def main():
# Process arguments.
parser = optparse.OptionParser()
parser.add_option( '-F', '--format', dest="input_format" )
(options, args) = parser.parse_args()
in_fname, out_fname = args
input_format = options.input_format.lower()
# Create dict of name-location pairings.
name_loc_dict = {}
if input_format in [ 'gff', 'gtf' ]:
# GTF/GFF format
# Create reader.
if input_format == 'gff':
in_reader = GFFReaderWrapper( open( in_fname, 'r' ) )
else: # input_format == 'gtf'
in_reader = read_unordered_gtf( open( in_fname, 'r' ) )
for feature in in_reader:
if isinstance( feature, Comment ):
continue
for name in feature.attributes:
val = feature.attributes[ name ]
try:
float( val )
continue
except:
convert_gff_coords_to_bed( feature )
# Value is not a number, so it can be indexed.
if val not in name_loc_dict:
# Value is not in dictionary.
name_loc_dict[ val ] = {
'contig': feature.chrom,
'start': feature.start,
'end': feature.end
}
else:
# Value already in dictionary, so update dictionary.
loc = name_loc_dict[ val ]
if feature.start < loc[ 'start' ]:
loc[ 'start' ] = feature.start
if feature.end > loc[ 'end' ]:
loc[ 'end' ] = feature.end
elif input_format == 'bed':
# BED format.
for line in open( in_fname, 'r' ):
# Ignore track lines.
if line.startswith("track"):
continue
fields = line.split()
# Ignore lines with no feature name.
if len( fields ) < 4:
continue
# Process line
name_loc_dict[ fields[3] ] = {
'contig': fields[0],
'start': int( fields[1] ),
'end': int( fields[2] )
}
# Create sorted list of entries.
out = open( out_fname, 'w' )
max_len = 0
entries = []
for name in sorted( name_loc_dict.iterkeys() ):
loc = name_loc_dict[ name ]
entry = '%s\t%s\t%s' % ( name.lower(), name, '%s:%i-%i' % ( loc[ 'contig' ], loc[ 'start' ], loc[ 'end' ] ) )
if len( entry ) > max_len:
max_len = len( entry )
entries.append( entry )
# Write padded entries.
out.write( str( max_len + 1 ).ljust( max_len ) + '\n' )
for entry in entries:
out.write( entry.ljust( max_len ) + '\n' )
out.close()
#!/usr/bin/env python
import sys
from galaxy import eggs
from galaxy.datatypes.util.gff_util import read_unordered_gtf
# Older py compatibility
try:
set()
except:
from sets import Set as set
assert sys.version_info[:2] >= ( 2, 4 )
#
# Process inputs.
#
in_fname = sys.argv[1]
out_fname = sys.argv[2]
out = open( out_fname, 'w' )
for feature in read_unordered_gtf( open( in_fname, 'r' ) ):
# Print feature.
for interval in feature.intervals:
out.write( "\t".join(interval.fields) )
out.close()
# TODO: print status information: how many lines processed and features found.
#!/usr/bin/env python
import sys
from galaxy.datatypes.util.gff_util import read_unordered_gtf
#
# Process inputs.
#
in_fname = sys.argv[1]
out_fname = sys.argv[2]
out = open( out_fname, 'w' )
for feature in read_unordered_gtf( open( in_fname, 'r' ) ):
# Print feature.
for interval in feature.intervals:
out.write( "\t".join(interval.fields) )
out.close()
# TODO: print status information: how many lines processed and features found.
def main():
# Process arguments.
parser = optparse.OptionParser()
parser.add_option('-F', '--format', dest="input_format")
(options, args) = parser.parse_args()
in_fname, out_fname = args
input_format = options.input_format.lower()
# Create dict of name-location pairings.
name_loc_dict = {}
if input_format in ['gff', 'gtf']:
# GTF/GFF format
# Create reader.
if input_format == 'gff':
in_reader = GFFReaderWrapper(open(in_fname, 'r'))
else: #input_format == 'gtf'
in_reader = read_unordered_gtf(open(in_fname, 'r'))
for feature in in_reader:
if isinstance(feature, Comment):
continue
for name in feature.attributes:
val = feature.attributes[name]
try:
float(val)
continue
except:
convert_gff_coords_to_bed(feature)
# Value is not a number, so it can be indexed.
if val not in name_loc_dict:
# Value is not in dictionary.
name_loc_dict[val] = {
'contig': feature.chrom,
'start': feature.start,
'end': feature.end
}
else:
# Value already in dictionary, so update dictionary.
loc = name_loc_dict[val]
if feature.start < loc['start']:
loc['start'] = feature.start
if feature.end > loc['end']:
loc['end'] = feature.end
elif input_format == 'bed':
# BED format.
for line in open(in_fname, 'r'):
# Ignore track lines.
if line.startswith("track"):
continue
fields = line.split()
# Ignore lines with no feature name.
if len(fields) < 4:
continue
# Process line
name_loc_dict[fields[3]] = {
'contig': fields[0],
'start': int(fields[1]),
'end': int(fields[2])
}
# Create sorted list of entries.
out = open(out_fname, 'w')
max_len = 0
entries = []
for name in sorted(name_loc_dict.iterkeys()):
loc = name_loc_dict[name]
entry = '%s\t%s\t%s' % (name.lower(), name, '%s:%i-%i' %
(loc['contig'], loc['start'], loc['end']))
if len(entry) > max_len:
max_len = len(entry)
entries.append(entry)
# Write padded entries.
out.write(str(max_len + 1).ljust(max_len) + '\n')
for entry in entries:
out.write(entry.ljust(max_len) + '\n')
out.close()
