Mercurial > repos > yufei-luo > s_mart

comparison commons/pyRepetUnit/hmmer/check/OldDetectFeatureConfigChecker.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 '''
2 Created on 14 avr. 2009
3
4 @author: oinizan
5 '''
6 import re
7 from commons.core.checker.IChecker import IChecker
8 from commons.core.checker.OldConfigChecker import ConfigChecker
9 from commons.core.checker.ConfigException import ConfigException
10 from commons.core.checker.CheckerException import CheckerException
11
12 class DetectFeatureConfigChecker (IChecker):
13 '''
14 classdocs
15 '''
16 def __init__(self):
17 '''
18 Constructor
19 '''
20 self._dict = {"te_hmmer" : "",
21 "te_blrn" : ""
22 }
23 self._specifiqueDict = {"te_hmmer_evalue" : "",
24 "te_hmm_profiles" : ""
25 }
26
27 def _appendMessageToConfigExceptionMessage(self, messages):
28 appendedMessages = []
29 for msg in messages:
30 if (re.match("\[detect_features\] - No option 'te_hmm_profiles' in section: 'detect_features'", msg)):
31 appendedMessages.append(msg + " whereas te_hmmer is set")
32
33 if (re.match("\[detect_features\] - No option 'te_hmmer_evalue' in section: 'detect_features'", msg)):
34 appendedMessages.append(msg + " whereas te_hmmer is set - Default value will be set")
35
36 return appendedMessages
37
38
39 def check(self, configFile):
40 chk = ConfigChecker("detect_features", self._dict)
41 try :
42 chk.check(configFile)
43 except ConfigException, e :
44 raise e
45
46 if self._dict["te_hmmer"] == "yes":
47 isErrorOccured = False
48 try:
49 chk = ConfigChecker("detect_features", self._specifiqueDict)
50 chk.check(configFile)
51 except ConfigException, e:
52 appendedMessages = self._appendMessageToConfigExceptionMessage(e.messages)
53 raise ConfigException("", appendedMessages)
54
55
56 if __name__ == "__main__":
57 pass