def main_wrapper(process_func, argv, ext):
args = parse_arguments(argv, ext)
args.regions = None
if args.regions_fpath:
args.regions = collect_bed_regions(args.regions_fpath)
sys.stderr.write("Opening %r\n" % (args.infile,))
with pysam.Samfile(args.infile) as handle:
sort_bed_by_bamfile(handle, args.regions)
return process_func(handle, args)
def main_wrapper(process_func, argv, ext):
args = parse_arguments(argv, ext)
args.regions = None
if args.regions_fpath:
args.regions = collect_bed_regions(args.regions_fpath)
sys.stderr.write("Opening %r\n" % (args.infile, ))
with pysam.Samfile(args.infile) as handle:
sort_bed_by_bamfile(handle, args.regions)
return process_func(handle, args)
def collect_regions(bedfile, bam_input_handle):
"""Returns the regions to be genotyped / pileup'd, as a list of bed-regions
in the form (contig, start, end), where start is zero-based, and end is
open based.
"""
if bedfile is not None:
regions = list(read_bed_file(bedfile))
sort_bed_by_bamfile(bam_input_handle, regions)
regions = merge_bed_regions(regions)
else:
regions = []
for (name, length) in zip(bam_input_handle.references, bam_input_handle.lengths):
regions.append((name, 0, length))
return regions
def collect_regions(bedfile, bam_input_handle):
"""Returns the regions to be genotyped / pileup'd, as a list of bed-regions
in the form (contig, start, end), where start is zero-based, and end is
open based.
"""
if bedfile is not None:
regions = list(read_bed_file(bedfile))
sort_bed_by_bamfile(bam_input_handle, regions)
regions = merge_bed_regions(regions)
else:
regions = []
for (name, length) in zip(bam_input_handle.references,
bam_input_handle.lengths):
regions.append((name, 0, length))
return regions
def main_wrapper(process_func, argv, ext):
args = parse_arguments(argv, ext)
args.regions = None
if args.regions_fpath:
try:
args.regions = collect_bed_regions(args.regions_fpath)
except ValueError, error:
sys.stderr.write("Failed to parse BED file %r:\n%s\n" %
(args.regions_fpath, error))
return 1
sys.stderr.write("Opening %r\n" % (args.infile, ))
with pysam.Samfile(args.infile) as handle:
sort_bed_by_bamfile(handle, args.regions)
return process_func(handle, args)
def _get_readgroup(record):
try:
return record.opt("RG")
except KeyError:
raise BAMStatsError("Record lacks readgroup tag ('RG'), use of "
"--ignore-readgroups is required to process this"
"file.\n Record = %r" % (record.qname, ))
def _get_readgroup_ignored(_):
return None
def main_wrapper(process_func, argv, ext):
args = parse_arguments(argv, ext)
args.regions = None
if args.regions_fpath:
try:
args.regions = collect_bed_regions(args.regions_fpath)
except ValueError, error:
sys.stderr.write("Failed to parse BED file %r:\n%s\n"
% (args.regions_fpath, error))
return 1
sys.stderr.write("Opening %r\n" % (args.infile,))
with pysam.Samfile(args.infile) as handle:
sort_bed_by_bamfile(handle, args.regions)
return process_func(handle, args)
def _get_readgroup(record):
try:
return record.opt("RG")
except KeyError:
raise BAMStatsError("Record lacks readgroup tag ('RG'), use of "
"--ignore-readgroups is required to process this"
"file.\n Record = %r" % (record.qname,))
def _get_readgroup_ignored(_):
return None
