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eKLIPse_fct.py
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eKLIPse_fct.py
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import sys
import os
import glob
import json
from string import split
#=================================================================================================================================================#
#=================================================================================================================================================#
#=================================================================================================================================================#
class Highlighter:
def __init__(self):
self._msgTypes={'black':'\033[0;30m', 'gray':'\033[1;30m', 'blue':'\033[0;34m', 'bold blue':'\033[1;34m', 'green':'\033[0;32m', 'bold green':'\033[1;32m', 'cyan':'\033[0;36m', 'bold cyan':'\033[1;36m', 'red':'\033[0;31m', 'bold red':'\033[1;31m', 'purple':'\033[0;35m', 'bold purple':'\033[1;35m', 'yellow':'\033[0;33m', 'bold yellow':'\033[1;33m', 'white':'\033[0;37m', 'bold white':'\033[1;37m'} ; self._reset='\033[0m' ; self._default='white'
def ColorMsg(self,msg,msgLevel='white'):
try:s=self._msgTypes[msgLevel]+msg+self._reset
except: s=s=self._msgTypes[self._default]+msg+self._reset
return s
def ColorOutput(msg,msgLevel='white'):
return Highlighter().ColorMsg(msg,msgLevel)
def printcolor(ToWrite,color,bool):
if bool==True: sys.stdout.write(ColorOutput(ToWrite,color))
else: sys.stdout.write(ToWrite)
sys.stdout.flush()
def printerror(lstError):
if len(lstError)!=0:
for error in lstError: sys.stderr.write("\n[ERROR] "+error+"\n")
exit("\n")
#=================================================================================================================================================#
#=================================================================================================================================================#
#=================================================================================================================================================#
def string_to_num(num):
try: a = int(num) ; return "int"
except ValueError:
try: a = float(num) ; return "float"
except ValueError: return "str"
def load_json(path):
# Read json file
json_data=open(path)
data = json.load(json_data)
json_data.close()
return byteify(data)
def byteify(input):
if isinstance(input, dict):
return {byteify(key): byteify(value)
for key, value in input.iteritems()}
elif isinstance(input, list):
return [byteify(element) for element in input]
elif isinstance(input, unicode):
return input.encode('utf-8')
else:
return input
def explain_sam_flags(iFlags):
lstFlags = [("read paired", 0x1),("read mapped in proper pair", 0x2),("read unmapped", 0x4),("mate unmapped", 0x8),\
("read reverse strand", 0x10),("mate reverse strand", 0x20),("first in pair", 0x40),("second in pair", 0x80),\
("not primary alignment", 0x100),("read fails platform/vendor quality checks", 0x200),\
("read is PCR or optical duplicate", 0x400),("supplementary alignment", 0x800)]
decodeflag = ""
for strFlagName, iMask in lstFlags:
if iFlags & iMask:
decodeflag = decodeflag+":"+strFlagName
return decodeflag
def cigar_list_to_tuple(cigar_list,align_start):
positionsLstTuple = []
posRead = 0
posmatch = 0
posRef = align_start
for cigar in cigar_list: #[(length,type), (length,type), (length,type)]
for i in range(cigar[0]):
if cigar[1]=="M":
positionsLstTuple.append([posRead,posRef])
posRead+=1
posRef+=1
posmatch+=1
elif cigar[1]=="D":
positionsLstTuple.append([None,posRef])
posRef+=1
else: # "I" & "S"
positionsLstTuple.append([posRead,None])
posRead+=1
return positionsLstTuple,posRef,posmatch
#=================================================================================================================================================#
#=================================================================================================================================================#
#=================================================================================================================================================#
def mean_coverage(dicoInit,lstError):
try:
pathMeanCov = os.path.join(dicoInit['pathTmpDir'],"mean.cov")
dicoMean = {}
nb_sample = 0
#***** BROWSE JSON files *****#
for pathJson in glob.glob(os.path.join(dicoInit['pathTmpDir'],"*_SC.json")):
dicoBam = load_json(pathJson)
nb_sample+=1
for key in dicoBam:
try: dicoMean[key]+=dicoBam[key]['nb_reads_F']+dicoBam[key]['nb_reads_R']
except: dicoMean[key] = dicoBam[key]['nb_reads_F']+dicoBam[key]['nb_reads_R']
# Write Mean coverage file
MEAN = open(pathMeanCov,'w')
for pos in range(dicoInit["dicoGbk"]['refLength']-1):
if str(pos) in dicoMean: ToWrite = "hsM\t"+str(pos)+"\t"+str(pos+1)+"\t"+str(float(dicoMean[str(pos)])/float(nb_sample))+"\n"
else: ToWrite = "hsM\t"+str(pos)+"\t"+str(pos+1)+"\t0.0\n"
MEAN.write(ToWrite)
MEAN.close()
except:
exc_type, exc_value, exc_traceback = sys.exc_info()
lstError.append("mean_coverage \": "+str(exc_value)+" (line "+str(exc_traceback.tb_lineno)+")")
#=================================================================================================================================================#
#=================================================================================================================================================#
#=================================================================================================================================================#
def Alignment_downsampling(titleBam,dicoInit,lstError):
try:
dicoInit['dicoBam'][titleBam]['path_downsampling'] = os.path.join(dicoInit['pathTmpDir'],titleBam+"_reduce.bam")
fraction = round((float(dicoInit['downCov'])/float(dicoInit['dicoBam'][titleBam]['nbReads'])),2)
cmd = dicoInit['pathSamtools']+" view -b -q "+str(dicoInit["minQ"])+" -s "+str(fraction)+" "+dicoInit['dicoBam'][titleBam]['path']+" > "+dicoInit['dicoBam'][titleBam]['path_downsampling']
os.system(cmd)
except:
exc_type, exc_value, exc_traceback = sys.exc_info()
lstError.append("Downsampling for BAM title \""+titleBam+"\": "+str(exc_value)+" (line "+str(exc_traceback.tb_lineno)+")")