Mercurial > repos > vipints > fml_gff3togtf

annotate gff_to_bed.py @ 11:5c6f33e20fcc default tip

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requirement tag added
author vipints <vipin@cbio.mskcc.org>
date Fri, 24 Apr 2015 18:04:27 -0400
parents c42c69aa81f8
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
10
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1 #!/usr/bin/env python
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2 """
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3 Convert genome annotation data in GFF/GTF to a 12 column BED format.
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4 BED format typically represents the transcript models.
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5
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6 Usage: python gff_to_bed.py in.gff > out.bed
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7
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8 Requirement:
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9 GFFParser.py: https://github.com/vipints/GFFtools-GX/blob/master/GFFParser.py
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10
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11 Copyright (C)
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12 2009-2012 Friedrich Miescher Laboratory of the Max Planck Society, Tubingen, Germany.
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13 2012-2015 Memorial Sloan Kettering Cancer Center New York City, USA.
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14 """
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15
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16 import re
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17 import sys
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18 import GFFParser
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19
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20 def limitBEDWrite(tinfo):
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21 """
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22 Write a three column BED file
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23
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24 @args tinfo: list of genes
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25 @type tinfo: numpy object
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26 """
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27
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28 for contig_id, feature in tinfo.items():
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29 uns_line = dict()
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30 for tid, tloc in feature.items():
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31 uns_line[(int(tloc[0])-1, int(tloc[1]))]=1
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32 for ele in sorted(uns_line):
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33 pline = [contig_id,
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34 str(ele[0]-1),
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35 str(ele[1])]
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36
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37 sys.stdout.write('\t'.join(pline)+"\n")
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38
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39
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40 def writeBED(tinfo):
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41 """
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42 writing result files in bed format
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43
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44 @args tinfo: list of genes
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45 @type tinfo: numpy object
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46 """
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47
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48 for ent1 in tinfo:
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49 child_flag = False
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50
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51 for idx, tid in enumerate(ent1['transcripts']):
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52 child_flag = True
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53 exon_cnt = len(ent1['exons'][idx])
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54 exon_len = ''
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55 exon_cod = ''
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56 rel_start = None
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57 rel_stop = None
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58 for idz, ex_cod in enumerate(ent1['exons'][idx]):#check for exons of corresponding transcript
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59 exon_len += '%d,' % (ex_cod[1]-ex_cod[0]+1)
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60 if idz == 0: #calculate the relative start position
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61 exon_cod += '0,'
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62 rel_start = int(ex_cod[0])-1
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63 rel_stop = int(ex_cod[1])
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64 else:
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65 exon_cod += '%d,' % (ex_cod[0]-1-rel_start) ## shifting the coordinates to zero
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66 rel_stop = int(ex_cod[1])
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67
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68 if exon_len:
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69 score = 0
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70 score = ent1['transcript_score'][idx] if ent1['transcript_score'].any() else score ## getting the transcript score
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71 out_print = [ent1['chr'],
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72 str(rel_start),
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73 str(rel_stop),
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74 tid[0],
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75 str(score),
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76 ent1['strand'],
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77 str(rel_start),
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78 str(rel_stop),
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79 '0',
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80 str(exon_cnt),
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81 exon_len,
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82 exon_cod]
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83 sys.stdout.write('\t'.join(out_print)+"\n")
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84
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85 if not child_flag: # file just contains only a single parent type i.e, gff3 defines only one feature type
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86 score = 0
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87 score = ent1['transcript_score'][0] if ent1['transcript_score'].any() else score
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88
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89 out_print = [ent1['chr'],
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90 '%d' % int(ent1['start'])-1,
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91 '%d' % int(ent1['stop']),
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92 ent1['name'],
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93 str(score),
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94 ent1['strand'],
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95 '%d' % int(ent1['start']),
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96 '%d' % int(ent1['stop']),
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97 '0',
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98 '1',
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99 '%d,' % (int(ent1['stop'])-int(ent1['start'])+1),
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100 '0,']
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101
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102 sys.stdout.write('\t'.join(out_print)+"\n")
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103
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104
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105 def __main__():
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106 try:
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107 query_file = sys.argv[1]
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108 except:
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109 print __doc__
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110 sys.exit(-1)
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111
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112 Transcriptdb = GFFParser.Parse(query_file)
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113 writeBED(Transcriptdb)
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114
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115 if __name__ == "__main__":
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116 __main__()