Mercurial > repos > artbio > mircounts
diff mature_mir_gff_translation.py @ 13:b045c30fb768 draft
"planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mircounts commit af48e9f6df2717ffd3731a974be1ec36e4eff779"
| author | artbio |
|---|---|
| date | Fri, 18 Oct 2019 19:18:50 -0400 |
| parents | de227b7307cf |
| children |
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--- a/mature_mir_gff_translation.py Sat May 12 09:06:24 2018 -0400 +++ b/mature_mir_gff_translation.py Fri Oct 18 19:18:50 2019 -0400 @@ -10,9 +10,6 @@ the_parser.add_argument( '--output', action="store", type=str, help="output GFF3 file with converted mature mir coordinates") - the_parser.add_argument( - '--basename', action="store", type=str, - help="basename of the parsed gff file returned") args = the_parser.parse_args() return args @@ -43,6 +40,8 @@ gff_dict[ID]["primary"] = line[:-1] gff_dict[ID]["miRNAs"] = [] elif gff_fields[2] == "miRNA": + if "_" in ID: + continue parent_ID = gff_fields[8].split("erives_from=")[1] gff_dict[parent_ID]["miRNAs"].append(line[:-1]) # Now reorganise features and recalculate coordinates of premirs and mirs @@ -70,8 +69,10 @@ # ensure their is only 2 child miRNAs at best if len(gff_dict[ID]["miRNAs"]) > 2: gff_dict[ID]["miRNAs"] = gff_dict[ID]["miRNAs"][:2] - # sort child miRNAs 5p first 3p second - if gff_dict[ID]["miRNAs"][0].find('5p') == -1: + # sort child miRNAs 5p first 3p second, + # if there are two miR mature at least ! + if len(gff_dict[ID]["miRNAs"]) > 1 and \ + gff_dict[ID]["miRNAs"][0].find('5p') == -1: gff_dict[ID]["miRNAs"] = gff_dict[ID]["miRNAs"][::-1] for mir in gff_dict[ID]["miRNAs"]: mir_fields = mir.split('\t')