mirror of
https://github.com/galaxyproject/galaxy.git
synced 2026-10-24 02:04:04 +08:00
James Taylor
09db8088dd
that use doc_optparse should now get it from bx-python. In general tools should never import things from inside Galaxy's lib directory.
47 lines
1.2 KiB
Python
47 lines
1.2 KiB
Python
#!/usr/bin/env python2.4
|
|
|
|
"""
|
|
Extract features from GFF file.
|
|
|
|
usage: %prog input1 out_file1 column features out_format
|
|
"""
|
|
|
|
import sys, os
|
|
|
|
import pkg_resources; pkg_resources.require( "bx-python" )
|
|
from bx.cookbook import doc_optparse
|
|
|
|
def main():
|
|
# Parsing Command Line here
|
|
options, args = doc_optparse.parse( __doc__ )
|
|
|
|
try:
|
|
inp_file, out_file, column, features = args
|
|
column = int(column)
|
|
except:
|
|
doc_optparse.exception()
|
|
|
|
if features == None:
|
|
print "Column %d has no features to display. Please select another column." %(column+1)
|
|
sys.exit()
|
|
|
|
try:
|
|
fo=open(out_file,'w')
|
|
for line in open(inp_file):
|
|
if line[0] == '#' or not(line) or line == "":
|
|
print >>fo, line.strip()
|
|
continue
|
|
try:
|
|
if line.split('\t')[column] in features.split(','):
|
|
print >>fo, line.strip()
|
|
except:
|
|
pass
|
|
fo.close()
|
|
except Exception, exc:
|
|
print >> sys.stderr, exc
|
|
|
|
print 'Field = Column %d and Features = %s' %(column+1, features)
|
|
|
|
if __name__ == "__main__":
|
|
main()
|