# HG changeset patch # User drosofff # Date 1433842643 14400 # Node ID 6af7f779eb559de76b4f6dc3d65b489415ce0357 planemo upload for repository https://bitbucket.org/drosofff/gedtools/ diff -r 000000000000 -r 6af7f779eb55 blastx_to_scaffold.py --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/blastx_to_scaffold.py Tue Jun 09 05:37:23 2015 -0400 @@ -0,0 +1,66 @@ +#!/usr/bin/python +import sys +import argparse + +def insert_newlines(string, every=60): + lines = [] + for i in xrange(0, len(string), every): + lines.append(string[i:i+every]) + return '\n'.join(lines) + +def Parser(): + the_parser = argparse.ArgumentParser( + description="Generate DNA scaffold from blastx alignment of Contigs") + the_parser.add_argument( + '--sequences', action="store", type=str, help="input sequence file in fasta format") + the_parser.add_argument( + '--blastx-tab', dest="blastx_tab", action="store", type=str, help="13-columns tabular blastx output") + the_parser.add_argument( + '--output', action="store", type=str, help="output file path, fasta format") + args = the_parser.parse_args() + return args + +def __main__(): + args = Parser() + protLenght = int (open (args.blastx_tab, "r").readline().split("\t")[12]) + BlastxOutput = open (args.blastx_tab, "r") + Contigs = open (args.sequences, "r") + ContigsDict = {} + protScaffold = {} + + for line in Contigs: + if line[0] == ">": + header = line[1:-1] + ContigsDict[header] = "" + else: + ContigsDict[header] += line[:-1] + + protScaffold = dict ( [(i,"NNN") for i in range (1, protLenght+1)] ) + + for line in BlastxOutput: + fields = line[:-1].split("\t") + queryStart = int(fields[6]) + queryStop = int(fields[7]) + subjectStart = int(fields[8]) + subjectStop = int(fields[9]) + seqHeader = fields[0] + sequence = ContigsDict[seqHeader] + for i in range (subjectStart, subjectStop): + del protScaffold[i] + protScaffold[subjectStop] = ContigsDict[seqHeader][queryStart -1: queryStop] + + finalSeqList = [] + for i in sorted (protScaffold): + finalSeqList.append(protScaffold[i]) + finalSequence = insert_newlines("".join(finalSeqList)) + + Out = open (args.output, "w") + print >> Out, ">Scaffold" + print >> Out, finalSequence + + BlastxOutput.close() + Contigs.close() + Out.close() + +if __name__ == "__main__": + __main__() diff -r 000000000000 -r 6af7f779eb55 blastx_to_scaffold.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/blastx_to_scaffold.xml Tue Jun 09 05:37:23 2015 -0400 @@ -0,0 +1,42 @@ + +Generate DNA scaffold from blastx alignment of Contigs + + + + blastx_to_scaffold.py --sequences $sequences + --blastx-tab $blastx_tab + --output $output + + + + + + + + + + + + + + + + + + + + + + + +**What it Does** +This tool start from DNA contigs that aligned to a subject protein sequence through blastx. +The contigs must be provided in fasta format. The blastx output must be tabular, the 12 standard column plus column 13 with the length of the blastx subject. +The final scaffold is a DNA sequence. +Sequences of the subject protein which were not aligned to the contigs are replaced by Ns in this scaffold. + +**Attribution** +This Galaxy tool was created by drosofff@gmail.com on 28/05/2015 + + + diff -r 000000000000 -r 6af7f779eb55 test-data/Blastx2scaffold_test1_input.xls --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/Blastx2scaffold_test1_input.xls Tue Jun 09 05:37:23 2015 -0400 @@ -0,0 +1,53 @@ +>Contig1 +TAGATAAGGTTTGCTCATTTCTTGAGGATACTTTACCAGGTATGGTCGAGCACGTTACGC +TCGTAGCACAAAATACATCCGCGTCAGCCAAGGTGTTATCTGACGAGTTGATCAAATCAA +TGCTTTGCATTGTTTTGATTTGCTTGTTGATTGAAACCAAGTTCTATAAGACCGCTTTCG +CGGTACTTATAGTGGTTGCTCTACGTGTTTTCGGGTACAGTGAGCAAATAATTGAGACAG +CTATGGACATGTATCGCGTAATTAGGGCTCCAAAGGCTCAAGGTAATATGGAAGATGTCG +TTTTCCATCCGTGGTTGAACACGTGTGGAAAGTTGATTTTCCTACTTATCGCTGTCCTGT +GTCTCAAGAAATTACCAGGAAAGAACGACGTAGACACTTTCATGCGCAGGCTCGACAGCT +TACCCAAAGCTGTTAAGGGTGCGACACAACTACATGAATGGGTGTCAAAATACTTCGATC +TCTCTTTGGATCACGTCAAGGCGATGATTGTTGGTAAATCTTGTGCCGAAATGAAGAAGG +CTGAATCATCAAGCGCCAAAGTTTTGGCTTGGGCCGCTAGAGTTCAAGATTTCGTCAGAT +TGGAACAACGAAGTAAAATCGATAGTGATATCGCTGTCGCCAACGAGGCTGAAGCCTTGT +ATCACACTGGATTGCAATTTGCAGGAGACACTCTGTTACCTCCAGAATTGCACAAGGTCG +TGAACAGTGCGCTAAGACCAGCCCGCGATATATATGAGTACGTCACCCGCTCCCCAATAA +AAGGAGGGAGTCGTAAGATGAGACCCTTGATGATTTGGCTAGCTGGCCAGTCAGGAATTG +GGAAAACCTCTATGGTGGATCCTCTATGTATCGATTTGCTTCGAGCAATGGGTTATGTGG +GACCTGAACATCTCCACTCGTTGGTGTATGGCCGCCAAGTTGAGACGGAGTACTGGGATG +GTTACAAAGCCCACAAGATAGTGATCTATGATGATGCTTTTCAGCTGAAAGATGATGCTG +TGAACAGGAATTTGGAGGTATTTGAGGTTATACGTTCTTGCAACACGTATCCTCAACACC +TTCATATGGCTTGTCTCTCGGATAAAAACACTTTTTCAGTAGCGGAAGTGTACATCTACA +CTACCAACGAAATGAATGTCAAACTTGAGTCGCTGACTCATGAACAAGCATTCTACAACC +GCATGAGTGAAAACGCGTTCACTGTGCGTCCAAAAGAGGCTTATCGTCTAGTCGAAGAAG +GATCAACCGGCAATAAGCAGTATCGTTTGGACAAAACGAAAACCAAAGGAGCTATCGATC +TCGATGTGTACGAATTCGTGCGC +>Contig2 +CTAGAATCACAGCTCAGATGAGTTTTGAGGCACCGAAGGACGCAATTGAAGGACCGTGTC +AAACCCCGGAAGGATTGTTCGCCCCTATTGGCAAAGCGCCGATAGGCGTAGGGATGTCCA +CCAAGACGGCTATACGACCTTCACGCTTGTATGGAAGAATAACTAAACCGACAACTGCAC +CATCATACTTGGGTAAAGACGCGCTTTATCGTGGATTGACCAAGTGTGGTGTTCGCACAG +TTAATATTCAACCAGAATACATAGACGCAGCGGCGAATGACGTCGCACGCTATGTGTTAA +ACCAGCATGTTGGTCACGTGGATAGGGAACGATACACACGTATATTGTCGTACGAGGAGG +CTGTTAAGGGCGTGCCGTACGATGATTTCATGAAGTCAGTGACTCGAGTCACTTCCCCTG +GTTACCCCTATTGCTTGGATACTGGAAACATGCCAGGGAAAAGCAAATGGATGGGGCTCG +AACAAGATTTCGATATGACAAGTCCAGCTGCTTTGGCTTTGAGGAAAGATGTTGAAAGTT +TGTTGGAAGATTGCAAAAATGGCTTAGTCCGTGATGTGGTGTTTGTCGACACTCTCAAGG +ATGAAAGGCGCGAGCTGATAAAGGTGGAAGCAAAGAAGACTCGAGTCTTTTCTGCTGGAC +CACAGCATTTTGTAATAGCTTTCCGGCAATACTTTCTTCCATTCTCTGCCTGGGTCATGC +ATAACAGAATCGAAAACGAAGTAGCCGTTGGAACAAACCCCTTCTCAATGGATTGGCACA +ACATTGCTGTGCGTATGCGTAGTAAAGGGAGACACATTATTGCTGGAGATTTTAGCAATT +TTGATGGATCCCTCAACGCCCAAGTTCTCTGGACAATATTTTGGAAGATATTTGTCCCGT +GGCTTAATGATATTGAACCACTTGGTACACCCAAGAATGAGGAGAATCTGCGGGTCTGCA +CGAGTCTATGGACGCACTTGGTGCACTCCGTGCACATTTGTGGAGATAACTTGTACATGT +GGACACATTCTCAACCATCGGGCAATCCCTTCACGGTGATAATCAATAGTTTGTATAACT +CAGTTATCATGCGTGTCGTGTGGCAATACATAATGGCGAAAGAAGAACCTAAGTTACGCA +CAATGAACCATTTCAATCAACATGTTGCTATGGTTTCATATGGTGATGACAATCTACTTA +ACATCTCGGAAGGGGTAATTGATATCTTCAACCAACTTACCATCTCGGAAGCCATGCGTT +GGATAGGACACGAATACACAGATGAAACGAAAACAGGCGAGGCTGCGCCCTATCGGACAT +TGGAAGAAGTCCGTTTCCTTAAAAGAGGGTTCAGAATGGATCACCTCTTGTGTCGGTGGG +TAGCTCCTTTGAAGAAGGATGTCATCTACGAAATGCTTAATTGGACGCGCAAAGGGATTA +ACCCAGATGATGTGACGATGATGATCATTGATACAGCATTTAGGGAGATCTCTTATCACG +GAAGGGAAGCTTTCGAGAAGCTGCGAGGGCAGATACTTGAGCAGCGGGATGTGTTGGTTG +AATATCCTCAA +