Mercurial > repos > drosofff > blastx_to_scaffold

comparison blastx_to_scaffold.py @ 0:a2e034f1638e draft

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planemo upload for repository https://bitbucket.org/drosofff/gedtools/
author drosofff
date Sun, 21 Jun 2015 14:40:10 -0400
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-1:000000000000 0:a2e034f1638e
1 #!/usr/bin/python
2 import sys
3 import argparse
4
5 def insert_newlines(string, every=60):
6 lines = []
7 for i in xrange(0, len(string), every):
8 lines.append(string[i:i+every])
9 return '\n'.join(lines)
10
11 def Parser():
12 the_parser = argparse.ArgumentParser(
13 description="Generate DNA scaffold from blastx alignment of Contigs")
14 the_parser.add_argument(
15 '--sequences', action="store", type=str, help="input sequence file in fasta format")
16 the_parser.add_argument(
17 '--blastx-tab', dest="blastx_tab", action="store", type=str, help="13-columns tabular blastx output")
18 the_parser.add_argument(
19 '--output', action="store", type=str, help="output file path, fasta format")
20 args = the_parser.parse_args()
21 return args
22
23 def __main__():
24 args = Parser()
25 protLenght = int (open (args.blastx_tab, "r").readline().split("\t")[12])
26 BlastxOutput = open (args.blastx_tab, "r")
27 Contigs = open (args.sequences, "r")
28 ContigsDict = {}
29 protScaffold = {}
30
31 for line in Contigs:
32 if line[0] == ">":
33 header = line[1:-1]
34 ContigsDict[header] = ""
35 else:
36 ContigsDict[header] += line[:-1]
37
38 protScaffold = dict ( [(i,"NNN") for i in range (1, protLenght+1)] )
39
40 for line in BlastxOutput:
41 fields = line[:-1].split("\t")
42 queryStart = int(fields[6])
43 queryStop = int(fields[7])
44 subjectStart = int(fields[8])
45 subjectStop = int(fields[9])
46 seqHeader = fields[0]
47 sequence = ContigsDict[seqHeader]
48 for i in range (subjectStart, subjectStop):
49 del protScaffold[i]
50 protScaffold[subjectStop] = ContigsDict[seqHeader][queryStart -1: queryStop]
51
52 finalSeqList = []
53 for i in sorted (protScaffold):
54 finalSeqList.append(protScaffold[i])
55 finalSequence = insert_newlines("".join(finalSeqList))
56
57 Out = open (args.output, "w")
58 print >> Out, ">Scaffold"
59 print >> Out, finalSequence
60
61 BlastxOutput.close()
62 Contigs.close()
63 Out.close()
64
65 if __name__ == "__main__":
66 __main__()