mirror of
https://github.com/galaxyproject/galaxy.git
synced 2026-10-24 12:13:33 +08:00
100 lines
3.2 KiB
Python
Executable File
100 lines
3.2 KiB
Python
Executable File
#!/usr/bin/env python
|
|
"""
|
|
Build a UCSC genome browser custom track file
|
|
"""
|
|
|
|
import sys, os
|
|
|
|
assert sys.version_info[:2] >= ( 2, 4 )
|
|
|
|
def stop_err( msg ):
|
|
sys.stderr.write( msg )
|
|
sys.exit()
|
|
|
|
FILE_TYPE_TO_TRACK_TYPE = { 'bed': None, 'bedstrict': None, 'bed6': None, 'bed12': None, 'bedgraph':'bedGraph', 'wig':'wiggle_0' }
|
|
CHUNK_SIZE = 2**20 #1mb
|
|
|
|
def get_track_line_is_interval( file_type, name, description, color, visibility ):
|
|
if file_type in FILE_TYPE_TO_TRACK_TYPE:
|
|
track_type = FILE_TYPE_TO_TRACK_TYPE[ file_type ]
|
|
is_interval = False
|
|
else:
|
|
track_type = None
|
|
is_interval = True
|
|
track_line = 'track '
|
|
if track_type:
|
|
track_line += 'type=%s ' % ( track_type )
|
|
track_line += 'name="%s" description="%s" color=%s visibility=%s\n' % ( name, description, color, visibility )
|
|
return track_line, is_interval
|
|
|
|
args = sys.argv[1:]
|
|
|
|
out_fname = args.pop(0)
|
|
out = open( out_fname, "w" )
|
|
|
|
num_tracks = 0
|
|
skipped_lines = 0
|
|
first_invalid_line = 0
|
|
while args:
|
|
# Suck in one dataset worth of arguments
|
|
in_fname = args.pop(0)
|
|
file_type = args.pop(0)
|
|
colspec = args.pop(0)
|
|
name = args.pop(0)
|
|
description = args.pop(0)
|
|
color = args.pop(0).replace( '-', ',' )
|
|
visibility = args.pop(0)
|
|
track_line, is_interval = get_track_line_is_interval( file_type, name, description, color, visibility )
|
|
# Do the work
|
|
in_file = open( in_fname )
|
|
out.write( track_line )
|
|
if not is_interval:
|
|
while True:
|
|
chunk = in_file.read( CHUNK_SIZE )
|
|
if chunk:
|
|
out.write( chunk )
|
|
else:
|
|
break
|
|
else:
|
|
# Assume type is interval (don't pass this script anything else!)
|
|
try:
|
|
c, s, e, st = [ int( x ) - 1 for x in colspec.split( "," ) ]
|
|
except:
|
|
try:
|
|
c, s, e = [ int( x ) - 1 for x in colspec.split( "," )[:3] ]
|
|
st = -1 #strand column is absent
|
|
except:
|
|
stop_err( "Columns in interval file invalid for UCSC custom track." )
|
|
|
|
i = 0
|
|
for i, line in enumerate( in_file ):
|
|
line = line.rstrip( '\r\n' )
|
|
if line and not line.startswith( '#' ):
|
|
fields = line.split( "\t" )
|
|
if st > 0:
|
|
#strand column is present
|
|
try:
|
|
out.write( "%s\t%s\t%s\t%d\t0\t%s\n" % ( fields[c], fields[s], fields[e], i, fields[st] ) )
|
|
except:
|
|
skipped_lines += 1
|
|
if not first_invalid_line:
|
|
first_invalid_line = i+1
|
|
else:
|
|
try:
|
|
out.write( "%s\t%s\t%s\n" % ( fields[c], fields[s], fields[e] ) )
|
|
except:
|
|
skipped_lines += 1
|
|
if not first_invalid_line:
|
|
first_invalid_line = i+1
|
|
out.write( "\n" ) #separating newline
|
|
num_tracks += 1
|
|
|
|
out.close()
|
|
|
|
print "Generated a custom track containing %d subtracks." % num_tracks
|
|
if skipped_lines:
|
|
print "Skipped %d invalid lines starting at #%d" % ( skipped_lines, first_invalid_line )
|
|
|
|
|
|
|