PECO:0000005,has_penetrance(FYPO_EXT:0000001)| FYPO:0002188,PECO:0000005/g' tab_phenotype.csv

# 67. (see 66)
# ESSENTIAL microcolonies rounded cells at 32 cells slightly misshapen at 25 (1)
# broad classifier: rounded 
echo "67."
perl -pi -e 's/ESSENTIAL microcolonies rounded cells at 32 cells slightly misshapen at 25/FYPO:0002187,PECO:0000005,has_penetrance(FYPO_EXT:0000001)| FYPO:0002188,PECO:0000005/g' tab_phenotype.csv

# 68. (see 66)
# ESSENTIAL microcolonies rounded cells at 32 colonies larger at 25 (1)
# broad classifier: rounded 
echo "68."
perl -pi -e 's/ESSENTIAL microcolonies rounded cells at 32 colonies larger at 25/FYPO:0002187,PECO:0000005,has_penetrance(FYPO_EXT:0000001)| FYPO:0002188,PECO:0000005/g' tab_phenotype.csv

# 69. (see 66)
# ESSENTIAL microcolonies rounded cells at 32- cells more WT at 25 (1)
# broad classifier: rounded 
echo "69."
perl -pi -e 's/ESSENTIAL microcolonies rounded cells at 32- cells more WT at 25/FYPO:0002187,PECO:0000005,has_penetrance(FYPO_EXT:0000001)| FYPO:0002188,PECO:0000005/g' tab_phenotype.csv

# 70. (see 66)
# ESSENTIAL microcolonies  rounded cells at 25-32 (4)
# broad classifier: rounded 
echo  "70."
perl -pi -e 's/ESSENTIAL microcolonies  rounded cells at 25-32/FYPO:0002187,PECO:0000005,has_penetrance(FYPO_EXT:0000001)| FYPO:0002188,PECO:0000005/g' tab_phenotype.csv


# 71. (see 66)
# ESSENTIAL microcolonies rounded cells- colonies appear dark at 25-32 (1) 
# broad classifier: rounded 
# cellular phenotype 
# FYPO:0000741 increased cellular pigment accumulation (additional cellular phenotype)
echo "71."
perl -pi -e 's/ESSENTIAL microcolonies rounded cells- colonies appear dark at 25-32/FYPO:0002187,PECO:0000005,has_penetrance(FYPO_EXT:0000001)| FYPO:0000741,PECO:0000005| FYPO:0002188,PECO:0000005/g' tab_phenotype.csv

# 72. (see 66)
# ESSENTIAL microcolonies slightly rounded cells appear to be dark edged at 25-32 (1) 
# broad classifier: rounded 
# cellular phenotype
# plus (low expressivity) for FYPO:***** inviable normal volume spheroid vegetative cell  (high penetrance) 
# plus FYPO:0000741 increased cellular pigment accumulation

echo  "72."
perl -pi -e 's/ESSENTIAL microcolonies slightly rounded cells appear to be dark edged at 25-32/FYPO:0002187,PECO:0000005,has_penetrance(FYPO_EXT:0000001),has_expressivity(FYPO_EXT:0000003)| FYPO:0000741,PECO:0000005| FYPO:0002188,PECO:0000005/g' tab_phenotype.csv

# 73. (see 66)
# ESSENTIAL microcolonies slightly misshapen rounded cells at 25-32  (1)  
# broad classifier: rounded 
# cellular phenotype
# plus (low expressivity) for  for FYPO:***** inviable normal volume spheroid vegetative cell  (high penetrance) 
 
echo "73."
perl -pi -e 's/ESSENTIAL microcolonies slightly misshapen rounded cells at 25-32/FYPO:0002187,PECO:0000005,has_penetrance(FYPO_EXT:0000001),has_expressivity(FYPO_EXT:0000003)| FYPO:0002188,PECO:0000005/g' tab_phenotype.csv

# 74. (see 66)
# ESSENTIAL microcolonies slightly rounded cells at 25-32 (1)
# broad classifier: rounded 
# cellular phenotype
# plus expressivity low for FYPO:***** inviable normal volume spheroid vegetative cell  (high penetrance) 

echo "74"
perl -pi -e 's/ESSENTIAL microcolonies slightly misshapen rounded cells at 25-32/FYPO:0002187,PECO:0000005,has_penetrance(FYPO_EXT:0000001),has_expressivity(FYPO_EXT:0000003)| FYPO:0002188,PECO:0000005/g' tab_phenotype.csv

# 75. (see 66)
# ESSENTIAL microcolonies rounded cells- lysis at 25- spores at 32 (1)
# broad classifier: rounded 
# cell phenotype
# FYPO:0002187 inviable normal volume spheroid vegetative cell  (high penetrance)  (low temp)
# ******** plus FYPO:0000647 cell lysis (low temp)
# *********plus spores (high temperature)
# population phenotype
# FYPO:0002188 microcolonies of normal volume inviable spheroid cells 
# *******  mixed population of rounded and lysed cells at low temp 
# ******** population of spores at high temp
# checked with Jacky, this is fine

echo "75."
perl -pi -e 's/ESSENTIAL microcolonies rounded cells at 25-32/FYPO:0002187,PECO:0000005,has_penetrance(FYPO_EXT:0000001)| FYPO:0002188,PECO:0000005/g' tab_phenotype.csv

# 76. (see 66)
# ESSENTIAL microcolonies rounded cells- lysis at 25-32  (3) 
# broad classifier: rounded
# cell phenotype
# plus FYPO:0000647 cell lysis

echo "76."
perl -pi -e 's/ESSENTIAL microcolonies rounded cells- lysis at 25-32/FYPO:0000951,PECO:0000005,has_penetrance(FYPO_EXT:0000001)| FYPO:0000647,PECO:0000005 | FYPO:0002188,PECO:0000005/g' tab_phenotype.csv

# 77. 
# ESSENTIAL germinated spores- microcolonies rounded cells at 25-32 (1)
# broad classifier: rounded
# https://sourceforge.net/p/pombase/fission-yeast-phenotype/836/
# cell phenotype
# FYPO:0000021 inviable spheroid vegetative cell (normal volume?) 
# FYPO:0000310 inviable after spore germination with normal germ tube morphology (836)
# population phenotype
# FYPO:0002181 inviable mixed population including germinated spores and spheroid cells (836)

# JAcky can't recall penetrance so leaving this

echo "77."
perl -pi -e 's/ESSENTIAL germinated spores- microcolonies rounded cells at 25-32/FYPO:0000021,PECO:0000005| FYPO:0000310,PECO:0000005| FYPO:0002181,PECO:0000005/g' tab_phenotype.csv


# 78.
# ESSENTIAL spores- germinated spores- microcolonies rounded cells at 25-32 (1)
# broad classifier: rounded
# https://sourceforge.net/p/pombase/fission-yeast-phenotype/837/
# cell phenotype
# FYPO:0000021 inviable spheroid vegetative cell
# FYPO:0000310 inviable after spore germination with normal germ tube morphology
# FYPO:0002151 inviable spore
# cell population phenotype
# FYPO:0002182 inviable mixed population including spores, germinated spores, and spheroid cells
# penetrance Jacky not sure so leaving
echo "78."
perl -pi -e 's/ESSENTIAL spores- germinated spores- microcolonies rounded cells at 25-32/FYPO:0000021,PECO:0000005,has_penetrance(FYPO_EXT:0000001)| FYPO:0000310,PECO:0000005| FYPO:0002182,PECO:0000005/g' tab_phenotype.csv


# 79. (see 80 below)
# ESSENTIAL germinated spores misshapen at 25,32, germinated spores occasionally long at 25

# 80.
# ESSENTIAL germinated spores misshapen at 25-32
# broad classifier: misshapen essential
# https://sourceforge.net/p/pombase/fission-yeast-phenotype/838/
# cell phenotype
# FYPO:0000313 inviable after spore germination with abnormal germ tube morphology
# population phenotype
# FYPO:0002214 inviable vegetative cell population after spore germination, abnormal germ tube morphology  (838)

echo "80."
perl -pi -e 's/ESSENTIAL germinated spores misshapen at 25-32/FYPO:0000313,PECO:0000005,has_penetrance(FYPO_EXT:0000001)|FYPO:0002214,PECO:0000005/g' tab_phenotype.csv

# 81.
# VIABLE slightly stubby cells at 25-32
# PECO:0000005 standard temperature 25-32
# https://sourceforge.net/p/pombase/fission-yeast-phenotype/801/
# broad classifier:  stubby
# cell phenotype
# FYPO:0002106 stubby viable cell  (low expressivity) (high penetrance)
# population phenotype
# FYPO:0002201 viable stubby vegetative cell population (801)

echo "81."
perl -pi -e 's/VIABLE slightly stubby cells at 25-32/FYPO:0002106,PECO:0000005,has_expressivity(FYPO_EXT:0000003),has_penetrance(FYPO_EXT:0000001)| FYPO:0002201,PECO:0000005/g' tab_phenotype.csv

# 82. 
# ESSENTIAL spores  at 25-32
# broad classifier: spores
# cell phenotype
# FYPO:0002151 inviable spore  (high penetrance)
# population phenotype
# FYPO:0002150 inviable spore population

echo "82"
perl -pi -e 's/ESSENTIAL spores  at 25-32/FYPO:0002120,PECO:0000005| FYPO:0002151,PECO:0000005,has_penetrance(FYPO_EXT:0000003)/g' tab_phenotype.csv

# 84a. 
# VIABLE slightly curved cells at 25,32, occasionally cells are T-shaped
# https://sourceforge.net/p/pombase/fission-yeast-phenotype/839/
# broad classifier: curved
# cell phenotype 
# FYPO:0002112 curved viable cell  (low expressivity)  (high penetrance)
# FYPO:0000013 T-shaped cell (low penetrance)
# population phenotype
# FYPO:0002216 viable curved vegetative cell population
echo "84a"
perl -pi -e 's/VIABLE slightly curved cells at 25,32, occasionally cells are T-shaped/FYPO:0002112,PECO:0000005,has_expressivity(FYPO_EXT:0000003),has_penetrance(FYPO_EXT:0000003)| FYPO:0000013,PECO:0000005,has_penetrance(FYPO_EXT:0000003)| FYPO:0002216,PECO:0000005/g' tab_phenotype.csv

# 84b. 
# VIABLE slightly curved cells at 25-32
# https://sourceforge.net/p/pombase/fission-yeast-phenotype/839/
# broad classifier: curved
# cell phenotype
# FYPO:0002112 curved viable cell  (low expressivity)  (high penetrance)
# population phenotype
# FYPO:0002216 viable curved vegetative cell population

echo "84b"
perl -pi -e 's/VIABLE slightly curved cells at 25-32/FYPO:0002112,PECO:0000005,has_expressivity(FYPO_EXT:0000003),has_penetrance(FYPO_EXT:0000003)| FYPO:0002216,PECO:0000005/g' tab_phenotype.csv

# 85.
# ESSENTIAL small colonies skittle cells at 25-32
# https://sourceforge.net/p/pombase/fission-yeast-phenotype/808/
# broad classifier: skittle
# cell phenotype
# FYPO:0002111 bottle-shaped inviable vegetative cell 
# population phenoype
# FYPO:0002210 inviable microcolony, bottle-shaped cells 
####### CHECK THIS ONE WItH JACKY why small?????
echo "85."
perl -pi -e 's/ESSENTIAL small colonies skittle cells at 25-32/FYPO:0002111,PECO:0000005| FYPO:0002210,PECO:0000005/g' tab_phenotype.csv

# 86.
# ESSENTIAL microcolonies skittle cells- small colonies WT cells at 25-32 (38)
# https://sourceforge.net/p/pombase/fission-yeast-phenotype/840/
# https://sourceforge.net/p/pombase/fission-yeast-phenotype/803/
# broad classifier: skittle
# cell phenotype
# FYPO:0002111 bottle-shaped inviable vegetative cell
# FYPO:0002199 inviable vegetative cells with normal morphology (840)
# population phenoype
# FYPO:******inviable mixed population of microcolonies of skittle cells, and small colonies of inviable cells with normal morphology (803)

echo "86."
perl -pi -e 's/ESSENTIAL microcolonies skittle cells- small colonies WT cells at 25-32/FYPO:0002111,PECO:0000005| FYPO:0002199,PECO:0000005| FYPO:******,PECO:0000005/g' tab_phenotype.csv

# 87. 
# VIABLE small colonies slightly misshapen cells at 25-32
# https://sourceforge.net/p/pombase/fission-yeast-phenotype/812/
# broad classifier: misshapen weak viable
# cell phenotype
# FYPO:0001510 viable vegetative cell, abnormal cell shape, normal cell size  (low expressivity) (high expressivity?)
# population phenotype
# FYPO:0002198 viable vegetative cell population with abnormal cell shape 

echo "87."
perl -pi -e 's/VIABLE small colonies slightly misshapen cells at 25-32/FYPO:0001510,PECO:0000005,has_expressivity(FYPO_EXT:0000003),has_penetrance(FYPO_EXT:0000001)| FYPO:0002198,PECO:0000005/g' tab_phenotype.csv

# 87.b.
# https://sourceforge.net/p/pombase/fission-yeast-phenotype/779/
# broad classifier: rounded
# VIABLE very small colonies rounded cells at 25-32
# cell phenotype
# FYPO:0000946 normal volume spheroid vegetative cell
# population phenotype
# NTR***** microcolonies of rounded viable cells

# check with jacky/ microsolonies rounded


echo "87.b."
perl -pi -e 's/VIABLE very small colonies rounded cells at 25-32/FYPO:0000946,PECO:0000005,has_penetrance(FYPO_EXT:0000001)| FYPO:******,PECO:0000005/g' tab_phenotype.csv

# 88.  (add high penetrance ?)
# VIABLE WT cells at 32
# https://sourceforge.net/p/pombase/fission-yeast-phenotype/777/
# https://sourceforge.net/p/pombase/fission-yeast-phenotype/824/
# cell phenotype
# FYPO:0002177 viable cell with normal morphology (777)
# population phenotype
# FYPO:0002195 normal morphology viable vegetative cell population  (824)

echo "88."
perl -pi -e 's/VIABLE WT cells at 32/FYPO:0002177,PECO:0000005| FYPO:0002195,PECO:0000005/g' tab_phenotype.csv

# 89.
# VIABLE small colonies WT cells at 25-32
# broad classifier: WT
# https://sourceforge.net/p/pombase/fission-yeast-phenotype/812/
# https://sourceforge.net/p/pombase/fission-yeast-phenotype/840/
# cell phenotype
# FYPO:0002199 inviable vegetative cells with normal morphology (840)  (high penetrance)
# population phenotype 
# FYPO:0002195 normal morphology viable vegetative cell population (812)

echo "89."
perl -pi -e 's/VIABLE small colonies WT cells at 25-32/FYPO:0002199,PECO:0000005| FYPO:0002195,PECO:0000005/g' tab_phenotype.csv


# 90. 
# VIABLE small colonies long cells at 25-32
# https://sourceforge.net/p/pombase/fission-yeast-phenotype/786/
# broad classifier: long high penetrance
# cell phenotype
# FYPO:0001492 elongated viable vegetative cell (high penetrance)
# FYPO:0000059 abnormal mitotic cell cycle progression
# population phenotype
# FYPO:0002233 population of elongated viable vegetative cells  

echo "90"
perl -pi -e 's/VIABLE small colonies long cells at 25-32/FYPO:0001492,PECO:0000005,has_penetrance(FYPO_EXT:0000001)| FYPO:0000059,PECO:0000005| FYPO:0002233,PECO:0000005/g' tab_phenotype.csv

# 91.
# ESSENTIAL microcolonies slightly misshapen cells- some long cells at 25-32
# https://sourceforge.net/p/pombase/fission-yeast-phenotype/841/
# broad classifier: long low penetrance
# cell phenotype 
# FYPO:0001490 elongated inviable vegetative cell (low penetrance)
# FYPO:0001511 inviable vegetative cell, abnormal cell shape, normal cell size   (high_penetrance/ low expressivity) 
# FYPO:0000059 abnormal mitotic cell cycle progression (standard temperature)
# cell population phenotype
# FYPO:0002180 microcolonies of inviable vegetative cells with abnormal morphology, occasionally long cells

echo "91."
perl -pi -e 's/ESSENTIAL microcolonies slightly misshapen cells- some long cells at 25-32/FYPO:0001490,PECO:0000005,has_penetrance(FYPO_EXT:0000003)| FYPO:0001511,PECO:0000005,has_penetrance(FYPO_EXT:0000001),has_expressivity(FYPO_EXT:0000003)| FYPO:0000059,PECO:0000004| FYPO:0002180,PECO:0000005/g' tab_phenotype.csv 

# 92.
# ESSENTIAL microcolonies slightly misshapen cells at 25-32
# https://sourceforge.net/p/pombase/fission-yeast-phenotype/831/
# broad classifier: essential misshapen
# cell phenotype
# FYPO:0001511 inviable vegetative cell, abnormal cell shape, normal cell size (high_penetrance/ low expressivity) 
# population phenotype
# FYPO:0002226 nviable microcolony, abnormal cell shape, normal cell size (831)

echo "92."
perl -pi -e 's/ESSENTIAL microcolonies slightly misshapen cells at 25-32/FYPO:0001511,PECO:0000005,has_penetrance(FYPO_EXT:0000001),has_expressivity(FYPO_EXT:0000003)| FYPO:0002226,PECO:0000005/g' tab_phenotype.csv

# 93. 
# ESSENTIAL microcolonies long cells at 25-32
# https://sourceforge.net/p/pombase/fission-yeast-phenotype/793/
# broad classifier: long high penetrance
# cell phenotype
# FYPO:0001490 elongated inviable vegetative cell (high penetrance) (high expressivity)
# FYPO:0000059 abnormal mitotic cell cycle progression (standard temperature)
# population phenotype
# FYPO:0002225 inviable microcolony, elongated cells

echo "93."
perl -pi -e 's/ESSENTIAL microcolonies long cells at 25-32/FYPO:0001490,PECO:0000005,has_penetrance(FYPO_EXT:0000001)| FYPO:0000059,PECO:0000005| FYPO:0002225,PECO:0000005/g' tab_phenotype.csv

# 94. 
# VIABLE WT cells with some long cells at 25-32 
# https://sourceforge.net/p/pombase/fission-yeast-phenotype/841/
# broad classifier: long low penetrance
# cell phenotype
# FYPO:0002104 viable cell with normal cell shape (high penetrance 1)
# FYPO:0001492 elongated viable vegetative cell (low penetrance 3)
# FYPO:0000059 abnormal mitotic cell cycle progression (standard temperature)
# population phenotype
# FYPO:0002180 viable mixed vegetative cell population including cell with normal morphology and long cells

echo "94."
perl -pi -e 's/VIABLE WT cells with some long cells at 25-32/FYPO:0001492,PECO:0000005,has_penetrance(FYPO_EXT:0000003)|FYPO:0002104,PECO:0000005,has_penetrance(FYPO_EXT:0000001)| FYPO:0000059,PECO:0000005| FYPO:0002180,PECO:0000005/g' tab_phenotype.csv

# 95.
# VIABLE slightly long cells at 32, microcolonies long cells at 25 (1)
# broad classifier: long high penetrance
# https://sourceforge.net/p/pombase/fission-yeast-phenotype/842/
# cell phenotype
# FYPO:0001492 elongated viable vegetative cell (high penetrance 1 low expressivity 3)
# FYPO:0000059 abnormal mitotic cell cycle progression (standard temperature)
# phenotype population
# FYPO:0002233 population of elongated viable vegetative cells (population phenotype)

echo "95."
perl -pi -e 's/VIABLE slightly long cells at 32, microcolonies long cells at 25/FYPO:0001492,PECO:0000005,has_penetrance(FYPO_EXT:0000001),has_expressivity(FYPO_EXT:0000003)| FYPO:0000059,PECO:0000005| FYPO:0002233,PECO:0000005/g' tab_phenotype.csv

# 96.
# VIABLE slightly long cells at 32, small colonies long cells at 25
# broad classifier: long high penetrance
# cell phenotype
# FYPO:0001492 elongated viable vegetative cell (high penetrance 1 low expressivity 3)
# FYPO:0000059 abnormal mitotic cell cycle progression (standard temperature)
# phenotype population
# FYPO:0002233 viable population of elongated vegetative cells (population phenotype)

echo "96."
perl -pi -e 's/VIABLE slightly long cells at 32- small colonies long cells at 25/FYPO:0001492,PECO:0000005,has_penetrance(FYPO_EXT:0000001),has_expressivity(FYPO_EXT:0000003)| FYPO:0000059,PECO:0000005| FYPO:0002233,PECO:0000005/g' tab_phenotype.csv

# 97. 
# VIABLE slightly long cells at 32
# broad classifier: long high penetrance
# cell phenotype
# FYPO:0001492 elongated viable vegetative cell (high penetrance 1 low expressivity 3)
# FYPO:0000059 abnormal mitotic cell cycle progression (standard temperature)
# phenotype population
# FYPO:0002233 viable population of elongated vegetative cells (population phenotype)

echo "97."
perl -pi -e 's/VIABLE slightly long cells at 32/FYPO:0001492,PECO:0000005,has_penetrance(FYPO_EXT:0000001),has_expressivity(FYPO_EXT:0000003)| FYPO:0000059,PECO:0000005| FYPO:0002233,PECO:0000005/g' tab_phenotype.csv

# 98. 
# ESSENTIAL microcolonies slightly long cells at 25-32
# https://sourceforge.net/p/pombase/fission-yeast-phenotype/793/
# broad classifier: long high penetrance
# cell phenotype
# FYPO:0001490 elongated inviable vegetative cell (high penetrance 1 low expressivity 3)
# FYPO:0000059 abnormal mitotic cell cycle progression (standard temperature)
# population phenotype
# FYPO:0002225 microcolonies of elongated inviable vegetative cells 

echo "98."
perl -pi -e 's/ESSENTIAL microcolonies slightly long cells at 25-32/FYPO:0001490,PECO:0000005,has_penetrance(FYPO_EXT:0000001),has_expressivity(FYPO_EXT:0000003)| FYPO:0000059,PECO:0000005| FYPO:0002225,PECO:0000005/g' tab_phenotype.csv

# 99. 
# VIABLE long cells at 25-32
# broad classifier: long high penetrance
# cell phenotype
# https://sourceforge.net/p/pombase/fission-yeast-phenotype/842/
# FYPO:0001492 elongated viable vegetative cell (high penetrance) (high expressivity??????)
# FYPO:0000059 abnormal mitotic cell cycle progression (standard temperature)
# population phenotype
# FYPO:0002233 elongated viable vegetative cell population

echo "99."
perl -pi -e 's/VIABLE long cells at 25-32/FYPO:0001492,PECO:0000005,has_penetrance(FYPO_EXT:0000001),has_expressivity(FYPO_EXT:0000001)| FYPO:0000059,PECO:0000005| FYPO:0002233,PECO:0000005/g' tab_phenotype.csv

# 100. 
# ESSENTIAL small colonies long cells at 25-32
# broad classifier: long high penetrance
# https://sourceforge.net/p/pombase/fission-yeast-phenotype/752/
# cell phenotype
# FYPO:0001490 elongated inviable vegetative cell (high penetrance 1) 
# FYPO:0000059 abnormal mitotic cell cycle progression (standard temperature)
# cell population phenotype  
# FYPO:0002225 inviable microcolony, elongated cells (cheek with JAcky)

echo "100."
perl -pi -e 's/ESSENTIAL small colonies long cells at 25-32/FYPO:0001490,PECO:0000005,has_penetrance(FYPO_EXT:0000001)| FYPO:0000059,PECO:0000005| FYPO:0002225,PECO:0000005/g' tab_phenotype.csv

# 101.
# VIABLE small colonies stubby cells at 25-32
# https://sourceforge.net/p/pombase/fission-yeast-phenotype/801/
# broad classifier: stubby
# cell phenotype
# FYPO:0002106 stubby viable cell  (high penetrance) 
# population phenotype
# FYPO:0002201 viable stubby vegetative cell population 

echo "101."
perl -pi -e 's/VIABLE small colonies stubby cells at 25-32/FYPO:0002106,PECO:0000005,has_penetrance(FYPO:0000001)| FYPO:0002201,PECO:0000005/g' tab_phenotype.csv


# 102a. 
# VIABLE stubby cells at 25-32- cells not growing at 36

# broad classifier: stubby
# https://sourceforge.net/p/pombase/fission-yeast-phenotype/801/
# cell phenotype
# FYPO:0002106 stubby viable cell  (high penetrance) 
# *****ADD INVIABLE AT HIGH TEMP
# population phenotype
# FYPO:0002201 viable stubby vegetative cell population 
# *****ADD INVIABLE POP AT HIGH TEMP

echo "102a"
perl -pi -e 's/VIABLE stubby cells at 25-32- cells not growing at 36/FYPO:0002106,PECO:0000005,has_penetrance(FYPO:0000001)| FYPO:0002201,PECO:0000005/g' tab_phenotype.csv


# 102b. 
# VIABLE stubby cells at 25-32
# broad classifier: stubby
# https://sourceforge.net/p/pombase/fission-yeast-phenotype/801/
# cell phenotype
# FYPO:0002106 stubby viable cell  (high penetrance) 
# population phenotype
# FYPO:0002201 viable stubby vegetative cell population 

echo "102b"
perl -pi -e 's/VIABLE stubby cells at 25-32- cells not growing at 36/FYPO:0002106,PECO:0000005,has_penetrance(FYPO:0000001)| FYPO:0002201,PECO:0000005/g' tab_phenotype.csv



# 102b. 
# VIABLE stubby cells at 25-32
# broad classifier: stubby
# https://sourceforge.net/p/pombase/fission-yeast-phenotype/801/
# cell phenotype
# FYPO:0002106 stubby viable cell  (high penetrance) 
# population phenotype
# FYPO:0002201 viable stubby vegetative cell population 

echo "102b"
perl -pi -e 's/VIABLE stubby cells at 25-32/FYPO:0002106,PECO:0000005,has_penetrance(FYPO:0000001)| FYPO:0002201,PECO:0000005/g' tab_phenotype.csv

# 103.
# broad classifier: long high penetrance
# https://sourceforge.net/p/pombase/fission-yeast-phenotype/842/
# VIABLE slightly long cells at 25-32
# VIABLE  slightly long cells at 25-32
# cell phenotype
# FYPO:0001492 elongated viable vegetative cell (high penetranhance 1 low expressivity 3)
# FYPO:0000059 abnormal mitotic cell cycle progression (standard temperature)
# population phenotype
# FYPO:0002233 viable population of elongated vegetative cells

echo "103."
perl -pi -e 's/VIABLE slightly long cells at 25-32/FYPO:0001492,PECO:0000005,has_penetrance(FYPO_EXT:0000001),has_expressivity(FYPO_EXT:0000003)| FYPO:0000059,PECO:0000005| FYPO:0002233,PECO:0000005/g' tab_phenotype.csv

echo "103.b"
perl -pi -e 's/VIABLE  slightly long cells at 25-32/FYPO:0001492,PECO:0000005,has_penetrance(FYPO_EXT:0000001),has_expressivity(FYPO_EXT:0000003)| FYPO:0000059,PECO:0000005| FYPO:0002233,PECO:0000005/g' tab_phenotype.csv

# 104. 
# VIABLE long cells at 32   (CARE THIS ISA SUBSTRING, ALL LONNGER STRINGS ARE ABOVE)
# https://sourceforge.net/p/pombase/fission-yeast-phenotype/842/
# broad classifier: long high penetrance
# cell phenotype
# FYPO:0001492 elongated viable vegetative cell (high penetrance 1 high expressivity )
# FYPO:0000059 abnormal mitotic cell cycle progression (standard temperature)
# population phenotype
# FYPO:0002233 viable population of elongated vegetative cells

echo "104."
perl -pi -e 's/VIABLE long cells at 32/FYPO:0001492,PECO:0000005,has_penetrance(FYPO_EXT:0000001)| FYPO:0000059,PECO:0000005| FYPO:0002233,PECO:0000005/g' tab_phenotype.csv


# 105. 
# VIABLE misshapen cells at 25-32
# broad classifier: misshapen viable
# https://sourceforge.net/p/pombase/fission-yeast-phenotype/825/
# cell phenotype
# FYPO:0001510 viable vegetative cell with abnormal cell shape, normal cell size  
# population phenotype
# FYPO:0002198 viable vegetative cell population with abnormal cell shape  (825/) (**normal size ?)

echo "105"
perl -pi -e 's/VIABLE misshapen cells at 25-32/FYPO:0001510,PECO:0000005| FYPO:0002198,PECO:0000005/g' tab_phenotype.csv


# 106.
# VIABLE slightly misshapen cells at 32
# broad classifier: misshapen weak viable
# https://sourceforge.net/p/pombase/fission-yeast-phenotype/825/
# cell phenotype
# FYPO:0001510 viable vegetative cell with abnormal cell shape, normal cell size (low expressivity)
# population phenotype
# FYPO:0002198 viable vegetative cell population with abnormal cell shape (825/) (** normal size ?)

echo "106."
perl -pi -e 's/VIABLE slightly misshapen cells at 32/FYPO:0001510,PECO:0000005,has_expressivity(FYPO_EXT:0000003)| FYPO:0002198,PECO:0000005/g' tab_phenotype.csv

# 107. 
# VIABLE small colonies slightly long cells at 25-32
# https://sourceforge.net/p/pombase/fission-yeast-phenotype/786/
# broad classifier: long high penetrance
# cell phenotype
# FYPO:0001492 elongated viable vegetative cell (high penetrance/low expressivity)
# FYPO:0000059 abnormal mitotic cell cycle progression (standard temperature)
# population phenotype
# FYPO:0002233 viable microcolonies of elongated vegetative cells (*****NEED TO CHECK WITH JACKY IF THIS IS OK)

echo "107"
perl -pi -e 's/VIABLE small colonies slightly long cells at 25-32/FYPO:0001492,PECO:0000005,has_penetrance(FYPO_EXT:0000001),has_expressivity(FYPO_EXT:0000003)| FYPO:0000059,PECO:0000005| FYPO:0002233,PECO:0000005/g' tab_phenotype.csv

# 108. 
# VIABLE curved slightly long cells at 32
# broad classifier: curved
# https://sourceforge.net/p/pombase/fission-yeast-phenotype/839/
# https://sourceforge.net/p/pombase/fission-yeast-phenotype/843/
# cell phenotype
# FYPO:****** long curved viable cell   (high penetracne, low expressivity, checked with Jacky) 843/
# FYPO:0000059 abnormal mitotic cell cycle progression (standard temperature)
# population phenotype
# FYPO:****** population of long curved viable cells  (low expressivity) ??????? (839)

echo "108."
perl -pi -e 's/VIABLE curved slightly long cells at 32/FYPO:000****,PECO:0000005,has_penetracne(FYPO_EXT:0000001),has_expressivity(FYPO_EXT00000003)| FYPO:0000059,PECO:0000005| FYPO:NTR******,PECO:0000005/g' tab_phenotype.csv




# 109.
# VIABLE curved slightly long cells at 25-32
# broad classifier: curved
# cell phenotype
# FYPO:****** long curved viable cell  ???????? asked Jacky *******penetracne? expressivity 843/
# FYPO:0000059 abnormal mitotic cell cycle progression (standard temperature)
# population phenotype
# FYPO:****** population of long curved viable cells  (low expressivity) ??????? (839)

echo "109"
perl -pi -e 's/VIABLE curved slightly long cells at 25-32/FYPO:000****,PECO:0000005| FYPO:0000059,PECO:0000005| FYPO:NTR******,PECO:0000005/g' tab_phenotype.csv


# 110. (asked jacky this should be small, not very small)
# VIABLE very small colonies long cells at 25-32
# broad classifier: long high penetrance
#
# FYPO:0001492 elongated viable vegetative cell (high penetrance)
# FYPO:0000059 abnormal mitotic cell cycle progression (standard temperature)
#
# FYPO:0002233 viable population of elongated vegetative cells

echo "110"
perl -pi -e 's/VIABLE very small colonies long cells at 25-32/FYPO:0001492,PECO:0000005,has_penetrance(FYPO_EXT:0000001)| FYPO:0000059,PECO:0000005| FYPO:0002233,PECO:0000005/g' tab_phenotype.csv


# 111. (make sure anything with this in the substring is higher up)
# ESSENTIAL swollen spores at 25-32
# https://sourceforge.net/p/pombase/fission-yeast-phenotype/802/
# general classifier in paper: misshapen essential changed to spores
# cell phenotype
# FYPO:0002208 inviable swollen spore with abnormal shape /802/ (high penetrance) (****remove abnormal she here)
# population phenotype
# FYPO:0002209 inviable swollen spore population with abnormal spore shape /802/ (****remove abnormal she here)
# the shape is not abnormal, it is just swollen

echo "111."
perl -pi -e 's/ESSENTIAL swollen spores at 25-32/FYPO:0002208,PECO:0000005,has_penetrance(FYPO_EXT:0000001)| FYPO:0002209,PECO:0000005/g' tab_phenotype.csv


# 112.
# VIABLE small colonies rounded cells at 25-32
# broad classifier: rounded
# https://sourceforge.net/p/pombase/fission-yeast-phenotype/800/
# https://sourceforge.net/p/pombase/fission-yeast-phenotype/779/
# cell phenotype
# FYPO:NEW normal volume rounded viable vegetative cell (high_penetrance) /800/
# population phenotype
# FYPO:NEW small colonies of rounded viable cells  (779)

echo "112."
perl -pi -e 's/VIABLE small colonies rounded cells at 25-32/FYPO:NTR****,PECO:0000005,has_penetrance(FYPO_EXT:0000001)| FYPO:NTR******,PECO:0000005/g' tab_phenotype.csv


# 113. 
# ESSENTIAL spores- some germinated spores at 25-32 (35)
# broad classifier: spores
# cell phenotype
# FYPO:*********** inviable after spore germination with normal unseptated germ tube morphology (low penetrance)
# FYPO:0002151 inviable spore (high penetrance)
# population phenotype
# FYPO:0000321 inviable mixed population including spores and undivided germinated spores

echo "113."
perl -pi -e 's/ESSENTIAL spores- some germinated spores at 25-32/FYPO:**********,PECO:0000005| FYPO:0000310,PECO:0000005,has_penetrance(FYPO_EXT:0000003)| FYPO:0002151,PECO:0000005,has_penetrance(FYPO_EXT:0000001)/g' tab_phenotype.csv
 
# 114. 
# ESSENTIAL spores- germinated spores at 25-32 (127)
# ESSENTIAL spores- germinated spores  at 25-32 (2)
# broad classifier: germination
# cell phenotype 
# FYPO:0000311 inviable after spore germination with normal, unseptated germ tube morphology (high penetrance)
# FYPO:0002151 inviable spore (low penetrance)
# population phenotype
# FYPO:0000321 inviable mixed population including spores and undivided germinated spores

echo "114."
perl -pi -e 's/ESSENTIAL spores- germinated spores at 25-32/FYPO:0000321,PECO:0000005| FYPO:0000311,PECO:0000005| FYPO:0002151,PECO:0000005/g' tab_phenotype.csv

# 115.
# ESSENTIAL germinated spores at 25-32 (69)
# broad classifier: germination  
# https://sourceforge.net/p/pombase/fission-yeast-phenotype/845/
# cell phenotype 
# FYPO:0000311 inviable after spore germination with normal, unseptated germ tube morphology (high penetracne)
# population phenotype
# FYPO:0002218 inviable vegetative cell population after spore germination, normal unseptated germ tube morphology (845)

echo "115."
perl -pi -e 's/ESSENTIAL germinated spores at 25-32/FYPO:0000311,PECO:0000005,has_penetrance(FYPO_EXT:0000001)| FYPO:0002218,PECO:0000005/g' tab_phenotype.csv


# 116.
# broad classifier: germination
# ESSENTIAL spores- germinated spores- some division at 25-32 (1)
# https://sourceforge.net/p/pombase/fission-yeast-phenotype/837/
# cell phenotype 
# FYPO:0002151 inviable spore (low penetrance)
# FYPO:0000320 inviable after spore germination, single cell division (low penetrance)
# FYPO:0000310 inviable after spore germination with normal germ tube morphology (high penetrate)
# population phenotype
# FYPO:0002183 inviable population including spores, germinated spores and cells with normal morphology

echo "116."
perl -pi -e 's/ESSENTIAL spores- germinated spores- some division at 25-32/FYPO:0002151,PECO:0000005,has_penetrance(FYPO_EXT:0000003)| FYPO:0000320,PECO:0000005,has_penetrance(FYPO_EXT:0000003)| FYPO:0000310,PECO:0000005,has_penetrance(FYPO_EXT:0000003)| FYPO:0002183,PECO:0000005/g' tab_phenotype.csv

# asked jacky, not microcolonies, only occasional division


# 117. 
# ESSENTIAL spores- germinated spores- microcolonies skittles cells at 25-32 (2)
# https://sourceforge.net/p/pombase/fission-yeast-phenotype/846/
# broad classifier: skittle
# cell phenotype 
# FYPO:0002151 inviable spore 
# FYPO:0000320 inviable skittle cells (high expressivity)
# FYPO:0000310 inviable after spore germination with normal germ tube morphology
# population phenotype
# mixed population of spores, germinated spores and microcolonies of inviable skittle cells (846)
# FYPO:0002184 inviable mixed population including spores, germinated spores and bottle-shaped cells
# penetrance probably split 3 way but not sure so ommitting

echo "117."
perl -pi -e 's/ESSENTIAL spores- germinated spores- microcolonies skittles cells at 25-32/FYPO:0002151,PECO:0000005| FYPO:0000320,PECO:0000005,has_expressivity(FYPO_EXT:0000001)| FYPO:0000310,PECO:0000005| FYPO:0002184,PECO:0000005/g' tab_phenotype.csv

# 118. 
# ESSENTIAL microcolonies skittle cells at 25-32
# https://sourceforge.net/p/pombase/fission-yeast-phenotype/808/
# cell phenotype
# FYPO:0002111 bottle-shaped inviable vegetative cell (high penetrance)
# cell population phenotype
# FYPO:0002210 inviable microcolony, bottle-shaped cells /808/
 
echo "118."
perl -pi -e 's/ESSENTIAL microcolonies skittle cells at 25-32/FYPO:0002111,PECO:0000005,has_penetrance(FYPO_EXT:0000001)| FYPO:0002210,PECO:0000005/g' tab_phenotype.csv

# 119.
# ESSENTIAL microcolonies skittle cells at 32- larger colonies at 25 (1)
# https://sourceforge.net/p/pombase/fission-yeast-phenotype/808/
# cell phenotype
# FYPO:0002111 bottle-shaped inviable vegetative cell
# cell population phenotype
# FYPO:0002210 inviable microcolony, bottle-shaped cells /808/

echo "119."
perl -pi -e 's/ESSENTIAL microcolonies skittle cells at 32- larger colonies at 25/FYPO:0002111,PECO:0000005| FYPO:0002210,PECO:0000005/g' tab_phenotype.csv

# 120.
# ESSENTIAL microcolonies skittle cells at 32- small colonies skittle cells at 25 (1)
# https://sourceforge.net/p/pombase/fission-yeast-phenotype/808/
# cell phenotype
# FYPO:0002111 bottle-shaped inviable vegetative cell (high penetracne?)
# cell population phenotype
# FYPO:0002210inviable microcolony, bottle-shaped cells  (808)

echo "120.a"
perl -pi -e 's/ESSENTIAL microcolonies skittle cells at 32- small colonies skittle cells at 25/FYPO:0002111,PECO:0000005,has_penetrance(FYPO_EXT:0000001)| FYPO:NTR****,PECO:0000005/g' tab_phenotype.csv

# 120.b
# ESSENTIAL microcolonies skittle slightly misshapen cells at 25-32 (5)
# https://sourceforge.net/p/pombase/fission-yeast-phenotype/808/
# cell phenotype
# FYPO:0002111 bottle-shaped inviable vegetative cell
# cell population phenotype
# FYPO:0002210 inviable microcolony, bottle-shaped cells /808/

echo "120.b"
perl -pi -e 's/ESSENTIAL microcolonies skittle slightly misshapen cells at 25-32/FYPO:0002111,PECO:0000005,has_penetrance(FYPO_EXT:0000001)| FYPO:0002210,PECO:0000005/g' tab_phenotype.csv

# 121.
# ESSENTIAL microcolonies slightly skittle cells at 25-32 (1)
# https://sourceforge.net/p/pombase/fission-yeast-phenotype/808/
# cell phenotype
# FYPO:0002111 bottle-shaped inviable vegetative cell (expressivity low)
# cell population phenotype
# FYPO:0002210 inviable microcolony, bottle-shaped cells /808/

echo "121."
perl -pi -e 's/ESSENTIAL microcolonies slightly skittle cells at 25-32/FYPO:0002111,PECO:0000005,has_penetrance(FYPO_EXT:0000001),has_expressivity(FYPO_EXT:0000003)| FYPO:0002210,PECO:0000005/g' tab_phenotype.csv


# 122.
# ESSENTIAL microcolonies small cells- often skittle at 25-32 (1) CHECK UP ON THIS (JACKY checking)


# 123. DUPLICATE OF 117
# ESSENTIAL spores- germinated spores- microcolonies skittle cells at 25-32 (1)


# 124.
# ESSENTIAL spores  at 32- microcolonies skittle cells at 25 (1) (JACKY checking)


# 125. 
# ESSENTIAL microcolonies rounded skittle cells at 25-32 (1)
# broad classifier: skittle
# https://sourceforge.net/p/pombase/fission-yeast-phenotype/808/
# cell phenotype
# FYPO:0002111 bottle-shaped inviable vegetative cell 
# cell population phenotype
# FYPO:0002210 inviable microcolony, bottle-shaped cells /808/

echo "125."
perl -pi -e 's/ESSENTIAL microcolonies rounded skittle cells at 25-32/FYPO:0002111,PECO:0000005,has_penetrance(FYPO_EXT:0000001)| FYPO:0002210,PECO:0000005/g' tab_phenotype.csv


# 126.
# ESSENTIAL microcolonies skittle- rounded cells at 25-32 (6)
# broad classifier: skittle
# https://sourceforge.net/p/pombase/fission-yeast-phenotype/808/
# cell phenotype
# FYPO:0002111 bottle-shaped inviable vegetative cell
# cell population phenotype
# FYPO:0002210 inviable microcolony, bottle-shaped cells /808/

echo "126"
perl -pi -e 's/ESSENTIAL microcolonies skittle- rounded cells at 25-32/FYPO:0002111,PECO:0000005,has_penetrance(FYPO_EXT:0000001)| FYPO:0002210,PECO:0000005/g' tab_phenotype.csv


# 127.
# ESSENTIAL microcolonies skittle cells 32- cells more rounded at 25 (1)
# broad classifier: skittle
# https://sourceforge.net/p/pombase/fission-yeast-phenotype/808/
# cell phenotype
# FYPO:0002111 bottle-shaped inviable vegetative cell 
# cell population phenotype 
# FYPO:0002210 inviable microcolony, bottle-shaped cells /808/

echo "127."
perl -pi -e 's/ESSENTIAL microcolonies skittle cells 32- cells more rounded at 25/FYPO:0002111,PECO:0000005,has_penetrance(FYPO_EXT:0000001)| FYPO:0002210,PECO:0000005/g' tab_phenotype.csv


# 128.
# ESSENTIAL microcolonies skittle cells at 32- cells more rounded at 25 (1)
# broad classifier: skittle
# https://sourceforge.net/p/pombase/fission-yeast-phenotype/808/
# cell phenotype
# FYPO:0002111 bottle-shaped inviable vegetative cell 
# cell population phenotype
# FYPO:0002210 inviable microcolony, bottle-shaped cells /808/
echo "128."
perl -pi -e 's/ESSENTIAL microcolonies skittle cells at 32- cells more rounded at 25/FYPO:0002111,PECO:0000005,has_penetrance(FYPO_EXT:0000001)| FYPO:0002210,PECO:0000005/g' tab_phenotype.csv

# 129
# ESSENTIAL germinated spores- microcolonies rounded skittle cells at 25-32 (1)
# https://sourceforge.net/p/pombase/fission-yeast-phenotype/847/
# broad classifier: skittle
# cell phenotype 
# FYPO:0000320 inviable skittle cells (penetrance??????)
# FYPO:0000310 inviable after spore germination with normal germ tube morphology (penetrance????)
# population phenotype
# FYPO:0002185 inviable mixed population including germinated spores and bottle-shaped cells (847)
echo  "129."
perl -pi -e 's/ESSENTIAL germinated spores- microcolonies rounded skittle cells at 25-32/FYPO:0000320,PECO:0000005|, FYPO:0000310,PECO:0000005| FYPO:0002185,PECO:0000005/g'  tab_phenotype.csv


# 130.  
# ESSENTIAL small colonies rounded cells at 25-32 (1)
# ESSENTIAL small colonies rounded cells at 25-32- lysis after 48h  PLUS  FYPO:0000647 cell lysis (1)
# ESSENTIAL small colonies rounded cells at 32- cells longer at 25 (1)
# ESSENTIAL small colonies rounded cells at 32- larger colonies at 25 (1)
# https://sourceforge.net/p/pombase/fission-yeast-phenotype/780/
# broad classification: rounded
# cell phenotype
# FYPO:0002187 inviable normal volume spheroid vegetative cell  (SF 780) (HIGH PENETRANT)
# population phenotype
# FYPO:0002188 inviable microcolony, normal volume spheroid cells   (SF 780)

echo "130 a."
perl -pi -e 's/ESSENTIAL small colonies rounded cells at 25-32/FYPO:0002187,PECO:0000005,has_penetrance(FYPO_EXT:0000001)| FYPO:0002188,PECO:0000005/g' tab_phenotype.csv

echo "130 b."
perl -pi -e 's/ESSENTIAL small colonies rounded cells at 25-32 lysis after 48 hours/FYPO:0002187,PECO:0000005,has_penetrance(FYPO_EXT:0000001)|FYPO:0000647,PECO:0000005| FYPO:0002188,PECO:0000005/g' tab_phenotype.csv

echo "130 c."
perl -pi -e 's/ESSENTIAL small colonies rounded cells at 32- cells longer at 25/FYPO:0002187,PECO:0000005,has_penetrance(FYPO_EXT:0000001)| FYPO:0002188,PECO:0000005/g' tab_phenotype.csv

echo "130 d."
perl -pi -e 's/ESSENTIAL small colonies rounded cells at 32- larger colonies at 25/FYPO:0002187,PECO:0000005,has_penetrance(FYPO_EXT:0000001)| FYPO:0002188,PECO:0000005/g' tab_phenotype.csv


# 131. 
# ESSENTIAL microcolonies rounded septated cells at 25-32 (1)
# https://sourceforge.net/p/pombase/fission-yeast-phenotype/806/
# broad classification: rounded
# cellular phenotype
# FYPO:0002193 inviable normal volume septated spheroid vegetative cell (806)
# population phenotype
# FYPO:0002192 inviable microcolony, normal volume septated spheroid cells  (780)

echo "131."
perl -pi -e 's/ESSENTIAL microcolonies rounded septated cells at 25-32/FYPO:0002193,PECO:0000005| FYPO:0002192,PECO:0000005/g' tab_phenotype.csv

# 132.
# ESSENTIAL microcolonies large rounded septated cells at 25-32 (1)
# broad classification: rounded
# https://sourceforge.net/p/pombase/fission-yeast-phenotype/806/
# https://sourceforge.net/p/pombase/fission-yeast-phenotype/780/
# cellular phenotype
# FYPO:0002240 swollen septated spheroid vegetative cell (806)
# population phenotype
# FYPO:0002194 inviable microcolony, swollen septated spheroid cells (780)


echo "132"
perl -pi -e 's/ESSENTIAL microcolonies large rounded septated cells at 25-32/FYPO:0002240,PECO:0000005| FYPO:0002194,PECO:0000005/g' tab_phenotype.csv

# 133. 
# LONG SKITTLE (weak)
# broad classification: long high penetrance
# ESSENTIAL microcolonies long- weak skittle cells at 25-32 (1)
# ESSENTIAL microcolonies long slight skittle cells at 25-32 (1)
# https://sourceforge.net/p/pombase/fission-yeast-phenotype/80
# cellular phenotype
# # FYPO:0000059 abnormal mitotic cell cycle progression (standard temperature)
# population phenotype
# FYPO:0000059,PECO:0000005| 

# 134. 
#  
#  https://sourceforge.net/p/pombase/fission-yeast-phenotype/801/
#  ESSENTIAL microcolonies stubby cells at 25-32 (1) 
#  ESSENTIAL microcolonies stubby cells at 25- cells slightly misshapen at 32 (1)
#  ESSENTIAL microcolonies stubby cells at 25-32 (1)
#  ESSENTIAL microcolonies stubby cells at 32 cells more misshapen at 25 (1)
#  broad classification: stubby
#  cell phenotype
#  FYPO:0002107 stubby inviable cell (high penetrance)
#  population phenotype
#  FYPO:0002202 inviable stubby vegetative cell population  (801)


echo "134.a"
perl -pi -e 's/ ESSENTIAL microcolonies stubby cells at 25-32/FYPO:0002107,PECO:0000005,has_penetrance(FYPO_EXT:0000001)| FYPO:0002202,PECO:0000005/g' tab_phenotype.csv

echo "134.b"
perl -pi -e 's/ESSENTIAL microcolonies stubby cells at 25- cells slightly misshapen at 32/FYPO:0002107,PECO:0000005,has_penetrance(FYPO_EXT:0000001)| FYPO:0002202,PECO:0000005/g' tab_phenotype.csv

echo "134.c"
perl -pi -e 's/ESSENTIAL microcolonies stubby cells at 25-32/FYPO:0002107,PECO:0000005,has_penetrance(FYPO_EXT:0000001)| FYPO:0002202,PECO:0000005/g' tab_phenotype.csv

echo "134.d"
perl -pi -e 's/microcolonies stubby cells at 32 cells more misshapen at 25/FYPO:0002107,PECO:0000005,has_penetrance(FYPO_EXT:0000001)| FYPO:0002202,PECO:0000005/g' tab_phenotype.csv


# 135. ignore long
# broad classification: stubby
# https://sourceforge.net/p/pombase/fission-yeast-phenotype/801/
# ESSENTIAL microcolonies stubby cells- occasionally long at 25-32 (1)
# cell phenotype
# FYPO:0002107 stubby inviable cell
# population phenotype
# FYPO:0002203 inviable microcolony, stubby cells (801)

echo "135."
perl -pi -e 's/ESSENTIAL microcolonies stubby cells- occasionally long at 25-32/FYPO:0002107,PECO:0000005,has_penetrance(FYPO_EXT:0000003)| FYPO:0002203,PECO:0000005/g' tab_phenotype.csv

# 136.
# broad classifier: stubby
# https://sourceforge.net/p/pombase/fission-yeast-phenotype/801/
# ESSENTIAL microcolonies stubby- septated cells at 25-32 (1) (high penetrance)
# ESSENTIAL microcolonies stubby- septated cells- some lysis at 25-32 (1) (high penetrance)
# cell phenotype
# ntr: inviable stubby septated cells
# FYPO:0002200 inviable stubby septated vegetative cell (801)
# population phenotype
# FYPO:0002204 inviable microcolony, stubby septated cells  

echo "136.a"
perl -pi -e 's/ESSENTIAL microcolonies stubby- septated cells at 25-32/FYPO:0002200,PECO:0000005,has_penetrance(FYPO_EXT:0000003)| FYPO:0002204,PECO:0000005/g' tab_phenotype.csv

echo "136.b"
perl -pi -e 's/ESSENTIAL microcolonies stubby- septated cells- some lysis at 25-32/FYPO:0002200,PECO:0000005,has_penetrance(FYPO_EXT:0000003)| FYPO:0002204,PECO:0000005/g' tab_phenotype.csv

#####add lysis

# 137. Asked Jacky if these really are small colonies (yes recheck numbes)
# ESSENTIAL small colonies stubby cells at 25-32 (1)
# https://sourceforge.net/p/pombase/fission-yeast-phenotype/801/
# broad classifier: stubby
# cell phenotype
# FYPO:0002107 stubby inviable cell (high penetrance ????)
# population phenotype
# FYPO:0002203 inviable microcolony, stubby cells (801)

echo "137."
perl -pi -e 's/ESSENTIAL small colonies stubby cells at 25-32/FYPO:0002107,PECO:0000005,has_penetrance(FYPO_EXT:0000001)| FYPO:0002203,PECO:0000005/g' tab_phenotype.csv

# 138.
# broad classifier: long high penetrance
# https://sourceforge.net/p/pombase/fission-yeast-phenotype/834/
# https://sourceforge.net/p/pombase/fission-yeast-phenotype/843/
# ESSENTIAL germinated spores long curved at 25-32 (1)
# ESSENTIAL germinated spores- often long and curved at 25-32 (1)
# cell phenotype
# FYPO:0002212 inviable after spore germination with elongated, curved germ tube (high penetrance) (843)
# FYPO:0000059 abnormal mitotic cell cycle progression (standard temperature)
# population phenotype
# FYPO:0002213 population of inviable germinated spores with curved elongated germ tube (834)

echo "138.a"
perl -pi -e 's/ESSENTIAL germinated spores long curved at 25-32/FYPO:0002212,PECO:0000005,has_penetrance(FYPO_EXT:0000001)| FYPO:0002213,PECO:0000005/g' tab_phenotype.csv
echo "138.b"
perl -pi -e 's/ESSENTIAL germinated spores- often long and curved at 25-32/FYPO:0002212,PECO:0000005,has_penetrance(FYPO_EXT:0000001)| FYPO:0000059,PECO:0000005| FYPO:0002213,PECO:0000005/g' tab_phenotype.csv

# 139.  ASKED JACKY
# broad classifier: long high penetrance
# ESSENTIAL germinated spores long curved- often divide at 25-32 (1)
# https://sourceforge.net/p/pombase/fission-yeast-phenotype/848/
# https://sourceforge.net/p/pombase/fission-yeast-phenotype/849/
# https://sourceforge.net/p/pombase/fission-yeast-phenotype/850/
# cellular phenotype
# FYPO:0002212  inviable after spore germination, with curved elongated germ tube (848) (high penetrance)
# FYPO:0000059 abnormal mitotic cell cycle progression (standard temperature)
# FYPO:NEW inviable after spore germination, with curved elongated germ tube, divides once  (849) (high penetrance)
# population phenotype
# ntr: population of germinated spores with elongated germ tube, some divide once (*****check inviable) 
perl -pi -e 's/ESSENTIAL germinated spores long curved- often divide at 25-32/FYPO:0002212,PECO:0000005| FYPO:NEW_849,PECO:0000005| FYPO:0000059,PECO:0000005| FYPO:NEW-850,PECO:0000005/g' tab_phenotype.csv


# 140.  need to decide how to represent (ask jacky)
# long high penetrance (with curved)
#   1 ESSENTIAL microcolonies long cells- often curved at 25-32
#  4 ESSENTIAL microcolonies long curved cells at 25-32
#  1 ESSENTIAL microcolonies long curved misshapen cells at 32- microcolonies with some long cells at 25
# 1 ESSENTIAL microcolonies long slightly curved cells at 25-32 
#  1 ESSENTIAL microcolonies long slightly curved cells- colonies appear dark at 25-32

# 141. (ask jacky)
# ESSENTIAL microcolonies slightly long curved cells at 25-32 (1)
# curved
# difficult because low expressivity only applied to  long


# 142. need to work on this one
#
# broad classifier: long low penetrance 
#   1 ESSENTIAL spores- germinated spores- some long curved at 25-32
#  spores
#  germinated
#  long curved see 55


# 143.
#  broad classifier: curved
#  ESSENTIAL microcolonies curved septated cells at 25- 32  (1) 
#  ESSENTIAL microcolonies curved septated cells at 25-32 (2) 
#  https://sourceforge.net/p/pombase/fission-yeast-phenotype/851/
#  https://sourceforge.net/p/pombase/fission-yeast-phenotype/852/
#  cell phenotype
#  NTR:****** curved inviable septated cell (851) (high penetrance)
#  population phenotype
#  NTR******* microcolonies curved septated cells (852)

echo "143.a"
perl -pi -e 's/ESSENTIAL microcolonies curved septated cells at 25- 32/FYPO:000****,PECO:0000005,has_penetrance(FYPO_EXT:0000001)| FYPO:xxxxxxx,PECO:0000005/g' tab_phenotype.csv
echo "143.b"
perl -pi -e 's/ESSENTIAL microcolonies curved septated cells at 25-32/FYPO:000****,PECO:0000005,has_penetrance(FYPO_EXT:0000001)| FYPO:xxxxxxx,PECO:0000005/g' tab_phenotype.csv


# 144.
# a. ESSENTIAL microcolonies curved cells at 32- cells more WT at 25 (1)
# b. ESSENTIAL microcolonies slightly misshapen curved cells  at 25-32 (1) 
# https://sourceforge.net/p/pombase/fission-yeast-phenotype/814/
# cell phenotype
# FYPO:0002113 curved inviable cell (high penetrance?)
# population phenotype
# FYPO:0002231 inviable microcolony, curved cells  (414)
# echo 144.a.
perl -pi -e 's/ESSENTIAL microcolonies curved cells at 32- cells more WT at 25/FYPO:0002113,PECO:0000005,has_penetrance(FYPO_EXT:0000001)| FYPO:0002231,PECO:0000005/g' tab_phenotype.csv
# echo 144.b.
perl -pi -e 's/ESSENTIAL microcolonies curved cells at 32- cells more WT at 25/FYPO:0002113,PECO:0000005,has_penetrance(FYPO_EXT:0000001),has_specificity(FYPO_EXT:0000003)| FYPO:0002231,PECO:0000005/g' tab_phenotype.csv

# 145.
# ESSENTIAL microcolonies curved misshapen cells- colonies have a dark edge at 25-32 (1)
# https://sourceforge.net/p/pombase/fission-yeast-phenotype/814/
# broad classifier: curved
# cell phenotype
# FYPO:0002113 curved inviable cell
# FYPO:0000741 increased  cellular pigment accumulation
# population phenotype
# FYPO:0002231 inviable microcolony, curved cells  (414)
echo "145."
perl -pi -e 's/ESSENTIAL microcolonies curved misshapen cells- colonies have a dark edge at 25-32/FYPO:0002113,PECO:0000005,has_penetrance(FYPO_EXT:0000003)| FYPO:0000741,PECO:0000005| FYPO:0002231,PECO:0000005/g' tab_phenotype.csv


# 146.
# ESSENTIAL microcolonies curved misshapen swollen cells at 25-32  (1)
# https://sourceforge.net/p/pombase/fission-yeast-phenotype/814/
# https://sourceforge.net/p/pombase/fission-yeast-phenotype/815/
# broad classifier: curved
# cell phenotype
# FYPO:0002230 inviable swollen curved vegetative cell  (814)  (high penetrance?) 
# population phenotype 
# FYPO:0002232 inviable microcolony, swollen curved cells  (814)
echo "146."
perl -pi -e 's/ESSENTIAL microcolonies curved misshapen swollen cells at 25-32/FYPO:0002230,PECO:0000005,has_penetrance(FYPO_EXT:0000001)| FYPO:0002232,PECO:0000005/g' tab_phenotype.csv


# 147. should this be mapped to curved?
# ESSENTIAL microcolonies misshapen curved cells at 25-32 (2)
# broad classifier: misshapen essential 
# cell phenotype
# general misshapen
# curved (low penetrance? ) jacky checking
# population phenotype

# 148.
# ESSENTIAL microcolonies slightly curved vacuolated cells at 25-32 (1)
# https://sourceforge.net/p/pombase/# fission-yeast-phenotype/815/
# https://sourceforge.net/p/pombase/fission-yeast-phenotype/814/
# broad classifier: curved
# cell phenotype
# FYPO:0002250:inviable curved vacuolated vegetative cell     LOW expressivity (815?)
# population phenotype 
# FYPO:0002231 inviable microcolony, curved cells  (814)

echo "148."
perl -pi -e 's/ESSENTIAL microcolonies slightly curved vacuolated cells at 25-32/FYPO:0002250,PECO:0000005,has_expressivity(FYPO_EXT:0000003)| FYPO:0002231,PECO:0000005/g' tab_phenotype.csv

# 149.
# VIABLE small colonies long curved cells at 32- ESSENTIAL microcolonies long cells at 25-36 (1)
# broad phenotype: long high penetrance
# http://sourceforge.net/p/pombase/fission-yeast-phenotype/843/
# https://sourceforge.net/p/pombase/fission-yeast-phenotype/853/ 839 
# https://sourceforge.net/p/pombase/fission-yeast-phenotype/854/
# https://sourceforge.net/p/pombase/fission-yeast-phenotype/856/
# cell phenotype
# FYPO:0002215 elongated curved viable vegetative cell (standard temp)  (843 OR 853)?
# FYPO:0001490 elongated inviable vegetative cell  (high temp/ low temperature) 
# FYPO:0000059 abnormal mitotic cell cycle progression (standard temperature)
# population  phenotypes
# small colonies viable elongated curved (standard temp) (854/855) 
# essential microcolonies long (high temperature/ low temperature)  (856)


echo "149."
perl -pi -e 's/VIABLE small colonies long curved cells at 32- ESSENTIAL microcolonies long cells at 25-36/FYPO:0002215,PECO:0000005| FYPO:0001490,PECO:0000004| FYPO:0001490,PECO:0000006| FYPO:xxxx854,PECO:0000005| FYPO:0000059,PECO:0000005| FYPO:000****,PECO:0000004| FYPO:000****,low temperature/g' tab_phenotype.csv


#150
# germination
# ESSENTIAL spores- germinated spores- occasionally microcolonies wee at 25-32 (1)
# ESSENTIAL spores- germinated spores- occasionally microcolonies small cells at 25-32 (1)
# cell phenotypes
# FYPO:0001991 inviable after spore germination, without cell division (high penetracne)
# FYPO:0000951 small inviable vegetative cell (low penetrance)
# FYPO:*** inviable spores (low penetracne)
# population phenotypes
# FYPO:NEW mixed population of spores, germinated undivided spores and microcolonies of small cells

echo "150 a ADD perl"
echo "150 b ADD perl"

# 151
# ESSENTIAL microcolonies slightly small cells at 25-32
# small
# FYPO:0000951 small inviable vegetative cell high penetrance, low expressivity
# FYPO:0002152 small inviable vegetative cell population low expressivity

echo "151."
perl -pi -e 's/ESSENTIAL microcolonies slightly small cells at 25-32/FYPO:0000951,PECO:0000005,has_penetrance(FYPO_EXT:0000001),has_expressivity(FYPO_EXT:0000003)| FYPO:0002152,PECO:0000005,has_expressivity(FYPO_EXT:0000003)/g' tab_phenotype.csv


# 83.
# VIABLE slightly misshapen cells at 25-32
# broad classifier: misshapen weak viable
# https://sourceforge.net/p/pombase/fission-yeast-phenotype/825/
# cell phenotype
# FYPO:0001510 viable vegetative cell, abnormal cell shape, normal cell size  (low expressivity) (high penetrance)
# poplulation phenotype
# FYPO:0002198 viable vegetative cell population with abnormal cell shape 

echo "83."
perl -pi -e 's/VIABLE slightly misshapen cells at 25-32/FYPO:0001510,PECO:0000005,has_expressivity(FYPO_EXT:0000003),has_penetrance(FYPO_EXT:0000001)| FYPO:0002198,PECO:0000005/g' tab_phenotype.csv



##########################################
##########################################

# 152
# ASked Jacky
# ESSENTIAL spores- some germinated spores long at 25-32 
# broad classifier: spores
# cell phenotype
# inviable spores (high pen)
# germinated spores with elongated germ tube (low pen)
# population phenotype
# mixed pop of ? 


# 153
# a) ESSENTIAL germinated spores long at 25- germinated spores slightly long at 32  (1) (expressivity low)
# b) ESSENTIAL germinated spores slightly long at 25-32 (2) (expressivity low)
# c) ESSENTIAL germinated spores long misshapen at 25-32 (2)
# d) ESSENTIAL germinated spores long often misshapen at 25-32 (1)
# long high penetrance
# cell phenotype
# FYPO:0000314 inviable after spore germination with elongated germ tube (expressivity low)
# FYPO:0000059 abnormal mitotic cell cycle progression (standard temperature)
# population phenotype
# FYPO:0002211 inviable vegetative cell population after spore germination, elongated germ tubes

echo "153a"
perl -pi -e 's/ESSENTIAL germinated spores long at 25- germinated spores slightly long at 32/FYPO:0000314,PECO:0000005, has_expressivity(FYPO_EXT:0000003)| FYPO:0000059,PECO:0000005| FYPO:0002211,PECO:0000005/g' tab_phenotype.csv
echo "153b"
perl -pi -e 's/ESSENTIAL germinated spores slightly long at 25-32/FYPO:0000314,PECO:0000005,has_expressivity(FYPO_EXT:0000003)| FYPO:0000059,PECO:0000005| FYPO:0002211,PECO:0000005/g' tab_phenotype.csv
echo "153c"
perl -pi -e 's/ESSENTIAL germinated spores long misshapen at 25-32/FYPO:0000314,PECO:0000005,has_expressivity(FYPO_EXT:0000003)| FYPO:0000059,PECO:0000005| FYPO:0002211,PECO:0000005/g' tab_phenotype.csv
echo "153d"
perl -pi -e 's/ESSENTIAL germinated spores long often misshapen at 25-32/FYPO:0000314,PECO:0000005,has_expressivity(FYPO_EXT:0000003)| FYPO:0000059,PECO:0000005| FYPO:0002211,PECO:0000005/g' tab_phenotype.csv

# 154
# a) ESSENTIAL germinated spores long- lysis at 25-32  (6) 
# b) ESSENTIAL germinated spores long misshapen- lysis at 25-32 (1) 
# long high penetrance
# https://sourceforge.net/p/pombase/fission-yeast-phenotype/874/
# cell phenotype
# FYPO:0000314 inviable after spore germination with elongated germ tube (expressivity low) (penetrance high)
# FYPO:0000059 abnormal mitotic cell cycle progression (standard temperature)
# FYPO:0000NEW lysed cell after spore germination with elongated germ tube  (expressivity low) (penetrance low) (874*******)
# population phenotype
# FYPO:0002211 inviable vegetative cell population after spore germination, elongated germ tubes 

echo "154a"
perl -pi -e 's/ESSENTIAL germinated spores long- lysis at 25-32/FYPO:0000314,PECO:0000005,has_expressivity(FYPO_EXT:0000003),has_penetrance(FYPO_EXT:0000001)| FYPO:0002211,PECO:0000005,has_expressivity(FYPO_EXT:0000003),has_penetrance(FYPO_EXT:0000002)| FYPO:0000059,PECO:0000005 /g' tab_phenotype.csv
echo "154b"
perl -pi -e 's/ESSENTIAL germinated spores long misshapen- lysis at 25-32/FYPO:0000314,PECO:0000005,has_expressivity(FYPO_EXT:0000003),has_penetrance(FYPO_EXT:0000001)| FYPO:0002211,PECO:0000005,has_expressivity(FYPO_EXT:0000003),has_penetrance(FYPO_EXT:0000002)| FYPO:0000059,PECO:0000005 /g' tab_phenotype.csv


# 155.
# long high penetrance
# a) 1 ESSENTIAL germinated spores long- some microcolonies long cells at 25-32
# b) 4 ESSENTIAL germinated spores long- microcolonies long cells at 25-32
# c) 5 ESSENTIAL germinated spores long- microcolonies with some long cells at 25-32
# d) 1 ESSENTIAL germinated spores long- some division at 32- microcolonies long cells at 25
# cell phenotype
# FYPO:0000314 inviable after spore germination with elongated germ tube 
# FYPO:0001490 inviable elongated vegetative cell (high pentrance)
# FYPO:0000059 abnormal mitotic cell cycle progression (standard temperature)
# population phenotype
# FYPO:0002149 inviable elongated vegetative cell population
# FYPO:0002225 inviable microcolony, elongated cells

echo "155a"
perl -pi -e 's/ESSENTIAL germinated spores long- some microcolonies long cells at 25-32/FYPO:0000314,PECO:0000005| FYPO:0002211,PECO:0000005,has_pentrance(FYPO_EXT:0000001)| FYPO:0000059,PECO:0000005| FYPO:0002149,PECO:0000005| FYPO:0002225,PECO:0000005/g' tab_phenotype.csv
echo "155b"
perl -pi -e 's/ESSENTIAL germinated spores long- microcolonies long cells at 25-32/FYPO:0000314,PECO:0000005| FYPO:0002211,PECO:0000005,has_pentrance(FYPO_EXT:0000001)| FYPO:0000059,PECO:0000005| FYPO:0002149,PECO:0000005| FYPO:0002225,PECO:0000005/g' tab_phenotype.csv
echo "155c"
perl -pi -e 's/ESSENTIAL germinated spores long- microcolonies with some long cells at 25-32/FYPO:0000314,PECO:0000005| FYPO:0002211,PECO:0000005,has_pentrance(FYPO_EXT:0000001)| FYPO:0000059,PECO:0000005| FYPO:0002149,PECO:0000005| FYPO:0002225,PECO:0000005/g' tab_phenotype.csv
echo "155d"
perl -pi -e 's/ESSENTIAL germinated spores long- some division at 32- microcolonies long cells at 25/FYPO:0000314,PECO:0000005| FYPO:0002211,PECO:0000005,has_pentrance(FYPO_EXT:0000001)| FYPO:0000059,PECO:0000005| FYPO:0002149,PECO:0000005| FYPO:0002225,PECO:0000005/g' tab_phenotype.csv


#156
# similar to 155
# 1 ESSENTIAL germinated spores long- some division at 25- microcolonies with some long cells at 32
# 1 ESSENTIAL germinated spores long at 32- microcolonies long cells at 25
# ==
#157
# 5 ESSENTIAL germinated spores- often long at 25-32
# 1 ESSENTIAL germinated spores- often long often divide at 25- 32 
# 1 ESSENTIAL germinated spores- often long- some division at 25-32
# jacky says slightly less penetrant but still high pentrant
# ====

# 158  
# broad classifier: long high penetrance
# https://sourceforge.net/p/pombase/fission-yeast-phenotype/875/
# a) 1 ESSENTIAL germinated spores long often divide at 25-32
# b) 1 ESSENTIAL germinated spores long at 32- more division at 25
# c) 2 ESSENTIAL germinated spores long- often divide 25-32
# d) 2 ESSENTIAL germinated spores long- often divide at 25-32
# e) 1 ESSENTIAL germinated spores long- often divide once at 25-32
# f) 8 ESSENTIAL germinated spores long- some division at 25-32
# g) 1 ESSENTIAL germinated spores long- occasionally divide 25-32
# h) 1 ESSENTIAL germinated spores long- occasionally divide at 25-32
# i) ESSENTIAL germinated spores long at 25-32- often divide at 32 (2) (I have ignored the dividing at 32, because it doesn't fit our temperature split well, might fix later)
# cell phenotypes
# FYPO:0000314 inviable after spore germination with elongated germ tube
# FYPO:0001042 inviable after spore germination, single or double cell division
# FYPO:0000059 abnormal mitotic cell cycle progression (standard temperature)

# population phenotype
# FYPO:0002149 inviable elongated vegetative cell population (this could be more specific, mixed population of spores with elongated germ tube and elongated inviable cells) (875)

echo "158a"
perl -pi -e 's/ESSENTIAL germinated spores long often divide at 25-32/FYPO:0000314,PECO:0000005| FYPO:0001042,PECO:0000005| FYPO:0000059,PECO:0000005| FYPO:0002149,PECO:0000005/g' tab_phenotype.csv
echo "158b"
perl -pi -e 's/ESSENTIAL germinated spores long at 32- more division at 25/FYPO:0000314,PECO:0000005| FYPO:0001042,PECO:0000005| FYPO:0000059,PECO:0000005| FYPO:0002149,PECO:0000005/g' tab_phenotype.csv
echo "158c"
perl -pi -e 's/ESSENTIAL germinated spores long- often divide 25-32/FYPO:0000314,PECO:0000005| FYPO:0001042,PECO:0000005| FYPO:0000059,PECO:0000005| FYPO:0002149,PECO:0000005/g' tab_phenotype.csv
echo "158d"
perl -pi -e 's/ESSENTIAL germinated spores long- often divide at 25-32/FYPO:0000314,PECO:0000005| FYPO:0001042,PECO:0000005| FYPO:0000059,PECO:0000005| FYPO:0002149,PECO:0000005/g' tab_phenotype.csv
echo "158e"
perl -pi -e 's/ESSENTIAL germinated spores long- often divide once at 25-32/FYPO:0000314,PECO:0000005| FYPO:0001042,PECO:0000005| FYPO:0000059,PECO:0000005| FYPO:0002149,PECO:0000005/g' tab_phenotype.csv
echo "158f"
perl -pi -e 's/ESSENTIAL germinated spores long- some division at 25-32/FYPO:0000314,PECO:0000005| FYPO:0001042,PECO:0000005| FYPO:0000059,PECO:0000005| FYPO:0002149,PECO:0000005/g' tab_phenotype.csv
echo "158g"
perl -pi -e 's/ESSENTIAL germinated spores long- occasionally divide 25-32/FYPO:0000314,PECO:0000005| FYPO:0001042,PECO:0000005| FYPO:0000059,PECO:0000005| FYPO:0002149,PECO:0000005/g' tab_phenotype.csv
echo "158h"
perl -pi -e 's/ESSENTIAL germinated spores long- occasionally divide at 25-32/FYPO:0000314,PECO:0000005| FYPO:0001042,PECO:0000005| FYPO:0000059,PECO:0000005| FYPO:0002149,PECO:0000005/g' tab_phenotype.csv
echo "158i"
perl -pi -e 's/ESSENTIAL germinated spores long at 25-32- often divide at 32/FYPO:0000314,PECO:0000005| FYPO:0001042,PECO:0000005| FYPO:0000059,PECO:0000005| FYPO:0002149,PECO:0000005/g' tab_phenotype.csv


# =====
#159.
# long low penetrance
# 1 ESSENTIAL germinated spores at 25- germinated spores- occasionally long at 32
# 2 ESSENTIAL germinated spores- occasionally long at 25-32
# 1 ESSENTIAL germinated spores- occasionally long- occasionally divide at 25-32
# 1 ESSENTIAL germinated spores- occasionally long- some division at 25-32 
# germinated spores with elongated germ tube (low pen)

#160
# long high penetracne cdc13
# 1 ESSENTIAL germinated spores long- swollen centre at 25-32
# swollen enviable elongated cell (check vegetative term) fully penetrant
# =====

#161
# misshapen essential
# 18 ESSENTIAL germinated spores misshapen at 25-32 
# non dividing 
# cell phenotype
# FYPO:0000313 inviable after spore germination, abnormal germ tube morphology (high_penetrance)
# population phenotype 
# FYPO:0002214 inviable vegetative cell population after spore germination, abnormal germ tube morphology

echo "161."
perl -pi -e 's/germinated spores misshapen at 25-32/FYPO:0000313,PECO:0000005,has_penetrance(FYPO_EXT:0000001)| FYPO:0002214,PECO:0000005/g' tab_phenotype.csv

# 162
# misshapen essential
# DIVIDE OCCASIONALLY = divides once
# a)  1 ESSENTIAL germinated spores slightly misshapen- occasionally divide at 25-32
# b) 12 ESSENTIAL germinated spores slightly misshapen- some division at 25-32
# c) 2 ESSENTIAL germinated spores misshapen- some division at 25-32
# d)  1 ESSENTIAL germinated spores slightly misshapen and divide once at 25-32
# e) 24 ESSENTIAL germinated spores slightly misshapen and divide once at 25-32
# f) 1 ESSENTIAL germinated spores slightly misshapen and divide once at 32- microcolonies misshapen cells at 25
# g) 2 ESSENTIAL germinated spores slightly misshapen- divide once at 25-32
# h) 5 ESSENTIAL germinated spores slightly misshapen- often divide once at 25-32
# i) 1 ESSENTIAL germinated spores slightly misshapen- often divide at 25-32

# cell phenotype
# FYPO:0000313 inviable after spore germination, abnormal germ tube morphology
# FYPO:0001042 inviable after spore germination, single or double cell division (are these abnormal morphology??)
# population phenotype 
# FYPO:000**** inviable vegetative cell population after spore germination, abnormal morphology

echo  "162 a"
perl -pi -e 's/ESSENTIAL germinated spores slightly misshapen- occasionally divide at 25-32/FYPO:0000313,PECO:0000005| FYPO:0001042,PECO:0000005/g' tab_phenotype.csv
echo "162 b"
perl -pi -e 's/ESSENTIAL germinated spores slightly misshapen- some division at 25-32/FYPO:0000313,PECO:0000005| FYPO:0001042,PECO:0000005/g' tab_phenotype.csv
echo "162 c"
perl -pi -e 's/ESSENTIAL germinated spores slightly misshapen and divide once at 25-32/FYPO:0000313,PECO:0000005| FYPO:0001042,PECO:0000005/g' tab_phenotype.csv
echo "162 d"
perl -pi -e 's/ESSENTIAL germinated spores slightly misshapen and divide once at 25-32/FYPO:0000313,PECO:0000005| FYPO:0001042,PECO:0000005/g' tab_phenotype.csv
echo "162 e"
perl -pi -e 's/ESSENTIAL germinated spores slightly misshapen and divide once at 25-32/FYPO:0000313,PECO:0000005| FYPO:0001042,PECO:0000005/g' tab_phenotype.csv
echo "162 f"
perl -pi -e 's/ESSENTIAL germinated spores slightly misshapen and divide once at 32- microcolonies misshapen cells at 25/FYPO:0000313,PECO:0000005| FYPO:0001042,PECO:0000005/g' tab_phenotype.csv
echo "162 g"
perl -pi -e 's/ESSENTIAL germinated spores slightly misshapen- divide once at 25-32/FYPO:0000313,PECO:0000005| FYPO:0001042,PECO:0000005/g' tab_phenotype.csv
echo "162 h"
perl -pi -e 's/ESSENTIAL germinated spores slightly misshapen- often divide once at 25-32/FYPO:0000313,PECO:0000005| FYPO:0001042,PECO:0000005/g' tab_phenotype.csv
echo "162 i"
perl -pi -e 's/ESSENTIAL germinated spores slightly misshapen- often divide at 25-32/FYPO:0000313,PECO:0000005| FYPO:0001042,PECO:0000005/g' tab_phenotype.csv


# CHECK THIS
# more specific cell phenotype: ntr: inviable after spore germination, single cell division, abnormal cell shape, normal cell size
#child of inviable after spore germination, single cell division, AND "inviable vegetative cell, abnormal cell shape, normal cell size
# population phenotype: ntr: Population of inviable germinated spores that divide once to give cells with abnormal cell shape, 
# normal cell size

# germination
# 2 ESSENTIAL germinated spores- occasionally divide at 25-32

# Misshapen essential
# DIVIDE ONCE OR TWICE
# 8 ESSENTIAL germinated spores slightly misshapen and divide once or twice at 25-32
# 1 ESSENTIAL germinated spores slightly misshapen- divide once or twice at 25-32
# 2 ESSENTIAL germinated spores slightly misshapen- occasionally divide once or twice- at 25-32

# ntr: inviable after spore germination, single or double cell division, abnormal cell shape, normal cell size
# child of
# inviable after spore germination, single or double cell division
# inviable vegetative cell, abnormal cell shape, normal cell size

# population phenotype ntr: mixed population of inviable germinated spores that divide once to give cells with abnormal cell shape, normal cell size

# 69F
# misshapen essential
# MICROCOLONIES 

# 1 ESSENTIAL germinated spores- microcolonies misshapen cells at 25-32
# 1 ESSENTIAL germinated spores- microcolonies slightly misshapen cells  at 25-32
# for above germinated spores  (low penetracne) misshapen vegetive cells (high penetrance) 

# 2 ESSENTIAL germinated spores- occasionally microcolonies misshapen cells at 25-32 
# 2 ESSENTIAL germinated spores- some microcolonies misshapen cells at 25-32 
# for above germinated spores  (high penetracne) misshapen vegetive cells (low penetrance) 

# 2 ESSENTIAL germinated spores misshapen- microcolonies misshapen cells at 25-32
# for above germinated misshapen spores  /misshapen vegetive cells (unknown penetrance)

# misshapen essential
# 1 ESSENTIAL microcolonies misshapen cells 32
# 1 ESSENTIAL microcolonies misshapen cells at 32
# 1 ESSENTIAL microcolonies misshapen cells- lysis at 25-32 ( add lysis)
# 1 ESSENTIAL microcolonies slightly misshapen cells- lysis at 25-32 ( add lysis) (add low expressivity)

# ntr: inviable after spore germination, multiple cell divisions, abnormal morphology, normal cell size
# child of
# inviable after spore germination, multiple cell divisions, abnormal morphology
# inviable vegetative cell, abnormal cell shape, normal cell size
# population phenotype
# ntr: Population of germinated spores producing inviable microcolonies of cells with abnormal cell shape, normal cell size

# misshapen essential
# MICROCOLONIES SEPTATED
#  3 ESSENTIAL microcolonies misshapen septated cells at 25-32
#  2 ESSENTIAL microcolonies misshapen- septated cells at 25-32
#   1 ESSENTIAL microcolonies septated misshapen cells at 32- cells  slightly misshapen at 25
#   3 ESSENTIAL microcolonies misshapen septated cells at 25-32
#   2 ESSENTIAL microcolonies misshapen- septated cells at 25-32
#   1 ESSENTIAL microcolonies septated misshapen cells at 32- cells  slightly misshapen at 25

# cell phenotype
# ntr: inviable after spore germination, multiple cell divisions, septated cells with abnormal morphology  (high penetrant)
# population phenotype
# ntr: Population of germinated spores producing inviable microcolonies of septated cells with abnormal cell shape, 


# misshapen essential
# This one looks mixed: possible some of the above are too?
# MIXED POPULATION
# 1 ESSENTIAL germinated spores misshapen- occasionally microcolonies septated cells at 25-32
# cell phenotypes 
# germinated spores with abnormal morphology (undivided) (high penetracne)
# germinated spores with abnormal morphology (divided spetated cell) (high penetracne)
