1 | #!/usr/bin/env python |
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2 | import sys |
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3 | from galaxy import eggs |
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4 | from galaxy.tools.util.gff_util import parse_gff_attributes |
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5 | |
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6 | assert sys.version_info[:2] >= ( 2, 4 ) |
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7 | |
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8 | def get_bed_line( chrom, name, strand, blocks ): |
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9 | """ Returns a BED line for given data. """ |
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10 | |
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11 | |
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12 | if len( blocks ) == 1: |
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13 | # Use simple BED format if there is only a single block: |
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14 | # chrom, chromStart, chromEnd, name, score, strand |
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15 | # |
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16 | start, end = blocks[0] |
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17 | return "%s\t%i\t%i\t%s\t0\t%s\n" % ( chrom, start, end, name, strand ) |
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18 | |
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19 | # |
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20 | # Build lists for transcript blocks' starts, sizes. |
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21 | # |
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22 | |
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23 | # Get transcript start, end. |
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24 | t_start = sys.maxint |
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25 | t_end = -1 |
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26 | for block_start, block_end in blocks: |
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27 | if block_start < t_start: |
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28 | t_start = block_start |
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29 | if block_end > t_end: |
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30 | t_end = block_end |
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31 | |
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32 | # Get block starts, sizes. |
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33 | block_starts = [] |
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34 | block_sizes = [] |
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35 | for block_start, block_end in blocks: |
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36 | block_starts.append( str( block_start - t_start ) ) |
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37 | block_sizes.append( str( block_end - block_start ) ) |
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38 | |
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39 | # |
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40 | # Create BED entry. |
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41 | # Bed format: chrom, chromStart, chromEnd, name, score, strand, \ |
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42 | # thickStart, thickEnd, itemRgb, blockCount, blockSizes, blockStarts |
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43 | # |
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44 | return "%s\t%i\t%i\t%s\t0\t%s\t%i\t%i\t0\t%i\t%s\t%s\n" % \ |
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45 | ( chrom, t_start, t_end, name, strand, t_start, t_start, len( block_starts ), |
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46 | ",".join( block_sizes ), ",".join( block_starts ) ) |
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47 | |
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48 | def __main__(): |
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49 | input_name = sys.argv[1] |
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50 | output_name = sys.argv[2] |
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51 | skipped_lines = 0 |
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52 | first_skipped_line = 0 |
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53 | out = open( output_name, 'w' ) |
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54 | i = 0 |
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55 | cur_transcript_chrom = None |
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56 | cur_transcript_id = None |
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57 | cur_transcript_strand = None |
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58 | cur_transcripts_blocks = [] # (start, end) for each block. |
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59 | for i, line in enumerate( file( input_name ) ): |
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60 | line = line.rstrip( '\r\n' ) |
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61 | if line and not line.startswith( '#' ): |
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62 | try: |
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63 | # GFF format: chrom source, name, chromStart, chromEnd, score, strand, attributes |
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64 | elems = line.split( '\t' ) |
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65 | start = str( long( elems[3] ) - 1 ) |
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66 | coords = [ long( start ), long( elems[4] ) ] |
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67 | strand = elems[6] |
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68 | if strand not in ['+', '-']: |
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69 | strand = '+' |
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70 | attributes = parse_gff_attributes( elems[8] ) |
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71 | t_id = attributes.get( "transcript_id", None ) |
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72 | |
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73 | if not t_id: |
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74 | # |
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75 | # No transcript ID, so write last transcript and write current line as its own line. |
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76 | # |
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77 | |
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78 | # Write previous transcript. |
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79 | if cur_transcript_id: |
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80 | # Write BED entry. |
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81 | out.write( get_bed_line( cur_transcript_chrome, cur_transcript_id, cur_transcript_strand, cur_transcripts_blocks ) ) |
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82 | |
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83 | # Replace any spaces in the name with underscores so UCSC will not complain. |
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84 | name = elems[2].replace(" ", "_") |
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85 | out.write( get_bed_line( elems[0], name, strand, [ coords ] ) ) |
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86 | continue |
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87 | |
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88 | # There is a transcript ID, so process line at transcript level. |
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89 | if t_id == cur_transcript_id: |
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90 | # Line is element of transcript and will be a block in the BED entry. |
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91 | cur_transcripts_blocks.append( coords ) |
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92 | continue |
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93 | |
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94 | # |
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95 | # Line is part of new transcript; write previous transcript and start |
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96 | # new transcript. |
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97 | # |
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98 | |
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99 | # Write previous transcript. |
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100 | if cur_transcript_id: |
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101 | # Write BED entry. |
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102 | out.write( get_bed_line( cur_transcript_chrome, cur_transcript_id, cur_transcript_strand, cur_transcripts_blocks ) ) |
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103 | |
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104 | # Start new transcript. |
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105 | cur_transcript_chrome = elems[0] |
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106 | cur_transcript_id = t_id |
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107 | cur_transcript_strand = strand |
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108 | cur_transcripts_blocks = [] |
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109 | cur_transcripts_blocks.append( coords ) |
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110 | except: |
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111 | skipped_lines += 1 |
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112 | if not first_skipped_line: |
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113 | first_skipped_line = i + 1 |
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114 | else: |
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115 | skipped_lines += 1 |
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116 | if not first_skipped_line: |
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117 | first_skipped_line = i + 1 |
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118 | |
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119 | # Write last transcript. |
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120 | if cur_transcript_id: |
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121 | # Write BED entry. |
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122 | out.write( get_bed_line( cur_transcript_chrome, cur_transcript_id, cur_transcript_strand, cur_transcripts_blocks ) ) |
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123 | out.close() |
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124 | info_msg = "%i lines converted to BED. " % ( i + 1 - skipped_lines ) |
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125 | if skipped_lines > 0: |
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126 | info_msg += "Skipped %d blank/comment/invalid lines starting with line #%d." %( skipped_lines, first_skipped_line ) |
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127 | print info_msg |
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128 | |
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129 | if __name__ == "__main__": __main__() |
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