Mercurial > repos > yufei-luo > s_mart

comparison smart_toolShed/commons/core/parsing/BlatFileParser.py @ 0:e0f8dcca02ed

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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
author yufei-luo
date Thu, 17 Jan 2013 10:52:14 -0500
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-1:000000000000 0:e0f8dcca02ed
1 from commons.core.parsing.BlatParser import BlatParser
2 import os
3
4 class BlatFileParser(object):
5
6 def __init__(self, blatFileName = None):
7 self._blatFileName = blatFileName
8 self._lBlatHits = []
9 self._dBlatHitsByQueries = {}
10 self._dQueries = {}
11
12 def getDictOfQueries(self):
13 return self._dQueries
14
15 def getResultLinesOfOneQuery(self, queryName):
16 return self._dBlatHitsByQueries[queryName]
17
18 def getDictOfBlatHitsByQueries(self):
19 return self._dBlatHitsByQueries
20
21 def getListsOfHits(self):
22 return self._lBlatHits
23
24 def parseBlatFile(self):
25 blatFile = open(self._blatFileName, 'r')
26 line = blatFile.readline()
27 n = 1
28 while line != "":
29 if self._isInteger(line.split("\t")[0]):
30 iBlatParser = BlatParser()
31 iBlatParser.setAttributesFromString(line, n)
32 queryHeader = iBlatParser.getQName()
33 self._dQueries[queryHeader] = 1
34 self._lBlatHits.append(iBlatParser)
35 line = blatFile.readline()
36 n += 1
37 return self._lBlatHits
38
39 def parseBlatFileByQueries(self):
40 blatFile = open(self._blatFileName, 'r')
41 line = blatFile.readline()
42 n = 1
43 while line != "":
44 if self._isInteger(line.split("\t")[0]):
45 iBlatParser = BlatParser()
46 iBlatParser.setAttributesFromString(line, n)
47 queryHeader = iBlatParser.getQName()
48 self._dQueries[queryHeader] = 1
49 if self._dBlatHitsByQueries.has_key(queryHeader):
50 self._dBlatHitsByQueries[queryHeader].append(iBlatParser)
51 else:
52 self._dBlatHitsByQueries[queryHeader] = [iBlatParser]
53 line = blatFile.readline()
54 n += 1
55 blatFile.close()
56 return self._dBlatHitsByQueries
57
58 def _isInteger(self, string):
59 try:
60 int(string)
61 return True
62 except ValueError:
63 return False