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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 intervals and a maf. Outputs a new set of intervals with statistics appended.
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5 """
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6
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7 import sys
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8 from galaxy import eggs
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9 import pkg_resources; pkg_resources.require( "bx-python" )
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10 import bx.intervals.io
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11 from bx.bitset import BitSet
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12 from galaxy.tools.util import maf_utilities
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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 maf_source_type = sys.argv.pop( 1 )
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18 input_maf_filename = sys.argv[1].strip()
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19 input_interval_filename = sys.argv[2].strip()
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20 output_filename = sys.argv[3].strip()
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21 dbkey = sys.argv[4].strip()
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22 try:
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23 chr_col = int( sys.argv[5].strip() ) - 1
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24 start_col = int( sys.argv[6].strip() ) - 1
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25 end_col = int( sys.argv[7].strip() ) - 1
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26 except:
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27 print >>sys.stderr, "You appear to be missing metadata. You can specify your metadata by clicking on the pencil icon associated with your interval file."
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28 sys.exit()
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29 summary = sys.argv[8].strip()
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30 if summary.lower() == "true": summary = True
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31 else: summary = False
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32
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33 mafIndexFile = "%s/maf_index.loc" % sys.argv[9]
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34 try:
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35 maf_index_filename = sys.argv[10].strip()
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36 except:
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37 maf_index_filename = None
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38 index = index_filename = None
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39 if maf_source_type == "user":
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40 #index maf for use here
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41 index, index_filename = maf_utilities.open_or_build_maf_index( input_maf_filename, maf_index_filename, species = [dbkey] )
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42 if index is None:
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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 elif maf_source_type == "cached":
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46 #access existing indexes
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47 index = maf_utilities.maf_index_by_uid( input_maf_filename, mafIndexFile )
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48 if index is None:
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49 print >> sys.stderr, "The MAF source specified (%s) appears to be invalid." % ( input_maf_filename )
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50 sys.exit()
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51 else:
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52 print >>sys.stdout, 'Invalid source type specified: %s' % maf_source_type
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53 sys.exit()
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54
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55 out = open(output_filename, 'w')
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56
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57 num_region = None
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58 species_summary = {}
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59 total_length = 0
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60 #loop through interval file
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61 for num_region, region in enumerate( bx.intervals.io.NiceReaderWrapper( open( input_interval_filename, 'r' ), chrom_col = chr_col, start_col = start_col, end_col = end_col, fix_strand = True, return_header = False, return_comments = False ) ):
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62 src = "%s.%s" % ( dbkey, region.chrom )
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63 region_length = region.end - region.start
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64 total_length += region_length
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65 coverage = { dbkey: BitSet( region_length ) }
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66
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67
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68 for block in index.get_as_iterator( src, region.start, region.end ):
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69 for spec in maf_utilities.get_species_in_block( block ):
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70 if spec not in coverage: coverage[spec] = BitSet( region_length )
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71 for block in maf_utilities.iter_blocks_split_by_species( block ):
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72 if maf_utilities.component_overlaps_region( block.get_component_by_src( src ), region ):
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73 #need to chop and orient the block
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74 block = maf_utilities.orient_block_by_region( maf_utilities.chop_block_by_region( block, src, region ), src, region, force_strand = '+' )
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75 start_offset, alignment = maf_utilities.reduce_block_by_primary_genome( block, dbkey, region.chrom, region.start )
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76 for i in range( len( alignment[dbkey] ) ):
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77 for spec, text in alignment.items():
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78 if text[i] != '-':
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79 coverage[spec].set( start_offset + i )
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80 if summary:
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81 #record summary
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82 for key in coverage.keys():
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83 if key not in species_summary: species_summary[key] = 0
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84 species_summary[key] = species_summary[key] + coverage[key].count_range()
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85 else:
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86 #print coverage for interval
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87 coverage_sum = coverage[dbkey].count_range()
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88 out.write( "%s\t%s\t%s\t%s\n" % ( "\t".join( region.fields ), dbkey, coverage_sum, region_length - coverage_sum ) )
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89 keys = coverage.keys()
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90 keys.remove( dbkey )
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91 keys.sort()
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92 for key in keys:
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93 coverage_sum = coverage[key].count_range()
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94 out.write( "%s\t%s\t%s\t%s\n" % ( "\t".join( region.fields ), key, coverage_sum, region_length - coverage_sum ) )
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95 if summary:
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96 out.write( "#species\tnucleotides\tcoverage\n" )
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97 for spec in species_summary:
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98 out.write( "%s\t%s\t%.4f\n" % ( spec, species_summary[spec], float( species_summary[spec] ) / total_length ) )
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99 out.close()
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100 if num_region is not None:
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101 print "%i regions were processed with a total length of %i." % ( num_region + 1, total_length )
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102 maf_utilities.remove_temp_index_file( index_filename )
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103
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104 if __name__ == "__main__": __main__()
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