[2] | 1 | #!/usr/bin/env python |
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| 2 | #Dan Blankenberg |
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| 3 | """ |
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| 4 | Reads a list of block numbers and a maf. Produces a new maf containing the |
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| 5 | blocks specified by number. |
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| 6 | """ |
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| 7 | |
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| 8 | import sys |
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| 9 | from galaxy import eggs |
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| 10 | import pkg_resources; pkg_resources.require( "bx-python" ) |
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| 11 | from galaxy.tools.util import maf_utilities |
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| 12 | import bx.align.maf |
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| 13 | |
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| 14 | assert sys.version_info[:2] >= ( 2, 4 ) |
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| 15 | |
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| 16 | def __main__(): |
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| 17 | input_block_filename = sys.argv[1].strip() |
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| 18 | input_maf_filename = sys.argv[2].strip() |
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| 19 | output_filename1 = sys.argv[3].strip() |
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| 20 | block_col = int( sys.argv[4].strip() ) - 1 |
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| 21 | if block_col < 0: |
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| 22 | print >> sys.stderr, "Invalid column specified" |
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| 23 | sys.exit(0) |
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| 24 | species = maf_utilities.parse_species_option( sys.argv[5].strip() ) |
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| 25 | |
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| 26 | maf_writer = bx.align.maf.Writer( open( output_filename1, 'w' ) ) |
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| 27 | #we want to maintain order of block file and write blocks as many times as they are listed |
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| 28 | failed_lines = [] |
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| 29 | for ctr, line in enumerate( open( input_block_filename, 'r' ) ): |
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| 30 | try: |
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| 31 | block_wanted = int( line.split( "\t" )[block_col].strip() ) |
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| 32 | except: |
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| 33 | failed_lines.append( str( ctr ) ) |
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| 34 | continue |
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| 35 | try: |
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| 36 | for count, block in enumerate( bx.align.maf.Reader( open( input_maf_filename, 'r' ) ) ): |
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| 37 | if count == block_wanted: |
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| 38 | if species: |
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| 39 | block = block.limit_to_species( species ) |
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| 40 | maf_writer.write( block ) |
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| 41 | break |
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| 42 | except: |
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| 43 | print >>sys.stderr, "Your MAF file appears to be malformed." |
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| 44 | sys.exit() |
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| 45 | if len( failed_lines ) > 0: print "Failed to extract from %i lines (%s)." % ( len( failed_lines ), ",".join( failed_lines ) ) |
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| 46 | if __name__ == "__main__": __main__() |
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