Mercurial > repos > iuc > tbl2gff3

annotate tbl2gff3.py @ 1:d9eb9f753fa6 draft default tip

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tbl2gff3 commit db75a8489a1f61ea30abe9b91f6febac8b34204f"
author iuc
date Thu, 03 Dec 2020 16:59:00 +0000
parents 63f6b6ca0e97
children
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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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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
1
d9eb9f753fa6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tbl2gff3 commit db75a8489a1f61ea30abe9b91f6febac8b34204f"
iuc
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3 import collections
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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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4 import csv
63f6b6ca0e97 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tbl2gff3 commit 725ff8b6a4f01bf532052ce46400f529551a317d"
iuc
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5 import sys
63f6b6ca0e97 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tbl2gff3 commit 725ff8b6a4f01bf532052ce46400f529551a317d"
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6
63f6b6ca0e97 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tbl2gff3 commit 725ff8b6a4f01bf532052ce46400f529551a317d"
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7 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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8 from Bio.Seq import Seq
63f6b6ca0e97 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tbl2gff3 commit 725ff8b6a4f01bf532052ce46400f529551a317d"
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9 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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10 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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11
63f6b6ca0e97 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tbl2gff3 commit 725ff8b6a4f01bf532052ce46400f529551a317d"
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12
63f6b6ca0e97 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tbl2gff3 commit 725ff8b6a4f01bf532052ce46400f529551a317d"
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13 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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14 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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15 return default
63f6b6ca0e97 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tbl2gff3 commit 725ff8b6a4f01bf532052ce46400f529551a317d"
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16
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17 try:
63f6b6ca0e97 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tbl2gff3 commit 725ff8b6a4f01bf532052ce46400f529551a317d"
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18 _ = int(v)
63f6b6ca0e97 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tbl2gff3 commit 725ff8b6a4f01bf532052ce46400f529551a317d"
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19 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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20 except ValueError:
63f6b6ca0e97 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tbl2gff3 commit 725ff8b6a4f01bf532052ce46400f529551a317d"
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21 return v
63f6b6ca0e97 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tbl2gff3 commit 725ff8b6a4f01bf532052ce46400f529551a317d"
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22
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24 def tbl2gff3(
63f6b6ca0e97 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tbl2gff3 commit 725ff8b6a4f01bf532052ce46400f529551a317d"
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25 table,
63f6b6ca0e97 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tbl2gff3 commit 725ff8b6a4f01bf532052ce46400f529551a317d"
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26 rid,
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27 begin,
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28 end,
63f6b6ca0e97 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tbl2gff3 commit 725ff8b6a4f01bf532052ce46400f529551a317d"
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29 source=None,
63f6b6ca0e97 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tbl2gff3 commit 725ff8b6a4f01bf532052ce46400f529551a317d"
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30 type=None,
63f6b6ca0e97 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tbl2gff3 commit 725ff8b6a4f01bf532052ce46400f529551a317d"
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31 score=None,
63f6b6ca0e97 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tbl2gff3 commit 725ff8b6a4f01bf532052ce46400f529551a317d"
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32 frame=None,
63f6b6ca0e97 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tbl2gff3 commit 725ff8b6a4f01bf532052ce46400f529551a317d"
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33 a=None,
63f6b6ca0e97 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tbl2gff3 commit 725ff8b6a4f01bf532052ce46400f529551a317d"
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34 strand_column=None,
63f6b6ca0e97 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tbl2gff3 commit 725ff8b6a4f01bf532052ce46400f529551a317d"
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35 strand_value=None,
1
d9eb9f753fa6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tbl2gff3 commit db75a8489a1f61ea30abe9b91f6febac8b34204f"
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36 strand_infer=False,
0
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37 ):
63f6b6ca0e97 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tbl2gff3 commit 725ff8b6a4f01bf532052ce46400f529551a317d"
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38
1
d9eb9f753fa6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tbl2gff3 commit db75a8489a1f61ea30abe9b91f6febac8b34204f"
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39 records = collections.OrderedDict()
0
63f6b6ca0e97 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tbl2gff3 commit 725ff8b6a4f01bf532052ce46400f529551a317d"
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40
63f6b6ca0e97 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tbl2gff3 commit 725ff8b6a4f01bf532052ce46400f529551a317d"
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41 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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42 # print(', '.join(row))
63f6b6ca0e97 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tbl2gff3 commit 725ff8b6a4f01bf532052ce46400f529551a317d"
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43
63f6b6ca0e97 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tbl2gff3 commit 725ff8b6a4f01bf532052ce46400f529551a317d"
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44 # 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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45 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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46 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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47 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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48
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49 r = records[recid]
63f6b6ca0e97 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tbl2gff3 commit 725ff8b6a4f01bf532052ce46400f529551a317d"
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50 q = {}
63f6b6ca0e97 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tbl2gff3 commit 725ff8b6a4f01bf532052ce46400f529551a317d"
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51 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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52 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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53
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54 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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55
1
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56 begin_i = int(c(row, begin))
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57 end_i = int(c(row, end))
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58
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59 begin_f = min(begin_i, end_i)
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60 end_f = max(begin_i, end_i)
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61
0
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62 _str = None
63f6b6ca0e97 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tbl2gff3 commit 725ff8b6a4f01bf532052ce46400f529551a317d"
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63 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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64 _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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65 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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66 _str = int(strand_value)
1
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67 if strand_infer:
d9eb9f753fa6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tbl2gff3 commit db75a8489a1f61ea30abe9b91f6febac8b34204f"
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68 if begin_i > begin_f:
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69 _str = -1
d9eb9f753fa6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tbl2gff3 commit db75a8489a1f61ea30abe9b91f6febac8b34204f"
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70 else:
d9eb9f753fa6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tbl2gff3 commit db75a8489a1f61ea30abe9b91f6febac8b34204f"
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71 _str = 1
0
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72
1
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73 if a is not None:
d9eb9f753fa6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tbl2gff3 commit db75a8489a1f61ea30abe9b91f6febac8b34204f"
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74 for x in a:
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75 k, v = x.split(":", 1)
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76 _v = c(row, v)
d9eb9f753fa6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tbl2gff3 commit db75a8489a1f61ea30abe9b91f6febac8b34204f"
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77 if k in q:
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78 q[k].append(_v)
d9eb9f753fa6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tbl2gff3 commit db75a8489a1f61ea30abe9b91f6febac8b34204f"
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79 else:
d9eb9f753fa6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tbl2gff3 commit db75a8489a1f61ea30abe9b91f6febac8b34204f"
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80 q[k] = [_v]
0
63f6b6ca0e97 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tbl2gff3 commit 725ff8b6a4f01bf532052ce46400f529551a317d"
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81
63f6b6ca0e97 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tbl2gff3 commit 725ff8b6a4f01bf532052ce46400f529551a317d"
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82 f = SeqFeature(
1
d9eb9f753fa6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tbl2gff3 commit db75a8489a1f61ea30abe9b91f6febac8b34204f"
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83 FeatureLocation(begin_f, end_f),
0
63f6b6ca0e97 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tbl2gff3 commit 725ff8b6a4f01bf532052ce46400f529551a317d"
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84 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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85 strand=_str,
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86 qualifiers=q,
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87 )
63f6b6ca0e97 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tbl2gff3 commit 725ff8b6a4f01bf532052ce46400f529551a317d"
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88 r.features.append(f)
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89
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90 return records
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91
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92
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93 if __name__ == "__main__":
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94 parser = argparse.ArgumentParser(description="Convert tables to gff3", epilog="")
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95 parser.add_argument("table", type=argparse.FileType("r"), help="Tabular Input")
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96 parser.add_argument("rid", help="id column")
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97 parser.add_argument("begin", help="begin column")
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98 parser.add_argument("end", help="end column")
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99 parser.add_argument("--type", help="feature type column")
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100 parser.add_argument("--score", help="score column")
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101 parser.add_argument("--source", help="source column")
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102 parser.add_argument("--strand_infer", action='store_true', help="infer strand")
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103 parser.add_argument("--strand_column", help="strand column")
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104 parser.add_argument("--strand_value", help="strand value")
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105 # parser.add_argument('--frame', help='frame column')
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106 parser.add_argument("-a", action="append", help="attribute column (-a k:v)")
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107 args = parser.parse_args()
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108
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109 for rid, rec in tbl2gff3(**vars(args)).items():
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110 GFF.write([rec], sys.stdout)