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comparison commons/pyRepetUnit/hmmer/hmmOutput/HmmscanOutputProcessing.py @ 18:94ab73e8a190

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author m-zytnicki
date Mon, 29 Apr 2013 03:20:15 -0400
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17:b0e8584489e6 18:94ab73e8a190
1 import re
2 from commons.pyRepetUnit.hmmer.hmmOutput.HmmOutput import HmmOutput
3 from commons.pyRepetUnit.hmmer.hmmOutput.HmmOutputProcessing import HmmOutputProcessing
4
5 ##Concrete implementation for hmmscan output specific methods
6 #
7 class HmmscanOutputProcessing (HmmOutputProcessing):
8
9 ## read an hmmscan output from a file, 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 3 on Linux
15 line = hmmerOutputFile.readline()
16 tabResult = None
17 if (line == ""):
18 tabResult = None
19 return tabResult
20 tabResult = HmmOutput()
21
22 while line != "":
23 line = hmmerOutputFile.readline()
24 if not(re.match("^#.*$", line)) and line != "":
25 lLines = re.split("\s+", line)
26 seqName = lLines[3]
27 profilName = lLines[0]
28 iValue = lLines[12]
29 score = lLines[13]
30 queryCoordStart =lLines[17]
31 queryCoordEnd = lLines[18]
32 subjectCoordStart = lLines[15]
33 subjectCoordEnd = lLines[16]
34 tabResult.append([seqName, queryCoordStart, queryCoordEnd, profilName, subjectCoordStart, subjectCoordEnd, iValue, score])
35 return tabResult
36