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eKLIPse_circos.py
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eKLIPse_circos.py
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import sys
import os
import shutil
from string import split
from eKLIPse_fct import *
#=================================================================================================================================================#
#=================================================================================================================================================#
#=================================================================================================================================================#
def circosConf(titleBam,dicoInit,lstError):
try:
#***** PATHS *****#
# Main conf Templates
pathConfTemplate = os.path.join(dicoInit['pathDataDir'],"circos_template","circos.conf")
# Copy static conf files
shutil.copy(os.path.join(dicoInit['pathDataDir'],"circos_template","ideogram.conf"),os.path.join(dicoInit['pathTmpDir'],"ideogram.conf"))
shutil.copy(os.path.join(dicoInit['pathDataDir'],"circos_template","ticks.conf"),os.path.join(dicoInit['pathTmpDir'],"ticks.conf"))
shutil.copy(os.path.join(dicoInit['pathDataDir'],"circos_template","bands.conf"),os.path.join(dicoInit['pathTmpDir'],"bands.conf"))
# Template created from gbk input file
pathKaryotypeTemplate = os.path.join(dicoInit['pathTmpDir'],titleBam+"_karyotype.colors.mt.txt")
pathTextBands = os.path.join(dicoInit['pathTmpDir'],titleBam+"_text.bands.txt")
TEMPLATE_KARYOTYPE = open(pathKaryotypeTemplate,'w')
TEMPLATE_TEXTBANDS = open(pathTextBands,'w')
TEMPLATE_KARYOTYPE.write("chr - hsM "+titleBam+" 0 "+str(dicoInit["dicoGbk"]['refLength']-1)+" chrM\n")
cpt = 1 ; previous_end = 0 ; previous_color = ""
for gene in dicoInit["dicoGbk"]['lstGene']:
# Assign color to gene type
if gene[3]=="trna":
if previous_color=="orange": color = "dorange"
else: color = "orange"
elif gene[3]=="rrna":
if previous_color=="purple": color = "vdpurple"
else: color = "purple"
else:
if previous_color=="green": color = "vdgreen"
else: color = "green"
previous_color = color
# Create karyotype and bands lines
if previous_end<gene[1]: TEMPLATE_KARYOTYPE.write("band hsM band"+str(cpt)+" band"+str(cpt)+" "+str(previous_end)+" "+str(gene[1])+" vdgrey\n") ; cpt+=1
if previous_end>gene[1]: TEMPLATE_KARYOTYPE.write("band hsM band"+str(cpt)+" band"+str(cpt)+" "+str(previous_end+1)+" "+str(gene[2])+" "+color+"\n")
else: TEMPLATE_KARYOTYPE.write("band hsM band"+str(cpt)+" band"+str(cpt)+" "+str(gene[1])+" "+str(gene[2])+" "+color+"\n")
TEMPLATE_TEXTBANDS.write("hsM "+str(gene[1])+" "+str(gene[2])+" "+gene[0]+"\n")
cpt+=1 ; previous_end = gene[2]
TEMPLATE_KARYOTYPE.write("band hsM band"+str(cpt)+" band"+str(cpt)+" "+str(previous_end+1)+" "+str(dicoInit["dicoGbk"]['refLength']-1)+" vdgrey\n")
# For human reference display replications origins
if dicoInit["dicoGbk"]['refName']=="NC_012920":
TEMPLATE_TEXTBANDS.write("hsM 407 408 *******OH\nhsM 5747 5748 *******OL")
TEMPLATE_KARYOTYPE.close()
TEMPLATE_TEXTBANDS.close()
# CurrenBAM specific files
pathConf = os.path.join(dicoInit['pathTmpDir'],titleBam+"_circos.conf")
pathCov = os.path.join(dicoInit["pathTmpDir"],titleBam+".cov")
pathMeanCov = os.path.join(dicoInit['pathTmpDir'],"mean.cov")
pathSCcircos = os.path.join(dicoInit['pathTmpDir'],titleBam+".sc")
pathSCblastCircos = os.path.join(dicoInit['pathTmpDir'],titleBam+"_blastCircos.txt")
pathSCblastCircos1 = os.path.join(dicoInit['pathTmpDir'],titleBam+"_blastCircos1.txt")
pathSCblastCircos2 = os.path.join(dicoInit['pathTmpDir'],titleBam+"_blastCircos2.txt")
pathSCblastCircos3 = os.path.join(dicoInit['pathTmpDir'],titleBam+"_blastCircos3.txt")
nbLineBlastLink = 0 ; nbLineBlastLink1 = 0 ; nbLineBlastLink2 = 0 ; nbLineBlastLink3 = 0
pathSCdelPred = os.path.join(dicoInit['pathTmpDir'],titleBam+"_SCdel.txt")
pathDelCumul = os.path.join(dicoInit['pathTmpDir'],titleBam+"_cumulFreq.txt")
#***** LOAD JSON files *****#
dicoBam = load_json(os.path.join(dicoInit['pathTmpDir'],titleBam+"_SC.json"))
dicoDel = load_json(os.path.join(dicoInit['pathTmpDir'],titleBam+"_BLAST.json"))
#***** COVERAGE (sample) *****#
COV = open(pathCov,'w')
for pos in range(0,dicoInit["dicoGbk"]['refLength']-2,1):
if str(pos+1) in dicoBam: ToWrite = "hsM\t"+str(pos+1)+"\t"+str(pos+2)+"\t"+str(dicoBam[str(pos+1)]['nb_reads_F']+dicoBam[str(pos+1)]['nb_reads_R'])+"\n"
else: ToWrite = "hsM\t"+str(pos+1)+"\t"+str(pos+2)+"\t0\n"
COV.write(ToWrite)
COV.close()
#***** SOFTCLIPPING (frequency peak) *****#
CIRCOS = open(pathSCcircos,'w')
for pos in range(dicoInit["dicoGbk"]['refLength']-1):
freqSC = 0.0
if str(pos+1) in dicoBam:
if dicoBam[str(pos+1)]['nb_sc_reads_F']>dicoBam[str(pos+1)]['nb_sc_reads_R'] and dicoBam[str(pos+1)]['nb_reads_F']>0: freqSC = float(dicoBam[str(pos+1)]['nb_sc_reads_F'])/float(dicoBam[str(pos+1)]['nb_reads_F'])
elif dicoBam[str(pos+1)]['nb_sc_reads_F']<dicoBam[str(pos+1)]['nb_sc_reads_R'] and dicoBam[str(pos+1)]['nb_reads_R']>0: freqSC = float(dicoBam[str(pos+1)]['nb_sc_reads_R'])/float(dicoBam[str(pos+1)]['nb_reads_R'])
ToWrite = "hsM\t"+str(pos)+"\t"+str(pos+1)+"\t"+str(freqSC)+"\n"
CIRCOS.write(ToWrite)
CIRCOS.close()
#***** BLAST Links *****#
CIRCOS = open(pathSCblastCircos,'w')
CIRCOS1 = open(pathSCblastCircos1,'w')
CIRCOS2 = open(pathSCblastCircos2,'w')
CIRCOS3 = open(pathSCblastCircos3,'w')
for key in dicoDel.keys():
start = int(split(key,"-")[0])
end = int(split(key,"-")[1])
meanFreq = (dicoDel[key]['freqF']+dicoDel[key]['freqR'])/2.0
if meanFreq >= 10:
CIRCOS.write("hsM\t"+str(dicoDel[key]['scrR']['limit'])+"\t"+str(start)+"\thsM\t"+str(end)+"\t"+str(dicoDel[key]['scrF']['limit'])+"\n")
nbLineBlastLink+=1
elif meanFreq >= 1:
CIRCOS1.write("hsM\t"+str(dicoDel[key]['scrR']['limit'])+"\t"+str(start)+"\thsM\t"+str(end)+"\t"+str(dicoDel[key]['scrF']['limit'])+"\n")
nbLineBlastLink1+=1
elif meanFreq >= 0.1:
CIRCOS2.write("hsM\t"+str(dicoDel[key]['scrR']['limit'])+"\t"+str(start)+"\thsM\t"+str(end)+"\t"+str(dicoDel[key]['scrF']['limit'])+"\n")
nbLineBlastLink2+=1
else:
CIRCOS3.write("hsM\t"+str(dicoDel[key]['scrR']['limit'])+"\t"+str(start)+"\thsM\t"+str(end)+"\t"+str(dicoDel[key]['scrF']['limit'])+"\n")
nbLineBlastLink3+=1
CIRCOS.close()
CIRCOS1.close()
CIRCOS2.close()
CIRCOS3.close()
#***** CUMULATIVE Frequency *****#
dicoCumulFreq = load_json(os.path.join(dicoInit['pathTmpDir'],titleBam+"_cumul.json"))
OUT = open(pathDelCumul,'w')
for pos in range(dicoInit["dicoGbk"]['refLength']-1):
if str(pos) in dicoCumulFreq:
if dicoCumulFreq[str(pos)]>1.0: dicoCumulFreq[str(pos)] = 1.0
OUT.write("hsM\t"+str(pos)+"\t"+str(pos+1)+"\t"+str(dicoCumulFreq[str(pos)])+"\n")
else: OUT.write("hsM\t"+str(pos)+"\t"+str(pos+1)+"\t0\n")
OUT.close()
#***** CREATE Main Circos Configuration File *****#
IN = open(pathConfTemplate,'r')
lst_lines = split(IN.read(),"\n")
IN.close()
OUT = open(pathConf,'w')
for line in lst_lines:
if line.__contains__("#KARYOTYPE"): new_line = line.replace("#KARYOTYPE",pathKaryotypeTemplate)
elif line.__contains__("#TEXTBANDS"): new_line = line.replace("#TEXTBANDS",pathTextBands)
elif line.__contains__("#BLASTLINKS0"): new_line = line.replace("#BLASTLINKS0",pathSCblastCircos)
elif line.__contains__("#LINKSNUMBER0"): new_line = line.replace("#LINKSNUMBER0",str(nbLineBlastLink))
elif line.__contains__("#BLASTLINKS1"): new_line = line.replace("#BLASTLINKS1",pathSCblastCircos1)
elif line.__contains__("#LINKSNUMBER1"): new_line = line.replace("#LINKSNUMBER1",str(nbLineBlastLink1))
elif line.__contains__("#BLASTLINKS2"): new_line = line.replace("#BLASTLINKS2",pathSCblastCircos2)
elif line.__contains__("#LINKSNUMBER2"): new_line = line.replace("#LINKSNUMBER2",str(nbLineBlastLink2))
elif line.__contains__("#BLASTLINKS3"): new_line = line.replace("#BLASTLINKS3",pathSCblastCircos3)
elif line.__contains__("#LINKSNUMBER3"): new_line = line.replace("#LINKSNUMBER3",str(nbLineBlastLink3))
elif line.__contains__("#SCFILE"): new_line = line.replace("#SCFILE",pathSCcircos)
elif line.__contains__("#DATACOV"): new_line = line.replace("#DATACOV",pathCov)
elif line.__contains__("#DATAMEDIANE"): new_line = line.replace("#DATAMEDIANE",pathMeanCov)
elif line.__contains__("#DATAFREQ"): new_line = line.replace("#DATAFREQ",pathDelCumul)
elif line.__contains__("#NAMEDIR"): new_line = line.replace("#NAMEDIR",dicoInit['pathOutputDir'])
elif line.__contains__("#NAMEFILE"): new_line = line.replace("#NAMEFILE","eKLIPse_"+titleBam+".png")
else: new_line = line
OUT.write(new_line+"\n")
OUT.close()
except:
exc_type, exc_value, exc_traceback = sys.exc_info()
lstError.append("ConfThread \""+titleBam+"\": "+str(exc_value)+" (line "+str(exc_traceback.tb_lineno)+")")
#=================================================================================================================================================#
#=================================================================================================================================================#
#=================================================================================================================================================#
def circosPlot(titleBam,dicoInit,lstError):
try:
pathConf = dicoInit['pathTmpDir']+"/"+titleBam+"_circos.conf"
pathLog = os.path.join(dicoInit["pathTmpDir"],titleBam+"_circos.log")
pathPng = os.path.join(dicoInit['pathOutputDir'],"eKLIPse_"+titleBam+".png")
cmd = dicoInit['pathCircosBin']+" -nosvg -conf "+pathConf+" > "+pathLog+" 2>&1"
os.system(cmd)
if not os.path.isfile(pathPng):
lstError.append("PlotThread \""+titleBam+"\": any output .png created (check log file)")
except:
exc_type, exc_value, exc_traceback = sys.exc_info()
lstError.append("PlotThread \""+titleBam+"\": "+str(exc_value)+" (line "+str(exc_traceback.tb_lineno)+")")