def main():
mincols = 1
upstream_pad = 0
downstream_pad = 0
options, args = cookbook.doc_optparse.parse( __doc__ )
try:
chr_col_1, start_col_1, end_col_1, strand_col_1 = parse_cols_arg( options.cols1 )
if options.mincols: mincols = int( options.mincols )
in_fname, out_fname = args
except:
cookbook.doc_optparse.exception()
g1 = GenomicIntervalReader( fileinput.FileInput( in_fname ),
chrom_col=chr_col_1,
start_col=start_col_1,
end_col=end_col_1,
strand_col = strand_col_1)
out_file = open( out_fname, "w" )
for line in merge(g1,mincols=mincols):
if type( line ) is GenomicInterval:
print >> out_file, "\t".join( line.fields )
elif type( line ) is list:
print >> out_file, "\t".join( line )
else:
print >> out_file, line
def main():
mincols = 1
upstream_pad = 0
downstream_pad = 0
options, args = cookbook.doc_optparse.parse(__doc__)
try:
chr_col_1, start_col_1, end_col_1, strand_col_1 = parse_cols_arg(
options.cols1)
if options.mincols: mincols = int(options.mincols)
in_fname, out_fname = args
except:
cookbook.doc_optparse.exception()
g1 = GenomicIntervalReader(fileinput.FileInput(in_fname),
chrom_col=chr_col_1,
start_col=start_col_1,
end_col=end_col_1,
strand_col=strand_col_1)
out_file = open(out_fname, "w")
for line in merge(g1, mincols=mincols):
if type(line) is GenomicInterval:
print >> out_file, "\t".join(line.fields)
elif type(line) is list:
print >> out_file, "\t".join(line)
else:
print >> out_file, line
def main():
mincols = 1
upstream_pad = 0
downstream_pad = 0
options, args = doc_optparse.parse(__doc__)
try:
chr_col_1, start_col_1, end_col_1, strand_col_1 = parse_cols_arg(
options.cols1)
if options.mincols: mincols = int(options.mincols)
in_fname, out_fname = args
except:
doc_optparse.exception()
g1 = NiceReaderWrapper(fileinput.FileInput(in_fname),
chrom_col=chr_col_1,
start_col=start_col_1,
end_col=end_col_1,
strand_col=strand_col_1,
fix_strand=True)
out_file = open(out_fname, "w")
try:
for line in merge(g1, mincols=mincols):
if options.threecol:
if type(line) is GenomicInterval:
out_file.write(
"%s\t%s\t%s\n" %
(line.chrom, str(line.startCol), str(line.endCol)))
elif type(line) is list:
out_file.write("%s\t%s\t%s\n" %
(line[chr_col_1], str(line[start_col_1]),
str(line[end_col_1])))
else:
out_file.write("%s\n" % line)
else:
if type(line) is GenomicInterval:
out_file.write("%s\n" % "\t".join(line.fields))
elif type(line) is list:
out_file.write("%s\n" % "\t".join(line))
else:
out_file.write("%s\n" % line)
except ParseError, exc:
out_file.close()
fail("Invalid file format: %s" % str(exc))
def main():
mincols = 1
upstream_pad = 0
downstream_pad = 0
options, args = doc_optparse.parse( __doc__ )
try:
chr_col_1, start_col_1, end_col_1, strand_col_1 = parse_cols_arg( options.cols1 )
if options.mincols: mincols = int( options.mincols )
in_fname, out_fname = args
except:
doc_optparse.exception()
g1 = NiceReaderWrapper( fileinput.FileInput( in_fname ),
chrom_col=chr_col_1,
start_col=start_col_1,
end_col=end_col_1,
strand_col = strand_col_1,
fix_strand=True )
out_file = open( out_fname, "w" )
try:
for line in merge(g1,mincols=mincols):
if options.threecol:
if type( line ) is GenomicInterval:
out_file.write( "%s\t%s\t%s\n" % ( line.chrom, str( line.startCol ), str( line.endCol ) ) )
elif type( line ) is list:
out_file.write( "%s\t%s\t%s\n" % ( line[chr_col_1], str( line[start_col_1] ), str( line[end_col_1] ) ) )
else:
out_file.write( "%s\n" % line )
else:
if type( line ) is GenomicInterval:
out_file.write( "%s\n" % "\t".join( line.fields ) )
elif type( line ) is list:
out_file.write( "%s\n" % "\t".join( line ) )
else:
out_file.write( "%s\n" % line )
except ParseError, exc:
out_file.close()
fail( "Invalid file format: %s" % str( exc ) )
