Mercurial > repos > artbio > mircounts
annotate mature_mir_gff_translation.py @ 15:ffcd42f85b61 draft default tip
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mircounts commit 5eb8570dce4e22fb2759cc16c8e1ce9d304508fe
author | artbio |
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date | Sat, 10 Feb 2024 17:15:04 +0000 |
parents | b045c30fb768 |
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rev | line source |
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5
9ea96a02c416
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mircounts commit 04980585c257ab5f8eb5d10de007316c47c5d1ce
artbio
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3
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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 |
0
da29af78a960
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mircounts commit d4d8106d66b65679a1a685ab94bfcf99cdb7b959
artbio
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changeset
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3 |
da29af78a960
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mircounts commit d4d8106d66b65679a1a685ab94bfcf99cdb7b959
artbio
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changeset
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4 |
da29af78a960
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mircounts commit d4d8106d66b65679a1a685ab94bfcf99cdb7b959
artbio
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changeset
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5 def Parser(): |
da29af78a960
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mircounts commit d4d8106d66b65679a1a685ab94bfcf99cdb7b959
artbio
parents:
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changeset
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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
artbio
parents:
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changeset
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7 the_parser.add_argument( |
10
de227b7307cf
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mircounts commit af0f70b8156c078cc0d832c54ebb678af10c42a0
artbio
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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
artbio
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9 help="path to miRBase GFF3 file") |
0
da29af78a960
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mircounts commit d4d8106d66b65679a1a685ab94bfcf99cdb7b959
artbio
parents:
diff
changeset
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10 the_parser.add_argument( |
3
6b8adacd4750
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mircounts commit fa65a844f9041a83767f5305ab360abfdf68f59f
artbio
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0
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changeset
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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
artbio
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0
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changeset
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12 help="output GFF3 file with converted mature mir coordinates") |
0
da29af78a960
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mircounts commit d4d8106d66b65679a1a685ab94bfcf99cdb7b959
artbio
parents:
diff
changeset
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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
artbio
parents:
diff
changeset
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14 return args |
da29af78a960
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mircounts commit d4d8106d66b65679a1a685ab94bfcf99cdb7b959
artbio
parents:
diff
changeset
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15 |
3
6b8adacd4750
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mircounts commit fa65a844f9041a83767f5305ab360abfdf68f59f
artbio
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16 |
9
2a08a6eb471c
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mircounts commit 6013aaf29ff7aa2d1aab434f2355da327c7ef102
artbio
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17 def convert_and_print_gff(gff_input_file, output): |
0
da29af78a960
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mircounts commit d4d8106d66b65679a1a685ab94bfcf99cdb7b959
artbio
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18 |
9
2a08a6eb471c
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mircounts commit 6013aaf29ff7aa2d1aab434f2355da327c7ef102
artbio
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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
artbio
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changeset
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20 string_list = [] |
2a08a6eb471c
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mircounts commit 6013aaf29ff7aa2d1aab434f2355da327c7ef102
artbio
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8
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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
artbio
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changeset
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22 if line[0] == '#': |
2a08a6eb471c
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mircounts commit 6013aaf29ff7aa2d1aab434f2355da327c7ef102
artbio
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changeset
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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
artbio
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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
artbio
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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
artbio
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26 return ''.join(string_list) |
3
6b8adacd4750
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mircounts commit fa65a844f9041a83767f5305ab360abfdf68f59f
artbio
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27 |
0
da29af78a960
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mircounts commit d4d8106d66b65679a1a685ab94bfcf99cdb7b959
artbio
parents:
diff
changeset
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28 gff_dict = {} |
9
2a08a6eb471c
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mircounts commit 6013aaf29ff7aa2d1aab434f2355da327c7ef102
artbio
parents:
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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
artbio
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30 # currently fixed by perl pretreatment or the gff3 file |
0
da29af78a960
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mircounts commit d4d8106d66b65679a1a685ab94bfcf99cdb7b959
artbio
parents:
diff
changeset
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31 for line in open(gff_input_file, "r"): |
3
6b8adacd4750
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mircounts commit fa65a844f9041a83767f5305ab360abfdf68f59f
artbio
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0
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changeset
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32 if line[0] == "#": |
0
da29af78a960
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mircounts commit d4d8106d66b65679a1a685ab94bfcf99cdb7b959
artbio
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changeset
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33 continue |
3
6b8adacd4750
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mircounts commit fa65a844f9041a83767f5305ab360abfdf68f59f
artbio
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changeset
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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
artbio
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35 ID = gff_fields[8].split("ID=")[1].split(";")[0] |
9
2a08a6eb471c
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mircounts commit 6013aaf29ff7aa2d1aab434f2355da327c7ef102
artbio
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changeset
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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
artbio
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8
diff
changeset
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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
artbio
parents:
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diff
changeset
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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
artbio
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changeset
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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
artbio
parents:
8
diff
changeset
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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
artbio
parents:
8
diff
changeset
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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
artbio
parents:
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diff
changeset
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42 elif gff_fields[2] == "miRNA": |
13
b045c30fb768
"planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mircounts commit af48e9f6df2717ffd3731a974be1ec36e4eff779"
artbio
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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"
artbio
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10
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44 continue |
9
2a08a6eb471c
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mircounts commit 6013aaf29ff7aa2d1aab434f2355da327c7ef102
artbio
parents:
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changeset
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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
artbio
parents:
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diff
changeset
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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
artbio
parents:
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diff
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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
artbio
parents:
8
diff
changeset
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48 gff_list = [] |
2a08a6eb471c
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mircounts commit 6013aaf29ff7aa2d1aab434f2355da327c7ef102
artbio
parents:
8
diff
changeset
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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
artbio
parents:
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diff
changeset
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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
artbio
parents:
8
diff
changeset
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51 if "_" in ID: |
2a08a6eb471c
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mircounts commit 6013aaf29ff7aa2d1aab434f2355da327c7ef102
artbio
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52 del gff_dict[ID] |
0
da29af78a960
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mircounts commit d4d8106d66b65679a1a685ab94bfcf99cdb7b959
artbio
parents:
diff
changeset
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53 else: |
9
2a08a6eb471c
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mircounts commit 6013aaf29ff7aa2d1aab434f2355da327c7ef102
artbio
parents:
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diff
changeset
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54 primary_fields = gff_dict[ID]["primary"].split('\t') |
2a08a6eb471c
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mircounts commit 6013aaf29ff7aa2d1aab434f2355da327c7ef102
artbio
parents:
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diff
changeset
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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
artbio
parents:
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diff
changeset
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56 source = primary_fields[1] |
2a08a6eb471c
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mircounts commit 6013aaf29ff7aa2d1aab434f2355da327c7ef102
artbio
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diff
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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
artbio
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diff
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58 start = primary_fields[3] |
2a08a6eb471c
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mircounts commit 6013aaf29ff7aa2d1aab434f2355da327c7ef102
artbio
parents:
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diff
changeset
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59 newstart = "1" |
2a08a6eb471c
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mircounts commit 6013aaf29ff7aa2d1aab434f2355da327c7ef102
artbio
parents:
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diff
changeset
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60 end = primary_fields[4] |
2a08a6eb471c
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mircounts commit 6013aaf29ff7aa2d1aab434f2355da327c7ef102
artbio
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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
artbio
parents:
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62 score = primary_fields[5] |
2a08a6eb471c
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mircounts commit 6013aaf29ff7aa2d1aab434f2355da327c7ef102
artbio
parents:
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diff
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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
artbio
parents:
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diff
changeset
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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
artbio
parents:
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diff
changeset
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65 attributes = primary_fields[8] |
2a08a6eb471c
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mircounts commit 6013aaf29ff7aa2d1aab434f2355da327c7ef102
artbio
parents:
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diff
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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
artbio
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diff
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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
artbio
parents:
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diff
changeset
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68 phase, attributes)) |
2a08a6eb471c
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mircounts commit 6013aaf29ff7aa2d1aab434f2355da327c7ef102
artbio
parents:
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diff
changeset
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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
artbio
parents:
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diff
changeset
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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
artbio
parents:
8
diff
changeset
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71 gff_dict[ID]["miRNAs"] = gff_dict[ID]["miRNAs"][:2] |
13
b045c30fb768
"planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mircounts commit af48e9f6df2717ffd3731a974be1ec36e4eff779"
artbio
parents:
10
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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"
artbio
parents:
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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"
artbio
parents:
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diff
changeset
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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"
artbio
parents:
10
diff
changeset
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75 gff_dict[ID]["miRNAs"][0].find('5p') == -1: |
9
2a08a6eb471c
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mircounts commit 6013aaf29ff7aa2d1aab434f2355da327c7ef102
artbio
parents:
8
diff
changeset
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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
artbio
parents:
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diff
changeset
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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
artbio
parents:
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diff
changeset
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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
parents:
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diff
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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
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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] |
2a08a6eb471c
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mircounts commit 6013aaf29ff7aa2d1aab434f2355da327c7ef102
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87 mir_strand = mir_fields[6] |
2a08a6eb471c
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mircounts commit 6013aaf29ff7aa2d1aab434f2355da327c7ef102
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88 mir_phase = mir_fields[7] |
2a08a6eb471c
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mircounts commit 6013aaf29ff7aa2d1aab434f2355da327c7ef102
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89 mir_attributes = mir_fields[8] |
2a08a6eb471c
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mircounts commit 6013aaf29ff7aa2d1aab434f2355da327c7ef102
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90 mir_sfx = ";Parent_mir_Name=%s" % gff_dict[ID]["premir_name"] |
2a08a6eb471c
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mircounts commit 6013aaf29ff7aa2d1aab434f2355da327c7ef102
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91 gff_list.append( |
2a08a6eb471c
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mircounts commit 6013aaf29ff7aa2d1aab434f2355da327c7ef102
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92 '%s\t%s\t%s\t%s\t%s\t%s\t%s\t%s\t%s%s' % ( |
2a08a6eb471c
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mircounts commit 6013aaf29ff7aa2d1aab434f2355da327c7ef102
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93 mir_seqid, mir_source, mir_type, |
2a08a6eb471c
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mircounts commit 6013aaf29ff7aa2d1aab434f2355da327c7ef102
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94 new_mir_start, new_mir_end, mir_score, |
2a08a6eb471c
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mircounts commit 6013aaf29ff7aa2d1aab434f2355da327c7ef102
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95 mir_strand, mir_phase, mir_attributes, |
2a08a6eb471c
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mircounts commit 6013aaf29ff7aa2d1aab434f2355da327c7ef102
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96 mir_sfx)) |
0
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planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mircounts commit d4d8106d66b65679a1a685ab94bfcf99cdb7b959
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97 with open(output, "w") as output: |
9
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planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mircounts commit 6013aaf29ff7aa2d1aab434f2355da327c7ef102
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98 output.write('%s' % 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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99 output.write('\n'.join(gff_list)) |
2a08a6eb471c
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mircounts commit 6013aaf29ff7aa2d1aab434f2355da327c7ef102
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100 output.write('\n') |
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planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mircounts commit d4d8106d66b65679a1a685ab94bfcf99cdb7b959
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101 |
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planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mircounts commit d4d8106d66b65679a1a685ab94bfcf99cdb7b959
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102 |
10
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planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mircounts commit af0f70b8156c078cc0d832c54ebb678af10c42a0
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103 def main(gff_path, outfile): |
de227b7307cf
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mircounts commit af0f70b8156c078cc0d832c54ebb678af10c42a0
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104 convert_and_print_gff(gff_path, outfile) |
0
da29af78a960
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mircounts commit d4d8106d66b65679a1a685ab94bfcf99cdb7b959
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105 |
da29af78a960
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mircounts commit d4d8106d66b65679a1a685ab94bfcf99cdb7b959
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106 |
da29af78a960
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mircounts commit d4d8106d66b65679a1a685ab94bfcf99cdb7b959
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107 if __name__ == "__main__": |
da29af78a960
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mircounts commit d4d8106d66b65679a1a685ab94bfcf99cdb7b959
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108 args = Parser() |
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planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mircounts commit af0f70b8156c078cc0d832c54ebb678af10c42a0
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109 main(args.gff_path, args.output) |