Mercurial > repos > vipints > fml_gff3togtf
comparison bed_to_gff.py @ 5:6e589f267c14
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| author | devteam |
|---|---|
| date | Tue, 04 Nov 2014 12:15:19 -0500 |
| parents | |
| children |
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| 4:619e0fcd9126 | 5:6e589f267c14 |
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| 1 #!/usr/bin/env python | |
| 2 """ | |
| 3 Convert genome annotation data in a 12 column BED format to GFF3. | |
| 4 | |
| 5 Usage: python bed_to_gff.py in.bed > out.gff | |
| 6 | |
| 7 Requirement: | |
| 8 helper.py : https://github.com/vipints/GFFtools-GX/blob/master/helper.py | |
| 9 | |
| 10 Copyright (C) | |
| 11 2009-2012 Friedrich Miescher Laboratory of the Max Planck Society, Tubingen, Germany. | |
| 12 2012-2014 Memorial Sloan Kettering Cancer Center New York City, USA. | |
| 13 """ | |
| 14 | |
| 15 import re | |
| 16 import sys | |
| 17 import helper | |
| 18 | |
| 19 def __main__(): | |
| 20 """ | |
| 21 main function | |
| 22 """ | |
| 23 | |
| 24 try: | |
| 25 bed_fname = sys.argv[1] | |
| 26 except: | |
| 27 print __doc__ | |
| 28 sys.exit(-1) | |
| 29 | |
| 30 bed_fh = helper.open_file(bed_fname) | |
| 31 | |
| 32 for line in bed_fh: | |
| 33 line = line.strip( '\n\r' ) | |
| 34 | |
| 35 if not line or line[0] in ['#']: | |
| 36 continue | |
| 37 | |
| 38 parts = line.split('\t') | |
| 39 assert len(parts) >= 12, line | |
| 40 | |
| 41 rstarts = parts[-1].split(',') | |
| 42 rstarts.pop() if rstarts[-1] == '' else rstarts | |
| 43 | |
| 44 exon_lens = parts[-2].split(',') | |
| 45 exon_lens.pop() if exon_lens[-1] == '' else exon_lens | |
| 46 | |
| 47 if len(rstarts) != len(exon_lens): | |
| 48 continue # checking the consistency col 11 and col 12 | |
| 49 | |
| 50 if len(rstarts) != int(parts[-3]): | |
| 51 continue # checking the number of exons and block count are same | |
| 52 | |
| 53 if not parts[5] in ['+', '-']: | |
| 54 parts[5] = '.' # replace the unknown strand with '.' | |
| 55 | |
| 56 # bed2gff result line | |
| 57 print '%s\tbed2gff\tgene\t%d\t%s\t%s\t%s\t.\tID=Gene:%s;Name=Gene:%s' % (parts[0], int(parts[1])+1, parts[2], parts[4], parts[5], parts[3], parts[3]) | |
| 58 print '%s\tbed2gff\ttranscript\t%d\t%s\t%s\t%s\t.\tID=%s;Name=%s;Parent=Gene:%s' % (parts[0], int(parts[1])+1, parts[2], parts[4], parts[5], parts[3], parts[3], parts[3]) | |
| 59 | |
| 60 st = int(parts[1]) | |
| 61 for ex_cnt in range(int(parts[-3])): | |
| 62 start = st + int(rstarts[ex_cnt]) + 1 | |
| 63 stop = start + int(exon_lens[ex_cnt]) - 1 | |
| 64 print '%s\tbed2gff\texon\t%d\t%d\t%s\t%s\t.\tParent=%s' % (parts[0], start, stop, parts[4], parts[5], parts[3]) | |
| 65 | |
| 66 bed_fh.close() | |
| 67 | |
| 68 | |
| 69 if __name__ == "__main__": | |
| 70 __main__() |