Mercurial > repos > artbio > blastparser_and_hits

comparison BlastParser_and_hits.py @ 5:5b7aa9f6fd59 draft default tip

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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
comparison
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4:d04fc71fb1b3 5:5b7aa9f6fd59
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: