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1 #Dan Blankenberg
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2 #Filters a MAF file according to the provided code file, which is generated in maf_filter.xml <configfiles>
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3 #Also allows filtering by number of columns in a block, and limiting output species
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4 import sys, os, shutil
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5 from galaxy import eggs
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6 import pkg_resources; pkg_resources.require( "bx-python" )
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7 import bx.align.maf
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8 from galaxy.tools.util import maf_utilities
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9
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10 def main():
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11 #Read command line arguments
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12 try:
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13 script_file = sys.argv.pop( 1 )
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14 maf_file = sys.argv.pop( 1 )
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15 out_file = sys.argv.pop( 1 )
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16 additional_files_path = sys.argv.pop( 1 )
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17 species = maf_utilities.parse_species_option( sys.argv.pop( 1 ) )
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18 min_size = int( sys.argv.pop( 1 ) )
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19 max_size = int( sys.argv.pop( 1 ) )
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20 if max_size < 1: max_size = sys.maxint
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21 min_species_per_block = int( sys.argv.pop( 1 ) )
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22 exclude_incomplete_blocks = int( sys.argv.pop( 1 ) )
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23 if species:
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24 num_species = len( species )
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25 else:
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26 num_species = len( sys.argv.pop( 1 ).split( ',') )
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27 except:
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28 print >>sys.stderr, "One or more arguments is missing.\nUsage: maf_filter.py maf_filter_file input_maf output_maf path_to_save_debug species_to_keep"
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29 sys.exit()
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30
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31 #Open input and output MAF files
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32 try:
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33 maf_reader = bx.align.maf.Reader( open( maf_file,'r' ) )
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34 maf_writer = bx.align.maf.Writer( open( out_file,'w' ) )
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35 except:
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36 print >>sys.stderr, "Your MAF file appears to be malformed."
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37 sys.exit()
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38
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39 #Save script file for debuging/verification info later
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40 os.mkdir( additional_files_path )
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41 shutil.copy( script_file, os.path.join( additional_files_path, 'debug.txt' ) )
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42
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43 #Loop through blocks, running filter on each
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44 #'maf_block' and 'ret_val' are used/shared in the provided code file
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45 #'ret_val' should be set to True if the block is to be kept
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46 i = 0
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47 blocks_kept = 0
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48 for i, maf_block in enumerate( maf_reader ):
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49 if min_size <= maf_block.text_size <= max_size:
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50 local = {'maf_block':maf_block, 'ret_val':False}
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51 execfile( script_file, {}, local )
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52 if local['ret_val']:
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53 #Species limiting must be done after filters as filters could be run on non-requested output species
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54 if species:
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55 maf_block = maf_block.limit_to_species( species )
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56 if len( maf_block.components ) >= min_species_per_block and ( not exclude_incomplete_blocks or len( maf_block.components ) >= num_species ):
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57 maf_writer.write( maf_block )
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58 blocks_kept += 1
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59 maf_writer.close()
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60 maf_reader.close()
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61 if i == 0: print "Your file contains no valid maf_blocks."
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62 else: print 'Kept %s of %s blocks (%.2f%%).' % ( blocks_kept, i + 1, float( blocks_kept ) / float( i + 1 ) * 100.0 )
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63
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64 if __name__ == "__main__":
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65 main()
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