Mercurial > repos > artbio > mircounts

annotate mature_mir_gff_translation.py @ 8:3f62272192f9 draft

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planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mircounts commit 0eaefbad21786cabed6791a6d06e9a0de8af10b0
author artbio
date Mon, 23 Apr 2018 13:21:16 -0400
parents 9ea96a02c416
children 2a08a6eb471c
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9ea96a02c416 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mircounts commit 04980585c257ab5f8eb5d10de007316c47c5d1ce
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diff changeset
1 import argparse
9ea96a02c416 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mircounts commit 04980585c257ab5f8eb5d10de007316c47c5d1ce
artbio
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2 from datetime import datetime
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da29af78a960 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mircounts commit d4d8106d66b65679a1a685ab94bfcf99cdb7b959
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5 def Parser():
da29af78a960 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mircounts commit d4d8106d66b65679a1a685ab94bfcf99cdb7b959
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6 the_parser = argparse.ArgumentParser()
da29af78a960 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mircounts commit d4d8106d66b65679a1a685ab94bfcf99cdb7b959
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7 the_parser.add_argument(
da29af78a960 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mircounts commit d4d8106d66b65679a1a685ab94bfcf99cdb7b959
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8 '--input', action="store", type=str, help="input miRBase GFF3 file")
da29af78a960 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mircounts commit d4d8106d66b65679a1a685ab94bfcf99cdb7b959
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9 the_parser.add_argument(
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10 '--output', action="store", type=str,
6b8adacd4750 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mircounts commit fa65a844f9041a83767f5305ab360abfdf68f59f
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11 help="output GFF3 file with converted mature mir coordinates")
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da29af78a960 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mircounts commit d4d8106d66b65679a1a685ab94bfcf99cdb7b959
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12 args = the_parser.parse_args()
da29af78a960 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mircounts commit d4d8106d66b65679a1a685ab94bfcf99cdb7b959
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13 return args
da29af78a960 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mircounts commit d4d8106d66b65679a1a685ab94bfcf99cdb7b959
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9ea96a02c416 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mircounts commit 04980585c257ab5f8eb5d10de007316c47c5d1ce
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16 def get_gff_header(gff_input_file):
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17 string_list = []
9ea96a02c416 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mircounts commit 04980585c257ab5f8eb5d10de007316c47c5d1ce
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18 for line in open(gff_input_file, "r"):
9ea96a02c416 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mircounts commit 04980585c257ab5f8eb5d10de007316c47c5d1ce
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19 if line[0] == '#':
9ea96a02c416 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mircounts commit 04980585c257ab5f8eb5d10de007316c47c5d1ce
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20 string_list.append(line)
9ea96a02c416 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mircounts commit 04980585c257ab5f8eb5d10de007316c47c5d1ce
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21 string_list.append('# generated by mature_mir_gff_translation.py %s\n#\n' %
9ea96a02c416 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mircounts commit 04980585c257ab5f8eb5d10de007316c47c5d1ce
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22 str(datetime.now()))
9ea96a02c416 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mircounts commit 04980585c257ab5f8eb5d10de007316c47c5d1ce
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23 return ''.join(string_list)
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da29af78a960 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mircounts commit d4d8106d66b65679a1a685ab94bfcf99cdb7b959
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26 def load_gff_in_dict(gff_input_file):
da29af78a960 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mircounts commit d4d8106d66b65679a1a685ab94bfcf99cdb7b959
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27 '''
da29af78a960 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mircounts commit d4d8106d66b65679a1a685ab94bfcf99cdb7b959
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28 Reads the gff3 file and return a dictionary of dictionaries
da29af78a960 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mircounts commit d4d8106d66b65679a1a685ab94bfcf99cdb7b959
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29 with keys equal to standard gff3 fields (9)
da29af78a960 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mircounts commit d4d8106d66b65679a1a685ab94bfcf99cdb7b959
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30 Note that the key of the primary dictionary is the ID
da29af78a960 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mircounts commit d4d8106d66b65679a1a685ab94bfcf99cdb7b959
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31 '''
da29af78a960 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mircounts commit d4d8106d66b65679a1a685ab94bfcf99cdb7b959
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32 gff_dict = {}
da29af78a960 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mircounts commit d4d8106d66b65679a1a685ab94bfcf99cdb7b959
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33 for line in open(gff_input_file, "r"):
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34 if line[0] == "#":
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da29af78a960 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mircounts commit d4d8106d66b65679a1a685ab94bfcf99cdb7b959
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35 continue
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6b8adacd4750 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mircounts commit fa65a844f9041a83767f5305ab360abfdf68f59f
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36 gff_fields = line[:-1].split("\t")
6b8adacd4750 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mircounts commit fa65a844f9041a83767f5305ab360abfdf68f59f
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37 ID = gff_fields[8].split("ID=")[1].split(";")[0]
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da29af78a960 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mircounts commit d4d8106d66b65679a1a685ab94bfcf99cdb7b959
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38 gff_dict[ID] = {}
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39 gff_dict[ID]["seqid"] = gff_fields[0]
6b8adacd4750 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mircounts commit fa65a844f9041a83767f5305ab360abfdf68f59f
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40 gff_dict[ID]["source"] = gff_fields[1]
6b8adacd4750 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mircounts commit fa65a844f9041a83767f5305ab360abfdf68f59f
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41 gff_dict[ID]["type"] = gff_fields[2]
6b8adacd4750 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mircounts commit fa65a844f9041a83767f5305ab360abfdf68f59f
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42 gff_dict[ID]["start"] = gff_fields[3]
6b8adacd4750 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mircounts commit fa65a844f9041a83767f5305ab360abfdf68f59f
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43 gff_dict[ID]["end"] = gff_fields[4]
6b8adacd4750 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mircounts commit fa65a844f9041a83767f5305ab360abfdf68f59f
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44 gff_dict[ID]["score"] = gff_fields[5]
6b8adacd4750 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mircounts commit fa65a844f9041a83767f5305ab360abfdf68f59f
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45 gff_dict[ID]["strand"] = gff_fields[6]
6b8adacd4750 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mircounts commit fa65a844f9041a83767f5305ab360abfdf68f59f
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46 gff_dict[ID]["phase"] = gff_fields[7]
6b8adacd4750 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mircounts commit fa65a844f9041a83767f5305ab360abfdf68f59f
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47 gff_dict[ID]["attributes"] = gff_fields[8]
5
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48 if "erives_from" in gff_dict[ID]["attributes"]:
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6b8adacd4750 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mircounts commit fa65a844f9041a83767f5305ab360abfdf68f59f
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49 parent_primary_transcript = gff_dict[ID]["attributes"].split(
5
9ea96a02c416 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mircounts commit 04980585c257ab5f8eb5d10de007316c47c5d1ce
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50 "erives_from=")[1]
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51 parent_primary_transcript = gff_dict[parent_primary_transcript][
6b8adacd4750 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mircounts commit fa65a844f9041a83767f5305ab360abfdf68f59f
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52 "attributes"].split("Name=")[1]
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53 gff_dict[ID]["attributes"] = "%s;Parent_mir_Name=%s" % (
6b8adacd4750 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mircounts commit fa65a844f9041a83767f5305ab360abfdf68f59f
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54 gff_dict[ID]["attributes"], parent_primary_transcript)
0
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55 return gff_dict
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56
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57
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9ea96a02c416 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mircounts commit 04980585c257ab5f8eb5d10de007316c47c5d1ce
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58 def genome_to_mir_gff(gff_dict, output, header):
0
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59 '''
da29af78a960 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mircounts commit d4d8106d66b65679a1a685ab94bfcf99cdb7b959
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60 Converts seqid field from chromosome to item Name
da29af78a960 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mircounts commit d4d8106d66b65679a1a685ab94bfcf99cdb7b959
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61 Then converts coordinates relative to "miRNA_primary_transcript"
da29af78a960 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mircounts commit d4d8106d66b65679a1a685ab94bfcf99cdb7b959
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62 Note that GFF files are 1-based coordinates
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63 '''
da29af78a960 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mircounts commit d4d8106d66b65679a1a685ab94bfcf99cdb7b959
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64 for key in gff_dict:
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65 name = gff_dict[key]["attributes"].split("Name=")[1].split(";")[0]
6b8adacd4750 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mircounts commit fa65a844f9041a83767f5305ab360abfdf68f59f
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66 gff_dict[key]["seqid"] = name
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67 if "erives_from=" in gff_dict[key]["attributes"]:
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6b8adacd4750 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mircounts commit fa65a844f9041a83767f5305ab360abfdf68f59f
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68 parent_ID = gff_dict[key]["attributes"].split(
5
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69 "erives_from=")[1].split(";")[0]
3
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70 gff_dict[key]["start"] = str(int(gff_dict[key]["start"])-int(
6b8adacd4750 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mircounts commit fa65a844f9041a83767f5305ab360abfdf68f59f
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71 gff_dict[parent_ID]["start"])+1)
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72 gff_dict[key]["end"] = str(int(gff_dict[key]["end"])-int(
6b8adacd4750 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mircounts commit fa65a844f9041a83767f5305ab360abfdf68f59f
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73 gff_dict[parent_ID]["start"])+1)
6b8adacd4750 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mircounts commit fa65a844f9041a83767f5305ab360abfdf68f59f
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74 hairpins = {}
6b8adacd4750 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mircounts commit fa65a844f9041a83767f5305ab360abfdf68f59f
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75 matures = {}
6b8adacd4750 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mircounts commit fa65a844f9041a83767f5305ab360abfdf68f59f
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76 # treats miRNA_primary_transcript coordinates
6b8adacd4750 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mircounts commit fa65a844f9041a83767f5305ab360abfdf68f59f
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77 # in a second loop to avoid errors in conversion
6b8adacd4750 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mircounts commit fa65a844f9041a83767f5305ab360abfdf68f59f
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78 for key in gff_dict:
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79 if gff_dict[key]["type"] == "miRNA_primary_transcript":
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80 gff_dict[key]["end"] = str(int(gff_dict[key]["end"])-int(
6b8adacd4750 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mircounts commit fa65a844f9041a83767f5305ab360abfdf68f59f
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81 gff_dict[key]["start"]) + 1)
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82 gff_dict[key]["start"] = '1'
0
da29af78a960 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mircounts commit d4d8106d66b65679a1a685ab94bfcf99cdb7b959
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83 # now, do a dict[ID]=Name but only for miRNA_primary_transcript
3
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84 hairpins[key] = gff_dict[key]["attributes"].split(
6b8adacd4750 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mircounts commit fa65a844f9041a83767f5305ab360abfdf68f59f
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85 "Name=")[1].split(
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86 ";")[0]
0
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87 else:
3
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88 matures[key] = gff_dict[key]["attributes"].split(
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89 "Name=")[1].split(
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90 ";")[0]
0
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91 with open(output, "w") as output:
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92 output.write(header)
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93 for ID in sorted(hairpins, key=hairpins.get):
3
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94 output.write("\t".join([gff_dict[ID]["seqid"],
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95 gff_dict[ID]["source"], gff_dict[ID]["type"],
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96 gff_dict[ID]["start"], gff_dict[ID]["end"],
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97 gff_dict[ID]["score"], gff_dict[ID]["strand"],
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98 gff_dict[ID]["phase"], gff_dict[ID]["attributes"]]))
0
da29af78a960 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mircounts commit d4d8106d66b65679a1a685ab94bfcf99cdb7b959
artbio
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99 output.write("\n")
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100 for id in sorted(matures, key=matures.get, reverse=True):
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101 if ID in gff_dict[id]["attributes"]:
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102 output.write("\t".join([gff_dict[id]["seqid"],
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103 gff_dict[id]["source"], gff_dict[id]["type"],
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104 gff_dict[id]["start"], gff_dict[id]["end"],
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105 gff_dict[id]["score"],
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106 gff_dict[id]["strand"],
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107 gff_dict[id]["phase"],
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108 gff_dict[id]["attributes"]]))
0
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109 output.write("\n")
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110
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111
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112 def main(infile, outfile):
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113 gff_dict = load_gff_in_dict(infile)
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114 genome_to_mir_gff(gff_dict, outfile, get_gff_header(infile))
0
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115
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116
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117 if __name__ == "__main__":
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118 args = Parser()
3
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119 main(args.input, args.output)