Mercurial > repos > drosofff > blastx_to_scaffold

annotate blastx_to_scaffold.py @ 1:940c0c669e96 draft default tip

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planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/blastx_to_scaffold commit b6de14061c479f0418cd89e26d6f5ac26e565a07
author drosofff
date Wed, 09 Nov 2016 11:39:20 -0500
parents a2e034f1638e
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
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1 #!/usr/bin/python
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2 import sys
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3 import argparse
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4
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5 def insert_newlines(string, every=60):
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6 lines = []
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7 for i in xrange(0, len(string), every):
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8 lines.append(string[i:i+every])
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9 return '\n'.join(lines)
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10
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11 def Parser():
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12 the_parser = argparse.ArgumentParser(
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13 description="Generate DNA scaffold from blastx alignment of Contigs")
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14 the_parser.add_argument(
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15 '--sequences', action="store", type=str, help="input sequence file in fasta format")
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16 the_parser.add_argument(
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17 '--blastx-tab', dest="blastx_tab", action="store", type=str, help="13-columns tabular blastx output")
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18 the_parser.add_argument(
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19 '--output', action="store", type=str, help="output file path, fasta format")
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20 args = the_parser.parse_args()
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21 return args
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22
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23 def __main__():
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24 args = Parser()
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25 protLenght = int (open (args.blastx_tab, "r").readline().split("\t")[12])
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26 BlastxOutput = open (args.blastx_tab, "r")
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27 Contigs = open (args.sequences, "r")
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28 ContigsDict = {}
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29 protScaffold = {}
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30
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31 for line in Contigs:
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32 if line[0] == ">":
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33 header = line[1:-1]
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34 ContigsDict[header] = ""
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35 else:
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36 ContigsDict[header] += line[:-1]
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37
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38 protScaffold = dict ( [(i,"NNN") for i in range (1, protLenght+1)] )
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39
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40 for line in BlastxOutput:
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41 fields = line[:-1].split("\t")
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42 queryStart = int(fields[6])
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43 queryStop = int(fields[7])
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44 subjectStart = int(fields[8])
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45 subjectStop = int(fields[9])
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46 seqHeader = fields[0]
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47 sequence = ContigsDict[seqHeader]
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48 for i in range (subjectStart, subjectStop):
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49 del protScaffold[i]
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50 protScaffold[subjectStop] = ContigsDict[seqHeader][queryStart -1: queryStop]
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51
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52 finalSeqList = []
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53 for i in sorted (protScaffold):
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54 finalSeqList.append(protScaffold[i])
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55 finalSequence = insert_newlines("".join(finalSeqList))
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56
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57 Out = open (args.output, "w")
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58 print >> Out, ">Scaffold"
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59 print >> Out, finalSequence
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60
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61 BlastxOutput.close()
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62 Contigs.close()
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63 Out.close()
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64
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65 if __name__ == "__main__":
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66 __main__()