def parse_MAT_xls (fhd):
"""Parse a tab-delimited xls file from MAT.
fhd is a file handler for MAT xls result.
Return a taolib.CoreLib.FeatIO.PeakIO object.
"""
peaks = PeakIO()
for row in fhd:
if row.startswith("Chr") or row.startswith("#") or row.startswith("track"):
continue
else:
f = row.split()
peaks.add(f[0],int(f[1]),int(f[2]),
int(f[8]),float(f[5]),
0,float(f[4]),0,float(f[7]))
break
for row in fhd:
f = row.split()
peaks.add(f[0],int(f[1]),int(f[2]),
int(f[8]),float(f[5]),
0,float(f[4]),0,float(f[7]))
return peaks
def parse_pMA2C_xls (fhd):
"""Parse a tab-delimited xls file from python version MA2C.
fhd is a file handler for python version of MA2C xls result.
Return a taolib.CoreLib.FeatIO.PeakIO object.
"""
reader = DictReader(Filter(fhd),dialect='excel-tab')
peaks = PeakIO()
for row in reader:
peaks.add(row['Chr'],int(row['Start']),int(row['End']),
int(row['Summit']),float(row['MA2Cscore']),
0,float(row['-10*log10(PValue)']),0,float(row['FDR']))
return peaks
def parse_pMA2C_xls(fhd):
"""Parse a tab-delimited xls file from python version MA2C.
fhd is a file handler for python version of MA2C xls result.
Return a taolib.CoreLib.FeatIO.PeakIO object.
"""
reader = DictReader(Filter(fhd), dialect='excel-tab')
peaks = PeakIO()
for row in reader:
peaks.add(row['Chr'], int(row['Start']), int(row['End']),
int(row['Summit']), float(row['MA2Cscore']), 0,
float(row['-10*log10(PValue)']), 0, float(row['FDR']))
return peaks
def parse_MACS_xls (fhd):
"""Parse a tab-delimited xls file from MACS.
fhd is a file handler for MACS xls result.
Return a taolib.CoreLib.FeatIO.PeakIO object.
"""
reader = DictReader(Filter(fhd),dialect='excel-tab')
peaks = PeakIO()
for row in reader:
peaks.add(row['chr'],int(row['start']),int(row['end']),
int(row['summit']),0,
int(row['tags']),float(row['-10*log10(pvalue)']),
float(row['fold_enrichment']),float(row['FDR(%)']))
return peaks
def parse_MACS_xls(fhd):
"""Parse a tab-delimited xls file from MACS.
fhd is a file handler for MACS xls result.
Return a taolib.CoreLib.FeatIO.PeakIO object.
"""
reader = DictReader(Filter(fhd), dialect='excel-tab')
peaks = PeakIO()
for row in reader:
peaks.add(row['chr'], int(row['start']), int(row['end']),
int(row['summit']), 0, int(row['tags']),
float(row['-10*log10(pvalue)']),
float(row['fold_enrichment']), float(row['FDR(%)']))
return peaks
def parse_BED (fhd):
"""Parse a tab-delimited bed file
Return a PeakIO object containing peak regions.
"""
peaks = PeakIO()
for thisline in fhd:
thisline = thisline.rstrip()
if not thisline: continue #return ("blank",None,None)
if thisline.startswith("#"): continue #return ("comment line",None,None) # comment line is skipped
if thisline.startswith("track"): continue
if thisline.startswith("browser"): continue
thisfields = thisline.split()
startpos = max(0,int(thisfields[1]))
peaks.add(thisfields[0],startpos,int(thisfields[2]),1,1,1,1,1,1)
return peaks
def parse_MAT_xls(fhd):
"""Parse a tab-delimited xls file from MAT.
fhd is a file handler for MAT xls result.
Return a taolib.CoreLib.FeatIO.PeakIO object.
"""
peaks = PeakIO()
for row in fhd:
if row.startswith("Chr") or row.startswith("#") or row.startswith(
"track"):
continue
else:
f = row.split()
peaks.add(f[0], int(f[1]), int(f[2]), int(f[8]), float(f[5]), 0,
float(f[4]), 0, float(f[7]))
break
for row in fhd:
f = row.split()
peaks.add(f[0], int(f[1]), int(f[2]), int(f[8]), float(f[5]), 0,
float(f[4]), 0, float(f[7]))
return peaks