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reduceMISOFileDimensions.py
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reduceMISOFileDimensions.py
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#!/usr/bin/env python
'''
ENAH.miso:
miso file format:
#isoforms=['ENAH@EXON1_ENAH@EXON2_ENAH@EXON3_ENAH@EXON4_ENAH@EXON5_ENAH@EXON6_ENAH@EXON7_ENAH@EXON8_ENAH@EXON9_ENAH@EXON10_ENAH@EXON11_ENAH@EXON12_ENAH@EXON13_ENAH@EXON14','ENAH@EXON15_ENAH@EXON16_ENAH@EXON17_ENAH@EXON18_ENAH@EXON19_ENAH@EXON20_ENAH@EXON21_ENAH@EXON22_ENAH@EXON23_ENAH@EXON24_ENAH@EXON25_ENAH@EXON26_ENAH@EXON27_ENAH@EXON28_ENAH@EXON29','ENAH@EXON30_ENAH@EXON31_ENAH@EXON32_ENAH@EXON33_ENAH@EXON34','ENAH@EXON35_ENAH@EXON36_ENAH@EXON37_ENAH@EXON38_ENAH@EXON39','ENAH@EXON40_ENAH@EXON41_ENAH@EXON42_ENAH@EXON43_ENAH@EXON44','ENAH@EXON45_ENAH@EXON46_ENAH@EXON47_ENAH@EXON48','ENAH@EXON49_ENAH@EXON50_ENAH@EXON51_ENAH@EXON52_ENAH@EXON53_ENAH@EXON54_ENAH@EXON55_ENAH@EXON56_ENAH@EXON57','ENAH@EXON58_ENAH@EXON59_ENAH@EXON60','ENAH@EXON61_ENAH@EXON62_ENAH@EXON63_ENAH@EXON64_ENAH@EXON65','ENAH@EXON66','ENAH@EXON67_ENAH@EXON68','ENAH@EXON69_ENAH@EXON70_ENAH@EXON71_ENAH@EXON72_ENAH@EXON73_ENAH@EXON74','ENAH@EXON75'] exon_lens=('ENAH@EXON1',10981),('ENAH@EXON2',58),('ENAH@EXON3',79),('ENAH@EXON4',67),('ENAH@EXON5',49),('ENAH@EXON6',58),('ENAH@EXON7',146),('ENAH@EXON8',305),('ENAH@EXON9',111),('ENAH@EXON10',368),('ENAH@EXON11',85),('ENAH@EXON12',178),('ENAH@EXON13',166),('ENAH@EXON14',458),('ENAH@EXON15',10981),('ENAH@EXON16',58),('ENAH@EXON17',79),('ENAH@EXON18',63),('ENAH@EXON19',67),('ENAH@EXON20',49),('ENAH@EXON21',58),('ENAH@EXON22',146),('ENAH@EXON23',305),('ENAH@EXON24',111),('ENAH@EXON25',368),('ENAH@EXON26',85),('ENAH@EXON27',178),('ENAH@EXON28',166),('ENAH@EXON29',461),('ENAH@EXON30',531),('ENAH@EXON31',46),('ENAH@EXON32',166),('ENAH@EXON33',155),('ENAH@EXON34',211),('ENAH@EXON35',736),('ENAH@EXON36',85),('ENAH@EXON37',178),('ENAH@EXON38',166),('ENAH@EXON39',82),('ENAH@EXON40',51),('ENAH@EXON41',178),('ENAH@EXON42',166),('ENAH@EXON43',58),('ENAH@EXON44',66),('ENAH@EXON45',475),('ENAH@EXON46',390),('ENAH@EXON47',58),('ENAH@EXON48',265),('ENAH@EXON49',2333),('ENAH@EXON50',58),('ENAH@EXON51',79),('ENAH@EXON52',63),('ENAH@EXON53',67),('ENAH@EXON54',49),('ENAH@EXON55',58),('ENAH@EXON56',146),('ENAH@EXON57',1457),('ENAH@EXON58',1081),('ENAH@EXON59',79),('ENAH@EXON60',67),('ENAH@EXON61',179),('ENAH@EXON62',58),('ENAH@EXON63',79),('ENAH@EXON64',67),('ENAH@EXON65',194),('ENAH@EXON66',1325),('ENAH@EXON67',168),('ENAH@EXON68',177),('ENAH@EXON69',592),('ENAH@EXON70',368),('ENAH@EXON71',85),('ENAH@EXON72',178),('ENAH@EXON73',166),('ENAH@EXON74',91),('ENAH@EXON75',708)
iters=5000 burn_in=500 lag=10 percent_accept=0.88 proposal_type=drift counts=(0,0,0,0,0,0,0,0,0,0,0,0,1):3,(0,0,0,0,0,0,0,0,0,0,0,1,0):3,(0,0,0,0,0,0,0,0,0,0,0,1,1):29,(0,0,0,0,0,0,0,0,0,0,1,0,0):13,(0,0,0,0,0,0,0,0,0,1,0,0,0):9,(0,0,0,0,0,0,0,1,0,0,0,0,0):1,(0,0,0,0,0,0,0,1,0,1,0,0,0):6,(0,0,0,0,0,0,1,0,0,0,0,0,0):6,(0,0,0,0,0,1,0,0,0,0,0,0,0):11,(0,0,0,1,0,0,0,0,0,0,0,0,0):6,(0,0,1,0,0,0,0,0,0,0,0,0,0):15,(0,1,0,0,0,0,1,0,0,0,0,0,0):38,(1,0,0,0,0,0,0,1,1,0,0,0,0):7,(1,1,0,0,0,0,0,0,0,0,0,0,0):586,(1,1,0,0,0,0,1,0,0,0,0,0,0):686,(1,1,0,0,0,0,1,0,0,0,1,0,0):187,(1,1,0,0,0,0,1,1,0,0,0,0,0):88,(1,1,0,0,0,0,1,1,1,0,0,0,0):41,(1,1,0,0,0,1,0,0,0,0,0,0,0):90,(1,1,0,0,0,1,1,1,0,0,0,0,0):105,(1,1,0,0,0,1,1,1,1,0,0,0,0):261,(1,1,0,0,0,1,1,1,1,1,0,0,0):14,(1,1,0,1,0,0,0,0,0,0,0,1,0):885,(1,1,0,1,1,0,0,0,0,0,0,1,0):223,(1,1,1,0,0,0,0,0,0,0,0,0,0):134,(1,1,1,0,0,0,1,0,0,0,0,0,0):121,(1,1,1,1,1,0,0,0,0,0,0,1,0):203 assigned_counts=0:308,1:848,2:167,3:1140,4:3,5:170,6:774,7:44,8:104,9:10,10:138,11:37,12:28
sampled_psi log_score
0.0216,0.0299,0.0376,0.5346,0.0055,0.0558,0.1322,0.0121,0.0420,0.0071,0.0097,0.0092,0.1027 -37479.0016
0.0216,0.0299,0.0376,0.5346,0.0055,0.0558,0.1322,0.0121,0.0420,0.0071,0.0097,0.0092,0.1027 -37424.9787
/lab/jaenisch_albert/genomes/hg18/annos$ acembly.pe.exonStringMap.make.sh
/lab/jaenisch_albert/genomes/hg18/annos/oldStuff/old.acembly$ grep ENAH acembly.pe.exonStringMap
/lab/jaenisch_albert/genomes/hg18/annos/oldStuff/old.acembly$ grep ENAH acembly.pe.exonStringMap > byGenes/acembly.pe.exonStringMap.ENAH
/lab/jaenisch_albert/genomes/hg18/annos/oldStuff/old.acembly$ less byGenes/acembly.pe.exonStringMap.ENAH
ENAH:mApr07-unspliced ENAH@EXON66
ENAH:bApr07 ENAH@EXON1_ENAH@EXON2_ENAH@EXON3_ENAH@EXON4_ENAH@EXON5_ENAH@EXON6_ENAH@EXON7_ENAH@EXON8_ENAH@EXON9_ENAH@EXON10_ENAH@EXON11_ENAH@EXON12_ENAH@EXON13_ENAH@EXON14
ENAH:iApr07 ENAH@EXON58_ENAH@EXON59_ENAH@EXON60
ENAH:fApr07-unspliced ENAH@EXON75
ENAH:jApr07 ENAH@EXON45_ENAH@EXON46_ENAH@EXON47_ENAH@EXON48
ENAH:eApr07 ENAH@EXON35_ENAH@EXON36_ENAH@EXON37_ENAH@EXON38_ENAH@EXON39
ENAH:dApr07 ENAH@EXON49_ENAH@EXON50_ENAH@EXON51_ENAH@EXON52_ENAH@EXON53_ENAH@EXON54_ENAH@EXON55_ENAH@EXON56_ENAH@EXON57
ENAH:hApr07 ENAH@EXON67_ENAH@EXON68
ENAH:aApr07 ENAH@EXON15_ENAH@EXON16_ENAH@EXON17_ENAH@EXON18_ENAH@EXON19_ENAH@EXON20_ENAH@EXON21_ENAH@EXON22_ENAH@EXON23_ENAH@EXON24_ENAH@EXON25_ENAH@EXON26_ENAH@EXON27_ENAH@EXON28_ENAH@EXON29
ENAH:lApr07 ENAH@EXON30_ENAH@EXON31_ENAH@EXON32_ENAH@EXON33_ENAH@EXON34
ENAH:gApr07 ENAH@EXON40_ENAH@EXON41_ENAH@EXON42_ENAH@EXON43_ENAH@EXON44
ENAH:cApr07 ENAH@EXON69_ENAH@EXON70_ENAH@EXON71_ENAH@EXON72_ENAH@EXON73_ENAH@EXON74
ENAH:kApr07 ENAH@EXON61_ENAH@EXON62_ENAH@EXON63_ENAH@EXON64_ENAH@EXON65
(END)
/lab/jaenisch_albert/genomes/hg18/SplidarEventGff$ makeTranscriptExonStringFromGff.py allEvents.pe.GFF3 > allEvents.pe.exonString
cat allEvents.EBED | tr " " "\t" > allEvents.tabbed.ebed
cheng@tak /lab/jaenisch_albert/genomes/hg18/SplidarEventGff$ less allEvents.tabbed.ebed
/lab/jaenisch_albert/genomes/hg18/SplidarEventGff$ rm events2Transcript.map; Splidar.Splicing.matchEventToTranscript.py allEvents.tabbed.ebed ../annos/acembly.ebed > events2Transcript.map
RI.ENAH.27053.1 ENAH.iApr07 chr1
RI.ENAH.27051.2 ENAH.jApr07 chr1
SE.ENAH.47366.2 ENAH.aApr07 chr1
RI.ENAH.27051.2 ENAH.kApr07 chr1
Alt3UTR.ENAH.2992.1 ENAH.aApr07 chr1
Alt3UTR.ENAH.2995.1 ENAH.aApr07 chr1
Alt3UTR.ENAH.2997.1 ENAH.aApr07 chr1
Alt3UTR.ENAH.2999.2 ENAH.aApr07 chr1
AFE.ENAH.43749.2 ENAH.aApr07 chr1
AFE.ENAH.43751.2 ENAH.aApr07 chr1
SE.ENAH.47366.1 ENAH.lApr07 chr1
RI.ENAH.27052.1 ENAH.iApr07 chr1
RI.ENAH.27052.2 ENAH.kApr07 chr1
Alt3UTR.ENAH.2993.1 ENAH.aApr07 chr1
Alt3UTR.ENAH.2996.1 ENAH.aApr07 chr1
Alt3UTR.ENAH.2998.1 ENAH.aApr07 chr1
Alt3UTR.ENAH.2999.1 ENAH.aApr07 chr1
RI.ENAH.27053.2 ENAH.jApr07 chr1
Alt3UTR.ENAH.2990.1 ENAH.aApr07 chr1
Alt3UTR.ENAH.2994.2 ENAH.aApr07 chr1
Alt3UTR.ENAH.2995.2 ENAH.aApr07 chr1
Alt3UTR.ENAH.2996.2 ENAH.aApr07 chr1
etc
/lab/jaenisch_albert/genomes/hg18/SplidarEventGff$ cat events2Transcript.map | tr "." ":" > events2Transcript.map.colon
rm ../annos/acembly.pe.exonStringMap.ENAH; grep ENAH ../annos/acembly.pe.exonStringMap > ../annos/acembly.pe.exonStringMap.ENAH
/lab/jaenisch_albert/genomes/hg18/SplidarEventGff$ rm events2Transcript.map.exonString.ENAH; joinu.py -1 2 -2 1 events2Transcript.map.colon ../annos/acembly.pe.exonStringMap.ENAH > events2Transcript.map.exonString.ENAH
RI.ENAH.27053.1 ENAH.iApr07 chr1 ENAH@EXON48_ENAH@EXON49_ENAH@EXON50
RI.ENAH.27051.2 ENAH.jApr07 chr1 ENAH@EXON30_ENAH@EXON31_ENAH@EXON32_ENAH@EXON33
SE.ENAH.47366.2 ENAH.aApr07 chr1 ENAH@EXON15_ENAH@EXON16_ENAH@EXON17_ENAH@EXON18_ENAH@EXON19_ENAH@EXON20_ENAH@EXON21_ENAH@EXON22_ENAH@EXON23_ENAH@EXON24_ENAH@EXON25_ENAH@EXON26_ENAH@EXON27_ENAH@EXON28_ENAH@EXON29
RI.ENAH.27051.2 ENAH.kApr07 chr1 ENAH@EXON51_ENAH@EXON52_ENAH@EXON53_ENAH@EXON54_ENAH@EXON55
Alt3UTR.ENAH.2992.1 ENAH.aApr07 chr1 ENAH@EXON15_ENAH@EXON16_ENAH@EXON17_ENAH@EXON18_ENAH@EXON19_ENAH@EXON20_ENAH@EXON21_ENAH@EXON22_ENAH@EXON23_ENAH@EXON24_ENAH@EXON25_ENAH@EXON26_ENAH@EXON27_ENAH@EXON28_ENAH@EXON29
Alt3UTR.ENAH.2995.1 ENAH.aApr07 chr1 ENAH@EXON15_ENAH@EXON16_ENAH@EXON17_ENAH@EXON18_ENAH@EXON19_ENAH@EXON20_ENAH@EXON21_ENAH@EXON22_ENAH@EXON23_ENAH@EXON24_ENAH@EXON25_ENAH@EXON26_ENAH@EXON27_ENAH@EXON28_ENAH@EXON29
Alt3UTR.ENAH.2997.1 ENAH.aApr07 chr1 ENAH@EXON15_ENAH@EXON16_ENAH@EXON17_ENAH@EXON18_ENAH@EXON19_ENAH@EXON20_ENAH@EXON21_ENAH@EXON22_ENAH@EXON23_ENAH@EXON24_ENAH@EXON25_ENAH@EXON26_ENAH@EXON27_ENAH@EXON28_ENAH@EXON29
Alt3UTR.ENAH.2999.2 ENAH.aApr07 chr1 ENAH@EXON15_ENAH@EXON16_ENAH@EXON17_ENAH@EXON18_ENAH@EXON19_ENAH@EXON20_ENAH@EXON21_ENAH@EXON22_ENAH@EXON23_ENAH@EXON24_ENAH@EXON25_ENAH@EXON26_ENAH@EXON27_ENAH@EXON28_ENAH@EXON29
AFE.ENAH.43749.2 ENAH.aApr07 chr1 ENAH@EXON15_ENAH@EXON16_ENAH@EXON17_ENAH@EXON18_ENAH@EXON19_ENAH@EXON20_ENAH@EXON21_ENAH@EXON22_ENAH@EXON23_ENAH@EXON24_ENAH@EXON25_ENAH@EXON26_ENAH@EXON27_ENAH@EXON28_ENAH@EXON29
AFE.ENAH.43751.2 ENAH.aApr07 chr1 ENAH@EXON15_ENAH@EXON16_ENAH@EXON17_ENAH@EXON18_ENAH@EXON19_ENAH@EXON20_ENAH@EXON21_ENAH@EXON22_ENAH@EXON23_ENAH@EXON24_ENAH@EXON25_ENAH@EXON26_ENAH@EXON27_ENAH@EXON28_ENAH@EXON29
SE.ENAH.47366.1 ENAH.lApr07 chr1 ENAH@EXON34_ENAH@EXON35_ENAH@EXON36_ENAH@EXON37_ENAH@EXON38
RI.ENAH.27052.1 ENAH.iApr07 chr1 ENAH@EXON48_ENAH@EXON49_ENAH@EXON50
RI.ENAH.27052.2 ENAH.kApr07 chr1 ENAH@EXON51_ENAH@EXON52_ENAH@EXON53_ENAH@EXON54_ENAH@EXON55
Alt3UTR.ENAH.2993.1 ENAH.aApr07 chr1 ENAH@EXON15_ENAH@EXON16_ENAH@EXON17_ENAH@EXON18_ENAH@EXON19_ENAH@EXON20_ENAH@EXON21_ENAH@EXON22_ENAH@EXON23_ENAH@EXON24_ENAH@EXON25_ENAH@EXON26_ENAH@EXON27_ENAH@EXON28_ENAH@EXON29
Alt3UTR.ENAH.2996.1 ENAH.aApr07 chr1 ENAH@EXON15_ENAH@EXON16_ENAH@EXON17_ENAH@EXON18_ENAH@EXON19_ENAH@EXON20_ENAH@EXON21_ENAH@EXON22_ENAH@EXON23_ENAH@EXON24_ENAH@EXON25_ENAH@EXON26_ENAH@EXON27_ENAH@EXON28_ENAH@EXON29
rm events2Transcript.map.exonString.ENAH.col; stickColValues.py --internalfs , events2Transcript.map.exonString.ENAH 1 > events2Transcript.map.exonString.ENAH.col
colStat.py -r2 events2Transcript.map.exonString.ENAH.col #events2TranscriptExonStringCol[::::: R 2 :::::]
Index Excel Field
----- ----- -----
1 A RI.ENAH.27051.2
2 B ENAH.jApr07,ENAH.kApr07,ENAH.dApr07,ENAH.bApr07,ENAH.aApr07
3 C chr1
4 D ENAH@EXON30_ENAH@EXON31_ENAH@EXON32_ENAH@EXON33,ENAH@EXON51_ENAH@EXON52_ENAH@EXON53_ENAH@EXON54_ENAH@EXON55,ENAH@EXON39_ENAH@EXON40_ENAH@EXON41_ENAH@EXON42_ENAH@EXON43_ENAH@EXON44_ENAH@EXON45_ENAH@EXON46_ENAH@EXON47,ENAH@EXON1_ENAH@EXON2_ENAH@EXON3_ENAH@EXON4_ENAH@EXON5_ENAH@EXON6_ENAH@EXON7_ENAH@EXON8_ENAH@EXON9_ENAH@EXON10_ENAH@EXON11_ENAH@EXON12_ENAH@EXON13_ENAH@EXON14,ENAH@EXON15_ENAH@EXON16_ENAH@EXON17_ENAH@EXON18_ENAH@EXON19_ENAH@EXON20_ENAH@EXON21_ENAH@EXON22_ENAH@EXON23_ENAH@EXON24_ENAH@EXON25_ENAH@EXON26_ENAH@EXON27_ENAH@EXON28_ENAH@EXON29
'''
from sys import *
import os.path
import os
from getopt import getopt
def parseMISOFile(filename):
#return (sampled_psi[exonString][MISORow]=float,logScore[MISORow]=float)
sampled_psi=dict()
log_scores=[]
fil=open(filename)
lines=fil.readlines()
fil.close()
#first parse header
header=lines[0].rstrip("\r\n")
try:
if header[0:11]!="#isoforms=[":
raise ValueError
headerIsoformString=header[10:].split("\t")[0]
isoformExonStrings=eval(headerIsoformString)
except:
print >> stderr,"MISO Header Format Error filename="+filename
exit()
#print >> stderr,"isoformExonStrings",isoformExonStrings
#now go to other lines
if lines[1].split("\t")[0]!="sampled_psi":
print >> stderr,"MISO Table Format Error filename="+filename
exit()
for isoformExonString in isoformExonStrings:
sampled_psi[isoformExonString]=[]
for lin in lines[2:]:
try:
sampled_psi_str,log_score=lin.rstrip("\r\n").split("\t")
sampled_psi_str=sampled_psi_str.split(",")
log_scores.append(log_score)
for isoformExonString,sampled_psi_stron in zip(isoformExonStrings,sampled_psi_str):
sampled_psi[isoformExonString].append(float(sampled_psi_stron))
except:
print >> stderr,"error at line:",lin
print >> stderr,"sampled_psi_str:",sampled_psi_str
exit()
return (sampled_psi,log_scores)
'''
misoFileDir=/lab/solexa_jaenisch/Albert2/mRNASeqLibs/EMT/MISOOnSE_acembly/MISOOutput.ENAH/Epithelial
events2TranscriptExonStringColFile=/lab/jaenisch_albert/genomes/hg18/SplidarEventGff/events2Transcript.map.exonString.ENAH.col
outputMISODir=/lab/solexa_jaenisch/Albert2/mRNASeqLibs/EMT/MISOOnSE_acembly_reduced/MISOOutput.ENAH/Epithelial
python reduceMISOFileDimensions.py $misoFileDir $events2TranscriptExonStringColFile $outputMISODir
'''
def printUsageAndExit(programName):
print >> stderr,"Usage:",programName,"[--abort-less-than default:100] misoFileDir events2TranscriptExonStringColFile outputMISODir"
exit()
if __name__=='__main__':
programName=argv[0]
opts,args=getopt(argv[1:],'',['abort-less-than='])
abortLessThan=100
for o,v in opts:
if o=='--abort-less-than':
abortLessThan=int(v)
try:
misoFileDir, events2TranscriptExonStringColFile, outputMISODir=args
except:
printUsageAndExit(programName)
if not os.path.isdir(outputMISODir):
os.makedirs(outputMISODir)
E2TXStrMap=dict()
GeneChromMap=dict()
#E2TXStrMap[eventGeneName][eventName][1|2...]=([transcriptID...],[exonString,..])
filE2TXStr=open(events2TranscriptExonStringColFile)
for lin in filE2TXStr:
fields=lin.rstrip("\r\n").split("\t")
eventID=fields[0].split(":")
eventGeneName=":".join(eventID[1:-2]) #Alt3UTR:ENAH:2995:1 -> ENAH
eventIDIsoformIdx=int(eventID[-1])
eventID=":".join(eventID[:-1])
transcriptIDs=fields[1].split(",")
exonStrings=fields[3].split(",")
chrom=fields[2]
try:
eventGeneStruct=E2TXStrMap[eventGeneName]
except KeyError:
eventGeneStruct=dict()
GeneChromMap[eventGeneName]=chrom
E2TXStrMap[eventGeneName]=eventGeneStruct
try:
eventStruct=eventGeneStruct[eventID]
except KeyError:
eventStruct=dict()
eventGeneStruct[eventID]=eventStruct
if eventStruct.has_key(eventIDIsoformIdx):
print >> stderr,"Error: event has been duplicated. Please col file before running"
exit()
eventStruct[eventIDIsoformIdx]=(transcriptIDs,exonStrings)
filE2TXStr.close()
#now go every event and process the corresponding eventGeneName.miso file
for eventGeneName,eventGeneStruct in E2TXStrMap.items():
chrom=GeneChromMap[eventGeneName]
misoFileName=misoFileDir+"/"+chrom+"/"+eventGeneName+".miso"
if not os.path.isfile(misoFileName):
print >> stderr,"miso file for gene",eventGeneName,"does not exists:",misoFileName
continue
sampled_psi,log_score=parseMISOFile(misoFileDir+"/"+chrom+"/"+eventGeneName+".miso")
for eventID,eventStruct in eventGeneStruct.items():
outputMISOPath=outputMISODir+"/"+chrom
if not os.path.isdir(outputMISOPath):
os.makedirs(outputMISOPath)
outputMISOFileName=outputMISOPath+"/"+eventID+".miso"
eventIsoforms=[]
eventIDIsoformIdxKeys=eventStruct.keys()
eventIDIsoformIdxKeys.sort()
if len(eventIDIsoformIdxKeys)<2: #only one isoform for this event mappable back to the transcript ignore
continue
foutputMISO=open(outputMISOFileName,"w")
for eventIDIsoformIdx in eventIDIsoformIdxKeys:
eventIsoforms.append("'"+eventID+"."+str(eventIDIsoformIdx)+"'")
#now write new header
new_header=["isoforms=["+",".join(eventIsoforms)+"]"]
print >> foutputMISO,"#"+"\t".join(new_header)
print >> foutputMISO,"sampled_psi\tlog_score"
numValidLines=0
numInvalidLines=0
sampled_psi_ave=[]
log_score_ave=0.0
for miso_row in range(0,len(log_score)):
sampled_psi_out=[]
isoform_cpsi=[]
ccpsi=0.0
for eventIDIsoformIdx in eventIDIsoformIdxKeys:
transcriptIDs,exonStrings=eventStruct[eventIDIsoformIdx]
cpsi=0.0
for exonString in exonStrings:
try:
cpsi+=sampled_psi[exonString][miso_row]
except KeyError:
print >> stderr,"exon string",exonString,"in gene ",eventGeneName," requested. Presumably due to overlapping genes. pass"
continue
isoform_cpsi.append(cpsi)
ccpsi+=cpsi
if ccpsi==0.0:
numInvalidLines+=1
continue
idxx=0
numValidLines+=1
for cpsi in isoform_cpsi:
norm_psi=cpsi/ccpsi
sampled_psi_out.append(str(norm_psi))
if numValidLines==1:
sampled_psi_ave.append(norm_psi)
else:
sampled_psi_ave[idxx]+=norm_psi
idxx+=1
thislogscore=log_score[miso_row]
log_score_ave+=float(thislogscore)
sampled_psi_out=",".join(sampled_psi_out)
print >> foutputMISO,sampled_psi_out+"\t"+thislogscore
if numValidLines<abortLessThan:
#delete this file:
foutputMISO.close()
os.remove(outputMISOFileName)
print >> stderr,"file",outputMISOFileName,"removed because numValidLines<",abortLessThan
else:
#now calculate the average and fill up
if numInvalidLines>0:
for i in range(0,len(sampled_psi_ave)):
sampled_psi_ave[i]=str(sampled_psi_ave[i]/numValidLines)
log_score_ave=str(log_score_ave/numValidLines)
outline=",".join(sampled_psi_ave)+"\t"+log_score_ave
for i in range(0,numInvalidLines):
print >> foutputMISO,outline
print >> stderr,"fill", numInvalidLines,"invalid rows with average for file",outputMISOFileName
foutputMISO.close()