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1 #!/usr/bin/env python
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2 """
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3 Find regions of first interval file that overlap regions in a second interval file.
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4 Interval files can either be BED or GFF format.
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5
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6 usage: %prog interval_file_1 interval_file_2 out_file
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7 -1, --cols1=N,N,N,N: Columns for start, end, strand in first file
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8 -2, --cols2=N,N,N,N: Columns for start, end, strand in second file
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9 -m, --mincols=N: Require this much overlap (default 1bp)
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10 -p, --pieces: just print pieces of second set (after padding)
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11 -G, --gff1: input 1 is GFF format, meaning start and end coordinates are 1-based, closed interval
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12 -H, --gff2: input 2 is GFF format, meaning start and end coordinates are 1-based, closed interval
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13 """
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14 import sys, traceback, fileinput
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15 from warnings import warn
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16 from bx.intervals import *
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17 from bx.intervals.io import *
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18 from bx.intervals.operations.intersect import *
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19 from bx.cookbook import doc_optparse
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20 from galaxy.tools.util.galaxyops import *
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21 from utils.gff_util import GFFFeature, GFFReaderWrapper, convert_bed_coords_to_gff
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22
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23 assert sys.version_info[:2] >= ( 2, 4 )
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24
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25 def main():
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26 mincols = 1
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27 upstream_pad = 0
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28 downstream_pad = 0
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29
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30 options, args = doc_optparse.parse( __doc__ )
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31 try:
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32 chr_col_1, start_col_1, end_col_1, strand_col_1 = parse_cols_arg( options.cols1 )
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33 chr_col_2, start_col_2, end_col_2, strand_col_2 = parse_cols_arg( options.cols2 )
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34 if options.mincols: mincols = int( options.mincols )
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35 pieces = bool( options.pieces )
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36 in1_gff_format = bool( options.gff1 )
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37 in2_gff_format = bool( options.gff2 )
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38 in_fname, in2_fname, out_fname = args
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39 except:
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40 doc_optparse.exception()
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41
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42 # Set readers to handle either GFF or default format.
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43 if in1_gff_format:
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44 in1_reader_wrapper = GFFReaderWrapper
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45 else:
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46 in1_reader_wrapper = NiceReaderWrapper
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47 if in2_gff_format:
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48 in2_reader_wrapper = GFFReaderWrapper
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49 else:
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50 in2_reader_wrapper = NiceReaderWrapper
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51
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52 g1 = in1_reader_wrapper( fileinput.FileInput( in_fname ),
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53 chrom_col=chr_col_1,
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54 start_col=start_col_1,
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55 end_col=end_col_1,
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56 strand_col=strand_col_1,
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57 fix_strand=True )
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58 if in1_gff_format:
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59 # Intersect requires coordinates in BED format.
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60 g1.convert_to_bed_coord=True
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61 g2 = in2_reader_wrapper( fileinput.FileInput( in2_fname ),
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62 chrom_col=chr_col_2,
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63 start_col=start_col_2,
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64 end_col=end_col_2,
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65 strand_col=strand_col_2,
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66 fix_strand=True )
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67 if in2_gff_format:
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68 # Intersect requires coordinates in BED format.
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69 g2.convert_to_bed_coord=True
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70
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71 out_file = open( out_fname, "w" )
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72 try:
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73 for feature in intersect( [g1,g2], pieces=pieces, mincols=mincols ):
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74 if isinstance( feature, GFFFeature ):
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75 # Convert back to GFF coordinates since reader converted automatically.
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76 convert_bed_coords_to_gff( feature )
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77 for interval in feature.intervals:
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78 out_file.write( "%s\n" % "\t".join( interval.fields ) )
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79 elif isinstance( feature, GenomicInterval ):
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80 out_file.write( "%s\n" % "\t".join( feature.fields ) )
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81 else:
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82 out_file.write( "%s\n" % feature )
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83 except ParseError, e:
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84 out_file.close()
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85 fail( "Invalid file format: %s" % str( e ) )
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86
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87 out_file.close()
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88
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89 if g1.skipped > 0:
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90 print skipped( g1, filedesc=" of 1st dataset" )
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91 if g2.skipped > 0:
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92 print skipped( g2, filedesc=" of 2nd dataset" )
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93
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94 if __name__ == "__main__":
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95 main()
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