def main():
description = """
Take a blast result table and output a subset of hits based on the
chosen filtering options. If more than one blast file given, use -O
to get multiple output files, otherwise all output data will be
concatenated into one output.
"""
# command line arguments
parser = argparse.ArgumentParser(
description=description,
conflict_handler='resolve')
add_hit_table_arguments(parser, flags='all')
parser.add_argument(
"-o",
"--outfilenome",
dest="outfilename",
default=None,
metavar="OUTFILENAME",
help="Write masked fasta output to OUTFILENAME.")
parser.add_argument(
'-O',
'--autoOutName',
default=False,
action='store_true',
help="Automatically generate output file name from input name "
"and options. Overridden by -o, cannot be used with data "
"from STDIN.")
parser.add_argument('-G', '--gff', default=False, action='store_true',
help="output GFF format instead of input format")
parser.add_argument('hit_table', nargs='*',
type=argparse.FileType('rU'), default=[sys.stdin, ],
help="Table of search results to be filtered. "
"If absent, data will be read from STDIN")
add_universal_arguments(parser)
arguments = parser.parse_args()
setup_logging(arguments)
# check that we have blast file as argument
# if we're not doing auto file names, wriate all outputs to same file
if not arguments.autoOutName:
if arguments.outfilename is not None:
logging.info("Writing data to %s" % (arguments.outfilename))
outfile_handle = open(arguments.outfilename, 'w')
else:
logging.info("writing data to STDOUT")
outfile_handle = sys.stdout
if arguments.gff:
logging.info("Converting to GFF")
# loop over inputs
for infile_handle in arguments.hit_table:
logging.info("reading data from %s" % (infile_handle.name))
if arguments.autoOutName:
outfile_handle = open(
getOutputFile(
infile_handle.name,
arguments),
'w')
# filter
params = FilterParams.create_from_arguments(arguments)
filterM8(infile_handle, outfile_handle, params, to_gff=arguments.gff)
if arguments.autoOutName:
outfile_handle.close()
infile_handle.close()
def main():
description = """
Take a blast result table and output a subset of hits based on the
chosen filtering options. If more than one blast file given, use -O
to get multiple output files, otherwise all output data will be
concatenated into one output.
"""
# command line arguments
parser = argparse.ArgumentParser(description=description,
conflict_handler='resolve')
add_hit_table_arguments(parser, flags='all')
parser.add_argument("-o",
"--outfilenome",
dest="outfilename",
default=None,
metavar="OUTFILENAME",
help="Write masked fasta output to OUTFILENAME.")
parser.add_argument(
'-O',
'--autoOutName',
default=False,
action='store_true',
help="Automatically generate output file name from input name "
"and options. Overridden by -o, cannot be used with data "
"from STDIN.")
parser.add_argument('-G',
'--gff',
default=False,
action='store_true',
help="output GFF format instead of input format")
parser.add_argument('hit_table',
nargs='*',
type=argparse.FileType('rU'),
default=[
sys.stdin,
],
help="Table of search results to be filtered. "
"If absent, data will be read from STDIN")
add_universal_arguments(parser)
arguments = parser.parse_args()
setup_logging(arguments)
# check that we have blast file as argument
# if we're not doing auto file names, wriate all outputs to same file
if not arguments.autoOutName:
if arguments.outfilename is not None:
logging.info("Writing data to %s" % (arguments.outfilename))
outfile_handle = open(arguments.outfilename, 'w')
else:
logging.info("writing data to STDOUT")
outfile_handle = sys.stdout
if arguments.gff:
logging.info("Converting to GFF")
# loop over inputs
for infile_handle in arguments.hit_table:
logging.info("reading data from %s" % (infile_handle.name))
if arguments.autoOutName:
outfile_handle = open(getOutputFile(infile_handle.name, arguments),
'w')
# filter
params = FilterParams.create_from_arguments(arguments)
filterM8(infile_handle, outfile_handle, params, to_gff=arguments.gff)
if arguments.autoOutName:
outfile_handle.close()
infile_handle.close()
def main():
usage = "usage: %prog [OPTIONS] BLAST_FILE"
description = """
Take a blast result table and output a subset of hits based on the chosen filtering options. If more than one blast file given, use -O to get multiple output files, otherwise all output data will be concatenated into one output.
"""
# command line options
parser = OptionParser(usage, description=description, conflict_handler='resolve')
addHitTableOptions(parser, flags='all')
parser.add_option("-o", "--outfilenome", dest="outfilename", default=None,
metavar="OUTFILENAME", help="Write masked fasta output to OUTFILENAME.")
parser.add_option('-O', '--autoOutName', default=False,
action='store_true',
help="Automatically generate output file name from input name and options. Overridden by -o, cannot be used with data from STDIN.")
addUniversalOptions(parser)
(options, args) = parser.parse_args()
setupLogging(options,description)
if options.hitTableFormat=='last':
if options.hitTableSort=='evalue':
parser.error("The last format has no evalue to sort by, sorry")
# check that we have blast file as argument
if len(args) <= 1:
# input
if len(args) == 1:
infile = args[0]
logging.info("reading data from %s" % (infile))
instream = open(infile,'rU')
else:
infile = './stdin'
logging.info("reading data from STDIN")
instream=sys.stdin
# output
if options.outfilename is not None:
logging.info("Writing data to %s" % (options.outfilename))
outstream=open(options.outfilename,'w')
elif options.autoOutName:
outfile=getOutputFile(infile,options)
logging.info("Writing data to %s" % (outfile))
outstream=open(outfile,'w')
else:
logging.info("writing data to STDOUT")
outstream=sys.stdout
# filter
params=FilterParams.createFromOptions(options)
filterM8(instream,outstream,params)
else:
if not options.autoOutName:
if options.outfilename is not None:
logging.info("Writing data to %s" % (options.outfilename))
outstream=open(options.outfilename,'w')
else:
logging.info("writing data to STDOUT")
outstream=sys.stdout
for infilename in args:
logging.info("reading data from %s" % (infilename))
instream=open(infilename,'rU')
if options.autoOutName:
outstream=open(getOutputFile(infilename,options),'w')
# filter
params=FilterParams.createFromOptions(options)
filterM8(instream,outstream,params)
if options.autoOutName:
outstream.close()
instream.close()