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 )
chr_col_2, start_col_2, end_col_2, strand_col_2 = parse_cols_arg( options.cols2 )
if options.mincols: mincols = int( options.mincols )
pieces = bool( options.pieces )
in_fname, in2_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)
g2 = GenomicIntervalReader( fileinput.FileInput( in2_fname ),
chrom_col=chr_col_2,
start_col=start_col_2,
end_col=end_col_2,
strand_col=strand_col_2)
out_file = open( out_fname, "w" )
for line in intersect([g1,g2], pieces=pieces, mincols=mincols):
if type( line ) is GenomicInterval:
print >> out_file, "\t".join( line.fields )
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)
chr_col_2, start_col_2, end_col_2, strand_col_2 = parse_cols_arg(
options.cols2)
if options.mincols: mincols = int(options.mincols)
pieces = bool(options.pieces)
in_fname, in2_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)
g2 = NiceReaderWrapper(fileinput.FileInput(in2_fname),
chrom_col=chr_col_2,
start_col=start_col_2,
end_col=end_col_2,
strand_col=strand_col_2,
fix_strand=True)
out_file = open(out_fname, "w")
try:
for line in intersect([g1, g2], pieces=pieces, mincols=mincols):
if type(line) == GenomicInterval:
out_file.write("%s\n" % "\t".join(line.fields))
else:
out_file.write("%s\n" % line)
except ParseError, e:
out_file.close()
fail("Invalid file format: %s" % str(e))
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)
chr_col_2, start_col_2, end_col_2, strand_col_2 = parse_cols_arg(
options.cols2)
if options.mincols: mincols = int(options.mincols)
pieces = bool(options.pieces)
in_fname, in2_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)
g2 = GenomicIntervalReader(fileinput.FileInput(in2_fname),
chrom_col=chr_col_2,
start_col=start_col_2,
end_col=end_col_2,
strand_col=strand_col_2)
out_file = open(out_fname, "w")
for line in intersect([g1, g2], pieces=pieces, mincols=mincols):
if type(line) is GenomicInterval:
print >> out_file, "\t".join(line.fields)
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 )
chr_col_2, start_col_2, end_col_2, strand_col_2 = parse_cols_arg( options.cols2 )
if options.mincols: mincols = int( options.mincols )
pieces = bool( options.pieces )
in1_gff_format = bool( options.gff1 )
in2_gff_format = bool( options.gff2 )
in_fname, in2_fname, out_fname = args
except:
doc_optparse.exception()
# Set readers to handle either GFF or default format.
if in1_gff_format:
in1_reader_wrapper = GFFReaderWrapper
else:
in1_reader_wrapper = NiceReaderWrapper
if in2_gff_format:
in2_reader_wrapper = GFFReaderWrapper
else:
in2_reader_wrapper = NiceReaderWrapper
g1 = in1_reader_wrapper( 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 )
if in1_gff_format:
# Intersect requires coordinates in BED format.
g1.convert_to_bed_coord=True
g2 = in2_reader_wrapper( fileinput.FileInput( in2_fname ),
chrom_col=chr_col_2,
start_col=start_col_2,
end_col=end_col_2,
strand_col=strand_col_2,
fix_strand=True )
if in2_gff_format:
# Intersect requires coordinates in BED format.
g2.convert_to_bed_coord=True
out_file = open( out_fname, "w" )
try:
for feature in intersect( [g1,g2], pieces=pieces, mincols=mincols ):
if isinstance( feature, GFFFeature ):
# Convert back to GFF coordinates since reader converted automatically.
convert_bed_coords_to_gff( feature )
for interval in feature.intervals:
out_file.write( "%s\n" % "\t".join( interval.fields ) )
elif isinstance( feature, GenomicInterval ):
out_file.write( "%s\n" % "\t".join( feature.fields ) )
else:
out_file.write( "%s\n" % feature )
except ParseError, e:
out_file.close()
fail( "Invalid file format: %s" % str( e ) )