/tools/maf/maf_by_block_number.py
https://bitbucket.org/cistrome/cistrome-harvard/ · Python · 46 lines · 35 code · 4 blank · 7 comment · 9 complexity · fcfbd12d42530b0f6579ba9333b68162 MD5 · raw file
- #!/usr/bin/env python
- #Dan Blankenberg
- """
- Reads a list of block numbers and a maf. Produces a new maf containing the
- blocks specified by number.
- """
- import sys
- from galaxy import eggs
- import pkg_resources; pkg_resources.require( "bx-python" )
- from galaxy.tools.util import maf_utilities
- import bx.align.maf
- assert sys.version_info[:2] >= ( 2, 4 )
- def __main__():
- input_block_filename = sys.argv[1].strip()
- input_maf_filename = sys.argv[2].strip()
- output_filename1 = sys.argv[3].strip()
- block_col = int( sys.argv[4].strip() ) - 1
- if block_col < 0:
- print >> sys.stderr, "Invalid column specified"
- sys.exit(0)
- species = maf_utilities.parse_species_option( sys.argv[5].strip() )
-
- maf_writer = bx.align.maf.Writer( open( output_filename1, 'w' ) )
- #we want to maintain order of block file and write blocks as many times as they are listed
- failed_lines = []
- for ctr, line in enumerate( open( input_block_filename, 'r' ) ):
- try:
- block_wanted = int( line.split( "\t" )[block_col].strip() )
- except:
- failed_lines.append( str( ctr ) )
- continue
- try:
- for count, block in enumerate( bx.align.maf.Reader( open( input_maf_filename, 'r' ) ) ):
- if count == block_wanted:
- if species:
- block = block.limit_to_species( species )
- maf_writer.write( block )
- break
- except:
- print >>sys.stderr, "Your MAF file appears to be malformed."
- sys.exit()
- if len( failed_lines ) > 0: print "Failed to extract from %i lines (%s)." % ( len( failed_lines ), ",".join( failed_lines ) )
- if __name__ == "__main__": __main__()