annotate commons/core/parsing/VarscanFileForGnpSNP.py @ 42:2abc37c27164

Deleted selected files
author m-zytnicki
date Wed, 18 Sep 2013 07:45:59 -0400
parents 769e306b7933
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
6
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
1 # Copyright INRA (Institut National de la Recherche Agronomique)
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
2 # http://www.inra.fr
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
3 # http://urgi.versailles.inra.fr
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
4 #
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
5 # This software is governed by the CeCILL license under French law and
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
6 # abiding by the rules of distribution of free software. You can use,
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
7 # modify and/ or redistribute the software under the terms of the CeCILL
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
8 # license as circulated by CEA, CNRS and INRIA at the following URL
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
9 # "http://www.cecill.info".
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
10 #
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
11 # As a counterpart to the access to the source code and rights to copy,
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
12 # modify and redistribute granted by the license, users are provided only
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
13 # with a limited warranty and the software's author, the holder of the
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
14 # economic rights, and the successive licensors have only limited
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
15 # liability.
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
16 #
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
17 # In this respect, the user's attention is drawn to the risks associated
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
18 # with loading, using, modifying and/or developing or reproducing the
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
19 # software by the user in light of its specific status of free software,
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
20 # that may mean that it is complicated to manipulate, and that also
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
21 # therefore means that it is reserved for developers and experienced
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
22 # professionals having in-depth computer knowledge. Users are therefore
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
23 # encouraged to load and test the software's suitability as regards their
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
24 # requirements in conditions enabling the security of their systems and/or
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
25 # data to be ensured and, more generally, to use and operate it in the
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
26 # same conditions as regards security.
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
27 #
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
28 # The fact that you are presently reading this means that you have had
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
29 # knowledge of the CeCILL license and that you accept its terms.
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
30
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
31
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
32 from commons.core.parsing.VarscanHitForGnpSNP import VarscanHitForGnpSNP
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
33 from commons.core.parsing.VarscanFile import VarscanFile
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
34
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
35 class VarscanFileForGnpSNP(VarscanFile):
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
36
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
37 def __init__(self, varscanFileName, fastqFileName="", refFastaFileName="", taxonName=""):
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
38 VarscanFile.__init__(self, varscanFileName)
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
39 self._fastqFileName = fastqFileName
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
40 self._refFastaFileName = refFastaFileName
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
41 self._taxonName = taxonName
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
42 self._previousVarscanHit = None
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
43
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
44 ## Equal operator
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
45 #
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
46 # @param o a VarscanFileAnalysis instance
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
47 #
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
48 def __eq__(self, o):
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
49 return VarscanFile.__eq__(self, o) and self._fastqFileName == o._fastqFileName \
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
50 and self._refFastaFileName == o._refFastaFileName and self._taxonName == o._taxonName
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
51
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
52 def getVarscanFieldSeparator(self):
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
53 return self._varscanFieldSeparator
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
54
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
55 def getFastqFileName(self):
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
56 return self._fastqFileName
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
57
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
58 def getRefFastaFileName(self):
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
59 return self._refFastaFileName
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
60
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
61 def getTaxonName(self):
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
62 return self._taxonName
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
63
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
64 def createVarscanHit(self, line, currentLineNumber):
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
65 line = line.strip()
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
66 lResults = line.split(self._varscanFieldSeparator)
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
67 iVarscanHit = VarscanHitForGnpSNP()
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
68 iVarscanHit.setAttributes(lResults, currentLineNumber)
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
69 iVarscanHit.formatAlleles2GnpSnp()
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
70 iVarscanHit.manageOccurrence(self._previousVarscanHit)
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
71 self._previousVarscanHit = iVarscanHit
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
72 return iVarscanHit