| Previous changeset 3:e279e53a3fde (2016-03-25) Next changeset 5:81ffa74cf96e (2016-11-09) |
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Commit message:
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/blast_to_scaffold commit fb47b9859a0703f1fa4a1e76b75b9dae29ca8329 |
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modified:
blast_to_scaffold.py blast_to_scaffold.xml test-data/assembly.fa |
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| diff -r e279e53a3fde -r 3288cc5a57e5 blast_to_scaffold.py --- a/blast_to_scaffold.py Fri Mar 25 19:14:20 2016 -0400 +++ b/blast_to_scaffold.py Fri Mar 25 19:21:26 2016 -0400 |
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| @@ -30,6 +30,10 @@ '--blast-tab', dest="blast_tab", action="store", type=str, help="13-columns tabular blastn or tblastx output") the_parser.add_argument( '--output', action="store", type=str, help="output file path, fasta format") + the_parser.add_argument( + '--scaffold_prefix', action="store", type=str, help="the prefix that will be used for the header of the fasta scaffold") + the_parser.add_argument( + '--scaffold_suffix', action="store", type=str, help="the sufix that will be used for the header of the fasta scaffold") args = the_parser.parse_args() return args @@ -98,13 +102,13 @@ for i, nucleotide in enumerate(sequence): GuideDict[i+subjectStart] = nucleotide -def finalAssembly (GuideDict, outputfile): +def finalAssembly (GuideDict, outputfile, prefix, suffix): finalSeqList = [] for keys in sorted(GuideDict): finalSeqList.append(GuideDict[keys]) finalSequence = insert_newlines("".join(finalSeqList) ) Out = open (outputfile, "w") - print >> Out, ">Scaffold" + print >> Out, ">Scaffold_from_%s_guided_by_%s" % (prefix, suffix) print >> Out, finalSequence Out.close() @@ -114,7 +118,7 @@ GuideDict = myGuide (args.guideSequence) blastlist = blatnInfo(args.blast_tab) updateGuide(blastlist, GuideDict, ContigsDict) - finalAssembly(GuideDict, args.output) + finalAssembly(GuideDict, args.output, args.scaffold_prefix, args.scaffold_suffix) if __name__ == "__main__": __main__() |
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| diff -r e279e53a3fde -r 3288cc5a57e5 blast_to_scaffold.xml --- a/blast_to_scaffold.xml Fri Mar 25 19:14:20 2016 -0400 +++ b/blast_to_scaffold.xml Fri Mar 25 19:21:26 2016 -0400 |
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| @@ -1,12 +1,14 @@ -<tool id="blast2scaffold" name="blast_to_scaffold" version="0.1.0"> +<tool id="blast2scaffold" name="blast_to_scaffold" version="0.9.0"> <description>Generate DNA scaffold from blastn or tblastx alignment of Contigs</description> <requirements> </requirements> <command interpreter="python"> blast_to_scaffold.py --sequences "$sequences" - --guideSequence "$guideSequence" - --blast-tab "$blast_tab" - --output "$output" + --guideSequence "$guideSequence" + --blast-tab "$blast_tab" + --output "$output" + --scaffold_prefix "$sequences.element_identifier" + --scaffold_suffix "$guideSequence.element_identifier" </command> <inputs> <param name="sequences" type="data" format="fasta" label="Select a fasta contigs file"/> |
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| diff -r e279e53a3fde -r 3288cc5a57e5 test-data/assembly.fa --- a/test-data/assembly.fa Fri Mar 25 19:14:20 2016 -0400 +++ b/test-data/assembly.fa Fri Mar 25 19:21:26 2016 -0400 |
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| @@ -1,4 +1,4 @@ ->Scaffold +>Scaffold_from_contigs.fa_guided_by_guideSequence.fa gcaaaaaggcccctgggGGGGGGTTAATGAGTACTGGAAAAAGAAGCGCGAGATACCACT TCGCTGATTATGCTGATTCTGGTATTAAGGATTAGTAGAGTATCGGAAGTGCCGAAGGGA ATAATGCTGGTCCGTTGTAAACAGGATACTTATGAGACCTCTTAACAGAAACTTTGAGCA |