| Previous changeset 1:35e2e6452cf7 (2016-01-15) Next changeset 3:e279e53a3fde (2016-03-25) |
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Commit message:
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/blast_to_scaffold commit e67f150062f2076d0879bcdd3376ef53ba639d91 |
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modified:
blast_to_scaffold.py blast_to_scaffold.xml |
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| diff -r 35e2e6452cf7 -r 61731b911f4e blast_to_scaffold.py --- a/blast_to_scaffold.py Fri Jan 15 12:35:45 2016 -0500 +++ b/blast_to_scaffold.py Fri Mar 25 17:01:52 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 35e2e6452cf7 -r 61731b911f4e blast_to_scaffold.xml --- a/blast_to_scaffold.xml Fri Jan 15 12:35:45 2016 -0500 +++ b/blast_to_scaffold.xml Fri Mar 25 17:01:52 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"/> |