Mercurial > repos > yufei-luo > s_mart

comparison commons/core/parsing/ParserChooser.py @ 36:44d5973c188c

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author m-zytnicki
date Tue, 30 Apr 2013 15:02:29 -0400
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35:d94018ca4ada 36:44d5973c188c
1 #
2 # Copyright INRA-URGI 2009-2010
3 #
4 # This software is governed by the CeCILL license under French law and
5 # abiding by the rules of distribution of free software. You can use,
6 # modify and/ or redistribute the software under the terms of the CeCILL
7 # license as circulated by CEA, CNRS and INRIA at the following URL
8 # "http://www.cecill.info".
9 #
10 # As a counterpart to the access to the source code and rights to copy,
11 # modify and redistribute granted by the license, users are provided only
12 # with a limited warranty and the software's author, the holder of the
13 # economic rights, and the successive licensors have only limited
14 # liability.
15 #
16 # In this respect, the user's attention is drawn to the risks associated
17 # with loading, using, modifying and/or developing or reproducing the
18 # software by the user in light of its specific status of free software,
19 # that may mean that it is complicated to manipulate, and that also
20 # therefore means that it is reserved for developers and experienced
21 # professionals having in-depth computer knowledge. Users are therefore
22 # encouraged to load and test the software's suitability as regards their
23 # requirements in conditions enabling the security of their systems and/or
24 # data to be ensured and, more generally, to use and operate it in the
25 # same conditions as regards security.
26 #
27 # The fact that you are presently reading this means that you have had
28 # knowledge of the CeCILL license and that you accept its terms.
29 #
30 import sys
31 from commons.core.parsing.TranscriptListParser import TranscriptListParser
32 from commons.core.parsing.MapperParser import MapperParser
33 from commons.core.parsing.SequenceListParser import SequenceListParser
34 from commons.core.parsing.BedParser import BedParser
35 from commons.core.parsing.GffParser import GffParser
36 from commons.core.parsing.MapperParser import MapperParser
37 from commons.core.parsing.CoordsParser import CoordsParser
38 from commons.core.parsing.SeqmapParser import SeqmapParser
39 from commons.core.parsing.SoapParser import SoapParser
40 from commons.core.parsing.Soap2Parser import Soap2Parser
41 from commons.core.parsing.BlastParser import BlastParser
42 from commons.core.parsing.PslParser import PslParser
43 from commons.core.parsing.RmapParser import RmapParser
44 from commons.core.parsing.ShrimpParser import ShrimpParser
45 from commons.core.parsing.AxtParser import AxtParser
46 from commons.core.parsing.ExoParser import ExoParser
47 from commons.core.parsing.MaqParser import MaqParser
48 from commons.core.parsing.SamParser import SamParser
49 from commons.core.parsing.BamParser import BamParser
50 from commons.core.parsing.BowtieParser import BowtieParser
51 from commons.core.parsing.ElandParser import ElandParser
52 from commons.core.parsing.GtfParser import GtfParser
53 from commons.core.parsing.FastaParser import FastaParser
54 from commons.core.parsing.FastqParser import FastqParser
55 from commons.core.parsing.MapParser import MapParser
56 from commons.core.parsing.WigParser import WigParser
57 from commons.core.parsing.NCListParser import NCListParser
58 from commons.core.parsing.PklParser import PklParser
59
60 #Attention!! Do not delete the imports!! They are used to know the type of file format!!!
61
62 class ParserChooser(object):
63 """
64 A class that finds the correct parser
65 @ivar format: the format
66 @type format: string
67 @ivar type: transcript / mapping / sequence parser
68 @type type: string
69 @ivar parser: the parser
70 @type parser: object
71 @ivar verbosity: verbosity
72 @type verbosity: int
73 """
74
75 def __init__(self, verbosity = 0):
76 """
77 Constructor
78 @param verbosity: verbosity
79 @type verbosity: int
80 """
81 self.type = None
82 self.parserClass = None
83 self.verbosity = verbosity
84
85
86 def findFormat(self, format, type = None):
87 """
88 Find the correct parser
89 @ivar format: the format
90 @type format: string
91 @ivar type: transcript / mapping / sequence parser (None is all)
92 @type type: string
93 @return: a parser
94 """
95 classes = {}
96 if (type == "transcript"):
97 classes = {TranscriptListParser: "transcript"}
98 elif (type == "mapping"):
99 classes = {MapperParser: "mapping"}
100 elif (type == "sequence"):
101 classes = {SequenceListParser: "sequence"}
102 elif (type == None):
103 classes = {TranscriptListParser: "transcript", MapperParser: "mapping", SequenceListParser: "sequence"}
104 else:
105 raise Exception("Do not understand format type '%s'" % (type))
106
107 for classType in classes:
108 for parserClass in classType.__subclasses__():
109 if format in parserClass.getFileFormats():
110 self.parserClass = parserClass
111 self.type = classes[classType]
112 return
113 raise Exception("Cannot get parser for format '%s'" % (format))
114
115
116 def getParser(self, fileName):
117 """
118 Get the parser previously found
119 @return: the parser
120 """
121 return self.parserClass(fileName, self.verbosity)
122
123
124 def getType(self):
125 """
126 Get the type of parser previously found
127 @return: the type of parser
128 """
129 return self.type