Mercurial > repos > iuc > tbl2gff3

annotate tbl2gff3.py @ 0:63f6b6ca0e97 draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tbl2gff3 commit 725ff8b6a4f01bf532052ce46400f529551a317d"
author iuc
date Tue, 07 Jul 2020 08:19:40 +0000
parents
children d9eb9f753fa6
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63f6b6ca0e97 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tbl2gff3 commit 725ff8b6a4f01bf532052ce46400f529551a317d"
iuc
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diff changeset
1 #!/usr/bin/env python
63f6b6ca0e97 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tbl2gff3 commit 725ff8b6a4f01bf532052ce46400f529551a317d"
iuc
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2 import argparse
63f6b6ca0e97 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tbl2gff3 commit 725ff8b6a4f01bf532052ce46400f529551a317d"
iuc
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3 import csv
63f6b6ca0e97 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tbl2gff3 commit 725ff8b6a4f01bf532052ce46400f529551a317d"
iuc
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4 import sys
63f6b6ca0e97 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tbl2gff3 commit 725ff8b6a4f01bf532052ce46400f529551a317d"
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5
63f6b6ca0e97 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tbl2gff3 commit 725ff8b6a4f01bf532052ce46400f529551a317d"
iuc
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6 from BCBio import GFF
63f6b6ca0e97 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tbl2gff3 commit 725ff8b6a4f01bf532052ce46400f529551a317d"
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7 from Bio.Seq import Seq
63f6b6ca0e97 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tbl2gff3 commit 725ff8b6a4f01bf532052ce46400f529551a317d"
iuc
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8 from Bio.SeqFeature import FeatureLocation, SeqFeature
63f6b6ca0e97 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tbl2gff3 commit 725ff8b6a4f01bf532052ce46400f529551a317d"
iuc
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9 from Bio.SeqRecord import SeqRecord
63f6b6ca0e97 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tbl2gff3 commit 725ff8b6a4f01bf532052ce46400f529551a317d"
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10
63f6b6ca0e97 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tbl2gff3 commit 725ff8b6a4f01bf532052ce46400f529551a317d"
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11
63f6b6ca0e97 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tbl2gff3 commit 725ff8b6a4f01bf532052ce46400f529551a317d"
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12 def c(row, v, default=None):
63f6b6ca0e97 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tbl2gff3 commit 725ff8b6a4f01bf532052ce46400f529551a317d"
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13 if v is None:
63f6b6ca0e97 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tbl2gff3 commit 725ff8b6a4f01bf532052ce46400f529551a317d"
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14 return default
63f6b6ca0e97 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tbl2gff3 commit 725ff8b6a4f01bf532052ce46400f529551a317d"
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15
63f6b6ca0e97 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tbl2gff3 commit 725ff8b6a4f01bf532052ce46400f529551a317d"
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16 try:
63f6b6ca0e97 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tbl2gff3 commit 725ff8b6a4f01bf532052ce46400f529551a317d"
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17 _ = int(v)
63f6b6ca0e97 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tbl2gff3 commit 725ff8b6a4f01bf532052ce46400f529551a317d"
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18 return row[int(v) - 1]
63f6b6ca0e97 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tbl2gff3 commit 725ff8b6a4f01bf532052ce46400f529551a317d"
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19 except ValueError:
63f6b6ca0e97 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tbl2gff3 commit 725ff8b6a4f01bf532052ce46400f529551a317d"
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20 return v
63f6b6ca0e97 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tbl2gff3 commit 725ff8b6a4f01bf532052ce46400f529551a317d"
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21
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22
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iuc
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23 def tbl2gff3(
63f6b6ca0e97 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tbl2gff3 commit 725ff8b6a4f01bf532052ce46400f529551a317d"
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24 table,
63f6b6ca0e97 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tbl2gff3 commit 725ff8b6a4f01bf532052ce46400f529551a317d"
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25 rid,
63f6b6ca0e97 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tbl2gff3 commit 725ff8b6a4f01bf532052ce46400f529551a317d"
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26 begin,
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27 end,
63f6b6ca0e97 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tbl2gff3 commit 725ff8b6a4f01bf532052ce46400f529551a317d"
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28 source=None,
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29 type=None,
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30 score=None,
63f6b6ca0e97 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tbl2gff3 commit 725ff8b6a4f01bf532052ce46400f529551a317d"
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31 frame=None,
63f6b6ca0e97 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tbl2gff3 commit 725ff8b6a4f01bf532052ce46400f529551a317d"
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32 a=None,
63f6b6ca0e97 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tbl2gff3 commit 725ff8b6a4f01bf532052ce46400f529551a317d"
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33 strand_column=None,
63f6b6ca0e97 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tbl2gff3 commit 725ff8b6a4f01bf532052ce46400f529551a317d"
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34 strand_value=None,
63f6b6ca0e97 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tbl2gff3 commit 725ff8b6a4f01bf532052ce46400f529551a317d"
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35 ):
63f6b6ca0e97 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tbl2gff3 commit 725ff8b6a4f01bf532052ce46400f529551a317d"
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36
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37 records = {}
63f6b6ca0e97 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tbl2gff3 commit 725ff8b6a4f01bf532052ce46400f529551a317d"
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38
63f6b6ca0e97 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tbl2gff3 commit 725ff8b6a4f01bf532052ce46400f529551a317d"
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39 for row in csv.reader(table, delimiter="\t"):
63f6b6ca0e97 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tbl2gff3 commit 725ff8b6a4f01bf532052ce46400f529551a317d"
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40 # print(', '.join(row))
63f6b6ca0e97 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tbl2gff3 commit 725ff8b6a4f01bf532052ce46400f529551a317d"
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41
63f6b6ca0e97 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tbl2gff3 commit 725ff8b6a4f01bf532052ce46400f529551a317d"
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42 # if we haven't seen this record before, populate it.
63f6b6ca0e97 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tbl2gff3 commit 725ff8b6a4f01bf532052ce46400f529551a317d"
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43 recid = c(row, rid)
63f6b6ca0e97 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tbl2gff3 commit 725ff8b6a4f01bf532052ce46400f529551a317d"
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44 if recid not in records:
63f6b6ca0e97 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tbl2gff3 commit 725ff8b6a4f01bf532052ce46400f529551a317d"
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45 records[recid] = SeqRecord(Seq("ACTG"), id=recid)
63f6b6ca0e97 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tbl2gff3 commit 725ff8b6a4f01bf532052ce46400f529551a317d"
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46
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47 r = records[recid]
63f6b6ca0e97 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tbl2gff3 commit 725ff8b6a4f01bf532052ce46400f529551a317d"
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48 q = {}
63f6b6ca0e97 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tbl2gff3 commit 725ff8b6a4f01bf532052ce46400f529551a317d"
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49 if c(row, score) is not None:
63f6b6ca0e97 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tbl2gff3 commit 725ff8b6a4f01bf532052ce46400f529551a317d"
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50 q["score"] = float(c(row, score))
63f6b6ca0e97 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tbl2gff3 commit 725ff8b6a4f01bf532052ce46400f529551a317d"
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51
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52 q["source"] = c(row, source, "tbl2gff3")
63f6b6ca0e97 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tbl2gff3 commit 725ff8b6a4f01bf532052ce46400f529551a317d"
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53
63f6b6ca0e97 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tbl2gff3 commit 725ff8b6a4f01bf532052ce46400f529551a317d"
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54 _str = None
63f6b6ca0e97 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tbl2gff3 commit 725ff8b6a4f01bf532052ce46400f529551a317d"
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55 if strand_column is not None:
63f6b6ca0e97 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tbl2gff3 commit 725ff8b6a4f01bf532052ce46400f529551a317d"
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56 _str = int(c(row, strand_column))
63f6b6ca0e97 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tbl2gff3 commit 725ff8b6a4f01bf532052ce46400f529551a317d"
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57 elif strand_value is not None:
63f6b6ca0e97 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tbl2gff3 commit 725ff8b6a4f01bf532052ce46400f529551a317d"
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58 _str = int(strand_value)
63f6b6ca0e97 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tbl2gff3 commit 725ff8b6a4f01bf532052ce46400f529551a317d"
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59
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60 for x in a:
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61 k, v = x.split(":", 1)
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62 _v = c(row, v)
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63 if k in q:
63f6b6ca0e97 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tbl2gff3 commit 725ff8b6a4f01bf532052ce46400f529551a317d"
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64 q[k].append(_v)
63f6b6ca0e97 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tbl2gff3 commit 725ff8b6a4f01bf532052ce46400f529551a317d"
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65 else:
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66 q[k] = [_v]
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67
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68 f = SeqFeature(
63f6b6ca0e97 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tbl2gff3 commit 725ff8b6a4f01bf532052ce46400f529551a317d"
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69 FeatureLocation(int(c(row, begin)), int(c(row, end))),
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70 type=c(row, type),
63f6b6ca0e97 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tbl2gff3 commit 725ff8b6a4f01bf532052ce46400f529551a317d"
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71 strand=_str,
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72 qualifiers=q,
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73 )
63f6b6ca0e97 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tbl2gff3 commit 725ff8b6a4f01bf532052ce46400f529551a317d"
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74 r.features.append(f)
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75
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76 return records
63f6b6ca0e97 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tbl2gff3 commit 725ff8b6a4f01bf532052ce46400f529551a317d"
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77
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78
63f6b6ca0e97 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tbl2gff3 commit 725ff8b6a4f01bf532052ce46400f529551a317d"
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79 if __name__ == "__main__":
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80 parser = argparse.ArgumentParser(description="Convert tables to gff3", epilog="")
63f6b6ca0e97 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tbl2gff3 commit 725ff8b6a4f01bf532052ce46400f529551a317d"
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81 parser.add_argument("table", type=argparse.FileType("r"), help="Tabular Input")
63f6b6ca0e97 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tbl2gff3 commit 725ff8b6a4f01bf532052ce46400f529551a317d"
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82 parser.add_argument("rid", help="id column")
63f6b6ca0e97 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tbl2gff3 commit 725ff8b6a4f01bf532052ce46400f529551a317d"
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83 parser.add_argument("begin", help="begin column")
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84 parser.add_argument("end", help="end column")
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85 parser.add_argument("--type", help="feature type column")
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86 parser.add_argument("--score", help="score column")
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87 parser.add_argument("--source", help="source column")
63f6b6ca0e97 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tbl2gff3 commit 725ff8b6a4f01bf532052ce46400f529551a317d"
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88 parser.add_argument("--strand_column", help="strand column")
63f6b6ca0e97 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tbl2gff3 commit 725ff8b6a4f01bf532052ce46400f529551a317d"
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89 parser.add_argument("--strand_value", help="strand value")
63f6b6ca0e97 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tbl2gff3 commit 725ff8b6a4f01bf532052ce46400f529551a317d"
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90 # parser.add_argument('--frame', help='frame column')
63f6b6ca0e97 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tbl2gff3 commit 725ff8b6a4f01bf532052ce46400f529551a317d"
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91 parser.add_argument("-a", action="append", help="attribute column (-a k:v)")
63f6b6ca0e97 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tbl2gff3 commit 725ff8b6a4f01bf532052ce46400f529551a317d"
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92 args = parser.parse_args()
63f6b6ca0e97 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tbl2gff3 commit 725ff8b6a4f01bf532052ce46400f529551a317d"
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93
63f6b6ca0e97 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tbl2gff3 commit 725ff8b6a4f01bf532052ce46400f529551a317d"
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94 for rid, rec in tbl2gff3(**vars(args)).items():
63f6b6ca0e97 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tbl2gff3 commit 725ff8b6a4f01bf532052ce46400f529551a317d"
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95 GFF.write([rec], sys.stdout)