def process_args(args=None):
args = parse_arguments().parse_args(args)
if args.correctedFile.name.endswith('bam'):
if not cfg.checkProgram(samtools, 'view',
'http://samtools.sourceforge.net/'):
exit(1)
if args.correctedFile.name.endswith('bw'):
if not cfg.checkProgram(bedgraph_to_bigwig, '-h',
'http://hgdownload.cse.ucsc.edu/admin/exe/'):
exit(1)
return args
def getChromSizes(bigwigFilesList):
"""
Get chromosome sizes from bigWig file by shell calling bigWigInfo
(UCSC tools).
Test dataset with two samples covering 200 bp.
>>> test = Tester()
Chromosome name(s) and size(s).
>>> getChromSizes([test.bwFile1, test.bwFile2])
[('3R', 200)]
"""
#The following lines are - with one exception ("bigWigInfo") -
#identical with the bw-reading part of deeptools/countReadsPerBin.py (FK)
# check that the path to USCS bedGraphToBigWig as set in the config
# is installed and is executable.
bigwig_info_cmd = cfg.config.get('external_tools', 'bigwig_info')
if not cfg.checkProgram(bigwig_info_cmd, '-h',
'http://hgdownload.cse.ucsc.edu/admin/exe/'):
exit()
cCommon = []
chromNamesAndSize = {}
for bw in bigwigFilesList:
inBlock = False
for line in os.popen("{} -chroms {}".format(bigwig_info_cmd, bw)).readlines():
if line[0:10] == "chromCount":
inBlock = True
continue
if line[0:5] == "bases":
break
if inBlock:
chromName, id, size = line.strip().split(" ")
size = int(size)
if chromName in chromNamesAndSize:
cCommon.append(chromName)
if chromNamesAndSize[chromName] != size:
print "\nWARNING\n" \
"Chromosome {} length reported in the " \
"bigwig files differ.\n{} for {}\n" \
"{} for {}.\n\nThe smallest " \
"length will be used".format(
chromName, chromNamesAndSize[chromName],
bw[0], size, bw[1])
chromNamesAndSize[chromName] = min(
chromNamesAndSize[chromName], size)
else:
chromNamesAndSize[chromName] = size
# get the list of common chromosome names and sizes
chromSizes = sorted([(k, v) for k, v in chromNamesAndSize.iteritems() \
if k in cCommon])
return chromSizes
def checkBigWig(string):
"""
Checks if the path to USCS bedGraphToBigWig as set in the config
is installed and is executable.
"""
if string == 'bigwig':
bedgraph_to_bigwig = cfg.config.get('external_tools',
'bedgraph_to_bigwig')
if not cfg.checkProgram(bedgraph_to_bigwig, 'h',
'http://hgdownload.cse.ucsc.edu/admin/exe/'):
msg = "The output is set by default to 'bedgraph'\n"
sys.stderr.write(msg)
return 'bedgraph'
return string
def checkBigWig(string):
"""
Checks if the path to USCS bedGraphToBigWig as set in the config
is installed and is executable.
"""
if string == 'bigwig':
bedgraph_to_bigwig = cfg.config.get('external_tools',
'bedgraph_to_bigwig')
if not cfg.checkProgram(bedgraph_to_bigwig, 'h',
'http://hgdownload.cse.ucsc.edu/admin/exe/'):
msg = "The output is set by default to 'bedgraph'\n"
sys.stderr.write(msg)
return 'bedgraph'
return string