Mercurial > repos > yufei-luo > s_mart

comparison commons/core/parsing/FastqParser.py @ 6:769e306b7933

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author yufei-luo
date Fri, 18 Jan 2013 04:54:14 -0500
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5:ea3082881bf8 6:769e306b7933
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.SequenceListParser import SequenceListParser
32 from SMART.Java.Python.structure.Sequence import Sequence
33
34 class FastqParser(SequenceListParser):
35 """A class that reads a list of sequences in FASTQ format"""
36
37 def __init__(self, fileName, verbosity = 0):
38 super(FastqParser, self).__init__(fileName, verbosity)
39
40
41 def getFileFormats():
42 return ["fastq", "mfq"]
43 getFileFormats = staticmethod(getFileFormats)
44
45
46 def getInfos(self):
47 """
48 Get some generic information about the sequences
49 """
50 self.nbSequences = 0
51 self.reset()
52 if self.verbosity >= 10:
53 print "Getting information on %s." % (self.fileName)
54
55 nbLines = 0
56 for line in self.handle:
57 line = line.strip()
58 if line == "":
59 continue
60 nbLines += 1
61 if self.verbosity >= 10 and nbLines % 400000 == 0:
62 sys.stdout.write(" %d sequences read\r" % (nbLines / 4))
63 sys.stdout.flush()
64 self.reset()
65 self.nbSequences = nbLines / 4
66 if self.verbosity >= 10:
67 print " %d sequences read" % (self.nbSequences)
68 print "Done."
69
70
71 def parseOne(self):
72 """
73 Parse only one element in the file
74 """
75 string = ""
76 quality = ""
77 lineType = 0
78
79 for line in self.handle:
80 line = line.strip()
81 if lineType == 0:
82 if line[0] != "@":
83 raise Exception("Line '%s' should start with '@'!" % (line))
84 name = line[1:]
85 inSequence = True
86 inQuality = False
87 elif lineType == 1:
88 string = line
89 elif lineType == 2:
90 if line[0] != "+":
91 sys.exit("Line '%s' should start with '+'!" % (line))
92 if line[1:] != name and line != "+":
93 sys.exit("Weird difference in sequence and quality names (%s and %s) while parsing FASTQ file %s." % (name, line[1:], self.fileName))
94 inQuality = True
95 inSequence = False
96 elif lineType == 3:
97 quality = line
98 lineType += 1
99 if lineType == 4:
100 sequence = Sequence(name, string)
101 sequence.setQuality(quality)
102 return sequence
103
104 return None