Mercurial > repos > fubar > bbgbigwig_dev

annotate gff_to_bed_converter.py @ 5:f132065ac170 draft

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planemo upload for repository https://www.encodeproject.org/software/bedgraphtobigwig/
author fubar
date Sat, 15 Jun 2024 08:34:13 +0000
parents 49c6f715bc82
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
1
49c6f715bc82 planemo upload for repository https://www.encodeproject.org/software/bedgraphtobigwig/
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1 #!/usr/bin/env python
49c6f715bc82 planemo upload for repository https://www.encodeproject.org/software/bedgraphtobigwig/
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2
49c6f715bc82 planemo upload for repository https://www.encodeproject.org/software/bedgraphtobigwig/
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3 import sys
49c6f715bc82 planemo upload for repository https://www.encodeproject.org/software/bedgraphtobigwig/
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4
49c6f715bc82 planemo upload for repository https://www.encodeproject.org/software/bedgraphtobigwig/
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5 assert sys.version_info[:2] >= (2, 6)
49c6f715bc82 planemo upload for repository https://www.encodeproject.org/software/bedgraphtobigwig/
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6
49c6f715bc82 planemo upload for repository https://www.encodeproject.org/software/bedgraphtobigwig/
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7
49c6f715bc82 planemo upload for repository https://www.encodeproject.org/software/bedgraphtobigwig/
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8 def __main__():
49c6f715bc82 planemo upload for repository https://www.encodeproject.org/software/bedgraphtobigwig/
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9 skipped_lines = 0
49c6f715bc82 planemo upload for repository https://www.encodeproject.org/software/bedgraphtobigwig/
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10 first_skipped_line = None
49c6f715bc82 planemo upload for repository https://www.encodeproject.org/software/bedgraphtobigwig/
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11 # was sys.argv[2] but we need stdout for a pipe in bam_bed_gff_to_bigwig.xml
49c6f715bc82 planemo upload for repository https://www.encodeproject.org/software/bedgraphtobigwig/
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12 for i, line in enumerate(sys.stdin):
49c6f715bc82 planemo upload for repository https://www.encodeproject.org/software/bedgraphtobigwig/
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13 line = line.rstrip("\r\n")
49c6f715bc82 planemo upload for repository https://www.encodeproject.org/software/bedgraphtobigwig/
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14 if line and not line.startswith("#"):
49c6f715bc82 planemo upload for repository https://www.encodeproject.org/software/bedgraphtobigwig/
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15 try:
49c6f715bc82 planemo upload for repository https://www.encodeproject.org/software/bedgraphtobigwig/
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16 elems = line.split("\t")
49c6f715bc82 planemo upload for repository https://www.encodeproject.org/software/bedgraphtobigwig/
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17 start = str(int(elems[3]) - 1)
49c6f715bc82 planemo upload for repository https://www.encodeproject.org/software/bedgraphtobigwig/
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18 endoff = str(int(elems[4]) - 1)
49c6f715bc82 planemo upload for repository https://www.encodeproject.org/software/bedgraphtobigwig/
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19 # GFF format: chrom, source, name, chromStart, chromEnd, score, strand
49c6f715bc82 planemo upload for repository https://www.encodeproject.org/software/bedgraphtobigwig/
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20 # bedtools puts out only 4 fields: chrom, chromStart, chromEnd, score
49c6f715bc82 planemo upload for repository https://www.encodeproject.org/software/bedgraphtobigwig/
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21 sys.stdout.write(f"{elems[0]}\t{start}\t{endoff}\t0\n")
49c6f715bc82 planemo upload for repository https://www.encodeproject.org/software/bedgraphtobigwig/
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22 except Exception:
49c6f715bc82 planemo upload for repository https://www.encodeproject.org/software/bedgraphtobigwig/
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23 skipped_lines += 1
49c6f715bc82 planemo upload for repository https://www.encodeproject.org/software/bedgraphtobigwig/
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24 if not first_skipped_line:
49c6f715bc82 planemo upload for repository https://www.encodeproject.org/software/bedgraphtobigwig/
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25 first_skipped_line = i + 1
49c6f715bc82 planemo upload for repository https://www.encodeproject.org/software/bedgraphtobigwig/
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26 else:
49c6f715bc82 planemo upload for repository https://www.encodeproject.org/software/bedgraphtobigwig/
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27 skipped_lines += 1
49c6f715bc82 planemo upload for repository https://www.encodeproject.org/software/bedgraphtobigwig/
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28 if not first_skipped_line:
49c6f715bc82 planemo upload for repository https://www.encodeproject.org/software/bedgraphtobigwig/
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29 first_skipped_line = i + 1
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30
49c6f715bc82 planemo upload for repository https://www.encodeproject.org/software/bedgraphtobigwig/
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31
49c6f715bc82 planemo upload for repository https://www.encodeproject.org/software/bedgraphtobigwig/
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32 if __name__ == "__main__":
49c6f715bc82 planemo upload for repository https://www.encodeproject.org/software/bedgraphtobigwig/
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33 __main__()