Mercurial > repos > artbio > mircounts

annotate mature_mir_gff_translation.py @ 15:ffcd42f85b61 draft default tip

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planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mircounts commit 5eb8570dce4e22fb2759cc16c8e1ce9d304508fe
author artbio
date Sat, 10 Feb 2024 17:15:04 +0000
parents b045c30fb768
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
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9ea96a02c416 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mircounts commit 04980585c257ab5f8eb5d10de007316c47c5d1ce
artbio
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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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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(
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de227b7307cf planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mircounts commit af0f70b8156c078cc0d832c54ebb678af10c42a0
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8 '--gff_path', action="store", type=str,
de227b7307cf planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mircounts commit af0f70b8156c078cc0d832c54ebb678af10c42a0
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9 help="path to miRBase GFF3 file")
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10 the_parser.add_argument(
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11 '--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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12 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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13 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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14 return args
da29af78a960 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mircounts commit d4d8106d66b65679a1a685ab94bfcf99cdb7b959
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17 def convert_and_print_gff(gff_input_file, output):
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19 def get_gff_header(gff_input_file):
2a08a6eb471c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mircounts commit 6013aaf29ff7aa2d1aab434f2355da327c7ef102
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20 string_list = []
2a08a6eb471c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mircounts commit 6013aaf29ff7aa2d1aab434f2355da327c7ef102
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21 for line in open(gff_input_file, "r"):
2a08a6eb471c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mircounts commit 6013aaf29ff7aa2d1aab434f2355da327c7ef102
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22 if line[0] == '#':
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23 string_list.append(line)
2a08a6eb471c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mircounts commit 6013aaf29ff7aa2d1aab434f2355da327c7ef102
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24 string_list.append('# generated by mature_mir_gff_translation.py \
2a08a6eb471c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mircounts commit 6013aaf29ff7aa2d1aab434f2355da327c7ef102
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25 %s\n#\n' % str(datetime.now()))
2a08a6eb471c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mircounts commit 6013aaf29ff7aa2d1aab434f2355da327c7ef102
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26 return ''.join(string_list)
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27
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28 gff_dict = {}
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2a08a6eb471c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mircounts commit 6013aaf29ff7aa2d1aab434f2355da327c7ef102
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29 # see https://github.com/ARTbio/tools-artbio/issues/246
2a08a6eb471c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mircounts commit 6013aaf29ff7aa2d1aab434f2355da327c7ef102
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30 # currently fixed by perl pretreatment or the gff3 file
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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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31 for line in open(gff_input_file, "r"):
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32 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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33 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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34 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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35 ID = gff_fields[8].split("ID=")[1].split(";")[0]
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36 if gff_fields[2] == "miRNA_primary_transcript":
2a08a6eb471c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mircounts commit 6013aaf29ff7aa2d1aab434f2355da327c7ef102
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37 gff_dict[ID] = {}
2a08a6eb471c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mircounts commit 6013aaf29ff7aa2d1aab434f2355da327c7ef102
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38 gff_dict[ID]["premir_name"] = gff_fields[8].split(
2a08a6eb471c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mircounts commit 6013aaf29ff7aa2d1aab434f2355da327c7ef102
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39 "Name=")[1].split(";")[0]
2a08a6eb471c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mircounts commit 6013aaf29ff7aa2d1aab434f2355da327c7ef102
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40 gff_dict[ID]["primary"] = line[:-1]
2a08a6eb471c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mircounts commit 6013aaf29ff7aa2d1aab434f2355da327c7ef102
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41 gff_dict[ID]["miRNAs"] = []
2a08a6eb471c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mircounts commit 6013aaf29ff7aa2d1aab434f2355da327c7ef102
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42 elif gff_fields[2] == "miRNA":
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43 if "_" in ID:
b045c30fb768 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mircounts commit af48e9f6df2717ffd3731a974be1ec36e4eff779"
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44 continue
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2a08a6eb471c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mircounts commit 6013aaf29ff7aa2d1aab434f2355da327c7ef102
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45 parent_ID = gff_fields[8].split("erives_from=")[1]
2a08a6eb471c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mircounts commit 6013aaf29ff7aa2d1aab434f2355da327c7ef102
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46 gff_dict[parent_ID]["miRNAs"].append(line[:-1])
2a08a6eb471c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mircounts commit 6013aaf29ff7aa2d1aab434f2355da327c7ef102
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47 # Now reorganise features and recalculate coordinates of premirs and mirs
2a08a6eb471c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mircounts commit 6013aaf29ff7aa2d1aab434f2355da327c7ef102
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48 gff_list = []
2a08a6eb471c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mircounts commit 6013aaf29ff7aa2d1aab434f2355da327c7ef102
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49 for ID in sorted(gff_dict, key=lambda x: (gff_dict[x]['premir_name'])):
2a08a6eb471c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mircounts commit 6013aaf29ff7aa2d1aab434f2355da327c7ef102
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50 # delete premir and their mir with ID containing "_"
2a08a6eb471c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mircounts commit 6013aaf29ff7aa2d1aab434f2355da327c7ef102
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51 if "_" in ID:
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52 del gff_dict[ID]
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53 else:
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54 primary_fields = gff_dict[ID]["primary"].split('\t')
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55 seqid = primary_fields[8].split("Name=")[1].split(";")[0]
2a08a6eb471c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mircounts commit 6013aaf29ff7aa2d1aab434f2355da327c7ef102
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56 source = primary_fields[1]
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57 type = primary_fields[2]
2a08a6eb471c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mircounts commit 6013aaf29ff7aa2d1aab434f2355da327c7ef102
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58 start = primary_fields[3]
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59 newstart = "1"
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60 end = primary_fields[4]
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61 newend = str(int(end)-int(start)+1)
2a08a6eb471c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mircounts commit 6013aaf29ff7aa2d1aab434f2355da327c7ef102
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62 score = primary_fields[5]
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63 strand = primary_fields[6]
2a08a6eb471c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mircounts commit 6013aaf29ff7aa2d1aab434f2355da327c7ef102
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64 phase = primary_fields[7]
2a08a6eb471c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mircounts commit 6013aaf29ff7aa2d1aab434f2355da327c7ef102
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65 attributes = primary_fields[8]
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66 gff_list.append('%s\t%s\t%s\t%s\t%s\t%s\t%s\t%s\t%s' % (seqid,
2a08a6eb471c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mircounts commit 6013aaf29ff7aa2d1aab434f2355da327c7ef102
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67 source, type, newstart, newend, score, strand,
2a08a6eb471c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mircounts commit 6013aaf29ff7aa2d1aab434f2355da327c7ef102
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68 phase, attributes))
2a08a6eb471c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mircounts commit 6013aaf29ff7aa2d1aab434f2355da327c7ef102
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69 # ensure their is only 2 child miRNAs at best
2a08a6eb471c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mircounts commit 6013aaf29ff7aa2d1aab434f2355da327c7ef102
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70 if len(gff_dict[ID]["miRNAs"]) > 2:
2a08a6eb471c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mircounts commit 6013aaf29ff7aa2d1aab434f2355da327c7ef102
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71 gff_dict[ID]["miRNAs"] = gff_dict[ID]["miRNAs"][:2]
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72 # sort child miRNAs 5p first 3p second,
b045c30fb768 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mircounts commit af48e9f6df2717ffd3731a974be1ec36e4eff779"
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73 # if there are two miR mature at least !
b045c30fb768 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mircounts commit af48e9f6df2717ffd3731a974be1ec36e4eff779"
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74 if len(gff_dict[ID]["miRNAs"]) > 1 and \
b045c30fb768 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mircounts commit af48e9f6df2717ffd3731a974be1ec36e4eff779"
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75 gff_dict[ID]["miRNAs"][0].find('5p') == -1:
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2a08a6eb471c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mircounts commit 6013aaf29ff7aa2d1aab434f2355da327c7ef102
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76 gff_dict[ID]["miRNAs"] = gff_dict[ID]["miRNAs"][::-1]
2a08a6eb471c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mircounts commit 6013aaf29ff7aa2d1aab434f2355da327c7ef102
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77 for mir in gff_dict[ID]["miRNAs"]:
2a08a6eb471c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mircounts commit 6013aaf29ff7aa2d1aab434f2355da327c7ef102
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78 mir_fields = mir.split('\t')
2a08a6eb471c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mircounts commit 6013aaf29ff7aa2d1aab434f2355da327c7ef102
artbio
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79 mir_seqid = mir_fields[8].split("Name=")[1].split(";")[0]
2a08a6eb471c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mircounts commit 6013aaf29ff7aa2d1aab434f2355da327c7ef102
artbio
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80 mir_source = mir_fields[1]
2a08a6eb471c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mircounts commit 6013aaf29ff7aa2d1aab434f2355da327c7ef102
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81 mir_type = mir_fields[2]
2a08a6eb471c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mircounts commit 6013aaf29ff7aa2d1aab434f2355da327c7ef102
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82 mir_start = mir_fields[3]
2a08a6eb471c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mircounts commit 6013aaf29ff7aa2d1aab434f2355da327c7ef102
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83 mir_end = mir_fields[4]
2a08a6eb471c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mircounts commit 6013aaf29ff7aa2d1aab434f2355da327c7ef102
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84 new_mir_start = str(int(mir_start)-int(start)+1)
2a08a6eb471c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mircounts commit 6013aaf29ff7aa2d1aab434f2355da327c7ef102
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85 new_mir_end = str(int(mir_end)-int(start)+1)
2a08a6eb471c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mircounts commit 6013aaf29ff7aa2d1aab434f2355da327c7ef102
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86 mir_score = mir_fields[5]
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87 mir_strand = mir_fields[6]
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88 mir_phase = mir_fields[7]
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89 mir_attributes = mir_fields[8]
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90 mir_sfx = ";Parent_mir_Name=%s" % gff_dict[ID]["premir_name"]
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91 gff_list.append(
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92 '%s\t%s\t%s\t%s\t%s\t%s\t%s\t%s\t%s%s' % (
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93 mir_seqid, mir_source, mir_type,
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94 new_mir_start, new_mir_end, mir_score,
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95 mir_strand, mir_phase, mir_attributes,
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96 mir_sfx))
0
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97 with open(output, "w") as output:
9
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98 output.write('%s' % get_gff_header(gff_input_file))
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99 output.write('\n'.join(gff_list))
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100 output.write('\n')
0
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101
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102
10
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103 def main(gff_path, outfile):
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104 convert_and_print_gff(gff_path, outfile)
0
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105
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106
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107 if __name__ == "__main__":
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108 args = Parser()
10
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109 main(args.gff_path, args.output)