Mercurial > repos > artbio > blastparser_and_hits
comparison BlastParser_and_hits.py @ 5:5b7aa9f6fd59 draft default tip
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/blastparser_and_hits commit 51a6a16f2b26ed1a44243a17fcd32e302e69cb62
| author | artbio |
|---|---|
| date | Thu, 22 Dec 2022 12:27:22 +0000 |
| parents | b4c9c085d709 |
| children |
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| 4:d04fc71fb1b3 | 5:5b7aa9f6fd59 |
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| 45 help="sequences that have been blast aligned") | 45 help="sequences that have been blast aligned") |
| 46 the_parser.add_argument('--un_sequences', action="store", type=str, | 46 the_parser.add_argument('--un_sequences', action="store", type=str, |
| 47 help="sequences that have not been blast aligned") | 47 help="sequences that have not been blast aligned") |
| 48 the_parser.add_argument('--dataset_name', action="store", type=str, | 48 the_parser.add_argument('--dataset_name', action="store", type=str, |
| 49 default="", | 49 default="", |
| 50 help="the name of the dataset that has been parsed,\ | 50 help="name of the dataset that has been parsed,\ |
| 51 to be reported in the output") | 51 to be reported in the output") |
| 52 args = the_parser.parse_args() | 52 args = the_parser.parse_args() |
| 53 if not all((args.sequences, args.blast, args.fastaOutput, | 53 if not all((args.sequences, args.blast, args.fastaOutput, |
| 54 args.tabularOutput)): | 54 args.tabularOutput)): |
| 55 the_parser.error('argument(s) missing, call the\ | 55 the_parser.error('argument(s) missing, call the\ |
| 192 filter_relativeCov=0, filter_maxScore=0, filter_meanScore=0, | 192 filter_relativeCov=0, filter_maxScore=0, filter_meanScore=0, |
| 193 filter_term_in="", filter_term_out="", mode="verbose"): | 193 filter_term_in="", filter_term_out="", mode="verbose"): |
| 194 def filter_results(results, filter_relativeCov=0, filter_maxScore=0, | 194 def filter_results(results, filter_relativeCov=0, filter_maxScore=0, |
| 195 filter_meanScore=0, filter_term_in="", | 195 filter_meanScore=0, filter_term_in="", |
| 196 filter_term_out=""): | 196 filter_term_out=""): |
| 197 for subject in results.keys(): | 197 for subject in list(results): |
| 198 if results[subject][ | 198 if results[subject][ |
| 199 "RelativeSubjectCoverage"] < filter_relativeCov: | 199 "RelativeSubjectCoverage"] < filter_relativeCov: |
| 200 del results[subject] | 200 del results[subject] |
| 201 continue | 201 continue |
| 202 if results[subject]["maxBitScores"] < filter_maxScore: | 202 if results[subject]["maxBitScores"] < filter_maxScore: |