Mercurial > repos > yufei-luo > s_mart
comparison commons/core/parsing/FastqParser.py @ 36:44d5973c188c
Uploaded
author | m-zytnicki |
---|---|
date | Tue, 30 Apr 2013 15:02:29 -0400 |
parents | 769e306b7933 |
children |
comparison
equal
deleted
inserted
replaced
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.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 |