| Previous changeset 6:3f7cfa1cf90c (2015-09-14) Next changeset 8:efb051ac0da9 (2015-10-19) |
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Commit message:
planemo upload for repository https://bitbucket.org/drosofff/gedtools/ commit 319fbe5bf4fe32ab9329a411a0d0bd70b83efd9a |
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modified:
BlastParser_and_hits.py BlastParser_and_hits.xml |
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| diff -r 3f7cfa1cf90c -r 72ef366ef55e BlastParser_and_hits.py --- a/BlastParser_and_hits.py Mon Sep 14 11:39:51 2015 -0400 +++ b/BlastParser_and_hits.py Wed Sep 16 06:11:35 2015 -0400 |
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| @@ -130,6 +130,13 @@ def outputParsing (F, Fasta, results, Xblastdict, fastadict, filter_relativeCov=0, filter_maxScore=0, filter_meanScore=0, mode="verbose"): F= open(F, "w") Fasta=open(Fasta, "w") + blasted_transcripts = [] + for subject in results: + if results[subject]["RelativeSubjectCoverage"]<filter_relativeCov or results[subject]["maxBitScores"]<filter_maxScore or results[subject]["meanBitScores"]<filter_meanScore: + continue + for transcript in Xblastdict[subject]: + blasted_transcripts.append(transcript) + blasted_transcripts = list( set( blasted_transcripts)) if mode == "verbose": print >>F, "# SeqId\t%Identity\tAlignLength\tStartSubject\tEndSubject\t%QueryHitCov\tE-value\tBitScore\n" for subject in sorted (results, key=lambda x: results[x]["meanBitScores"], reverse=True): @@ -172,18 +179,14 @@ print >> Fasta, "" # final carriage return for the sequence F.close() Fasta.close() + return blasted_transcripts -def sort_sequences (fastadict, blastdict, matched_sequences, unmatched_sequences): +def dispatch_sequences (fastadict, blasted_transcripts, matched_sequences, unmatched_sequences): '''to output the sequences that matched and did not matched in the blast''' - blasted_transcripts = [] - for subject in blastdict: - for transcript in blastdict[subject]: - blasted_transcripts.append(transcript) - blasted_transcripts = list( set( blasted_transcripts)) F_matched = open (matched_sequences, "w") F_unmatched = open (unmatched_sequences, "w") for transcript in fastadict: - if transcript in blasted_transcripts: + if transcript in blasted_transcripts: # le list of blasted_transcripts is generated by the outputParsing function print >> F_matched, ">%s\n%s" % (transcript, insert_newlines(fastadict[transcript]) ) else: print >> F_unmatched, ">%s\n%s" % (transcript, insert_newlines(fastadict[transcript]) ) @@ -195,11 +198,12 @@ args = Parser() fastadict = getfasta (args.sequences) Xblastdict = getblast (args.blast) - sort_sequences (fastadict, Xblastdict, args.al_sequences, args.un_sequences) results = defaultdict(dict) for subject in Xblastdict: results[subject]["HitDic"], results[subject]["subjectLength"], results[subject]["TotalCoverage"], results[subject]["RelativeSubjectCoverage"], results[subject]["maxBitScores"], results[subject]["meanBitScores"] = subjectCoverage(fastadict, Xblastdict, subject, args.flanking) - outputParsing (args.tabularOutput, args.fastaOutput, results, Xblastdict, fastadict, - filter_relativeCov=args.filter_relativeCov, filter_maxScore=args.filter_maxScore, - filter_meanScore=args.filter_meanScore, mode=args.mode) + blasted_transcripts = outputParsing (args.tabularOutput, args.fastaOutput, results, Xblastdict, fastadict, + filter_relativeCov=args.filter_relativeCov, filter_maxScore=args.filter_maxScore, + filter_meanScore=args.filter_meanScore, mode=args.mode) + dispatch_sequences (fastadict, blasted_transcripts, args.al_sequences, args.un_sequences) + if __name__=="__main__": __main__() |
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| diff -r 3f7cfa1cf90c -r 72ef366ef55e BlastParser_and_hits.xml --- a/BlastParser_and_hits.xml Mon Sep 14 11:39:51 2015 -0400 +++ b/BlastParser_and_hits.xml Wed Sep 16 06:11:35 2015 -0400 |
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| @@ -1,4 +1,4 @@ -<tool id="BlastParser_and_hits" name="Parse blast output and compile hits" version="2.3.0"> +<tool id="BlastParser_and_hits" name="Parse blast output and compile hits" version="2.3.1"> <description>for virus discovery</description> <requirements></requirements> <command interpreter="python"> @@ -66,7 +66,7 @@ **What it does** -Parse blast outputs for viruses genome assembly. Outputs analysis and hit sequences for further assembly. Output also the contig sequences which have or not been blast aligned with the indicated cut-off +Parse blast outputs for viruses genome assembly. Outputs analysis and hit sequences for further assembly. Outputs also the contig sequences which have or not been blast aligned taking into account all indicated cut-offs </help> </tool> |