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comparison commons/pyRepetUnit/hmmer/hmmOutput/HmmpfamOutputProcessing.py @ 31:0ab839023fe4

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Uploaded
author m-zytnicki
date Tue, 30 Apr 2013 14:33:21 -0400
parents 94ab73e8a190
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30:5677346472b5 31:0ab839023fe4
1 from commons.pyRepetUnit.hmmer.hmmOutput.HmmOutput import HmmOutput
2 import re
3 from commons.pyRepetUnit.hmmer.hmmOutput.HmmOutputProcessing import HmmOutputProcessing
4
5 ##Concrete implementation for specific methods
6 #
7 class HmmpfamOutputProcessing (HmmOutputProcessing):
8
9 ##read an output from hmmpfam and return a array with results useful to build a .align file
10 #
11 # @param file handle of file generated by software searching hmm profiles
12 #
13 def readHmmOutput( self, hmmerOutputFile ):
14 #Tested with HMMER 2.3.2 on Linux (Debian) and on Unix (Solaris)
15 line = hmmerOutputFile.readline()
16 tabResult = None
17 aRecup = 0
18 if (line == ""):
19 tabResult = None
20 return tabResult
21 tabResult = HmmOutput()
22 while not re.match("Alignments of top-scoring domains:.*", line):
23 line = hmmerOutputFile.readline()
24 m = re.match("Query sequence:\s*(.*)", line)
25 if m:
26 seqName = m.group(1)
27 #warning : do no use a return character because they change between several OS
28 if re.match("--------\s+-------\s+-----\s+-----\s+-----\s+-----\s+-----\s+-------.*", line):
29 aRecup = 1
30 m = re.match("(\S+)\s+\d+\/\d+\s+(\d+)\s+(\d+)\s+.+\s+(\d+)\s+(\d+)\s+.+\s+(.+\.\d)\s+(.+)", line)
31 if m and aRecup == 1:
32 tabResult.append([seqName, m.group(2), m.group(3), m.group(1), m.group(4), m.group(5), m.group(7), m.group(6)])
33 if line == "":
34 tabResult = None
35 return tabResult
36 return tabResult