annotate SMART/Java/Python/removeEmptySequences.py @ 31:0ab839023fe4

Uploaded
author m-zytnicki
date Tue, 30 Apr 2013 14:33:21 -0400
parents 94ab73e8a190
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 #! /usr/bin/env python
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
2 #
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
3 # Copyright INRA-URGI 2009-2010
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 Remove empty sequences from a FASTA or FASTQ file
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
33 """
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
34
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
35 import os, random
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
36 from optparse import OptionParser
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
37 from commons.core.parsing.FastaParser import *
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
38 from commons.core.parsing.FastqParser import *
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
39 from commons.core.writer.FastaWriter import *
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
40 from commons.core.writer.FastqWriter import *
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
41 from SMART.Java.Python.misc.Progress import *
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
42
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
43
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
44 class EmptySequenceRemover(object):
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
45
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
46 def __init__(self, verbosity = 1):
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
47 self.verbosity = verbosity
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
48 self.inputFileName = None
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
49 self.parser = None
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
50 self.format = None
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
51 self.writer = None
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
52 self.forbiddenNames = {}
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
53 self.removedNames = {}
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
54
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
55
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
56 def setInputFileName(self, fileName, format):
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
57 self.inputFileName = fileName
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
58 self.format = format
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
59 if options.format == "fasta":
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
60 self.parser = FastaParser(self.inputFileName, self.verbosity)
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
61 elif options.format == "fastq":
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
62 self.parser = FastqParser(self.inputFileName, self.verbosity)
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
63 else:
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
64 sys.exit("Do not understand '%s' file format." % (self.format))
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
65
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
66
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
67 def setOutputFileName(self, fileName):
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
68 if options.format == "fasta":
31
0ab839023fe4 Uploaded
m-zytnicki
parents: 18
diff changeset
69 self.writer = FastaWriter("%s.mfa" % (fileName), self.verbosity)
6
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
70 elif options.format == "fastq":
31
0ab839023fe4 Uploaded
m-zytnicki
parents: 18
diff changeset
71 self.writer = FastqWriter("%s.mfq" % (fileName), self.verbosity)
6
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
72
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
73
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
74 def parse(self):
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
75 progress = Progress(self.parser.getNbSequences(), "Reading sequences in %s" % (options.inputFileName), options.verbosity)
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
76 for sequence in self.parser.getIterator():
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
77 name = sequence.name.split("/")[0]
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
78 if name not in self.forbiddenNames:
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
79 if sequence.sequence == "":
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
80 self.removedNames[name] = 1
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
81 else:
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
82 self.writer.addSequence(sequence)
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
83 progress.inc()
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
84 progress.done()
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
85 self.writer.write()
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
86
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
87
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
88 if __name__ == "__main__":
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
89
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
90 # parse command line
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
91 description = "Remove Empty Sequences v1.0.2: Remove all the empty sequences in a list. [Category: Personal]"
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
92
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
93 parser = OptionParser(description = description)
31
0ab839023fe4 Uploaded
m-zytnicki
parents: 18
diff changeset
94 parser.add_option("-i", "--input", dest="inputFileName", action="store", type="string", help="input file [compulsory] [format: file in sequence format given by -f]")
0ab839023fe4 Uploaded
m-zytnicki
parents: 18
diff changeset
95 parser.add_option("-f", "--format", dest="format", action="store", type="string", help="format of the input file [compulsory] [format: sequence file format]")
0ab839023fe4 Uploaded
m-zytnicki
parents: 18
diff changeset
96 parser.add_option("-j", "--input2", dest="inputFileName2", action="store", type="string", help="input file 2 (in case of pair end reads) [format: file in sequence format given by -f] [default: None]")
0ab839023fe4 Uploaded
m-zytnicki
parents: 18
diff changeset
97 parser.add_option("-o", "--output", dest="outputFileName", action="store", default=None, type="string", help="output file [compulsory] [format: output file in format given by -f]")
0ab839023fe4 Uploaded
m-zytnicki
parents: 18
diff changeset
98 parser.add_option("-p", "--output2", dest="outputFileName2", action="store", default=None, type="string", help="output file 2 (in case of pair end reads) [format: output file in sequence format given by -f] [default: None]")
0ab839023fe4 Uploaded
m-zytnicki
parents: 18
diff changeset
99 parser.add_option("-v", "--verbosity", dest="verbosity", action="store", default=1, type="int", help="trace level [format: int] [default: 1]")
0ab839023fe4 Uploaded
m-zytnicki
parents: 18
diff changeset
100 parser.add_option("-l", "--log", dest="log", action="store_true", default=False, help="write a log file [format: bool] [default: false]")
6
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
101 (options, args) = parser.parse_args()
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
102
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
103 if options.log:
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
104 logHandle = open("%s.log" % options.outputFileName, "w")
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
105
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
106 remover = EmptySequenceRemover(options.verbosity)
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
107 remover.setInputFileName(options.inputFileName, options.format)
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
108 remover.setOutputFileName(options.outputFileName)
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
109 remover.parse()
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
110 removedNames = remover.removedNames
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
111 if options.log:
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
112 for name in removedNames:
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
113 logHandle.write("Removed '%s' in %s\n" % (name, options.inputFileName))
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
114 nbSequences = remover.parser.getNbSequences()
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
115
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
116 newRemovedNames = {}
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
117 if options.inputFileName2 != None:
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
118 remover = EmptySequenceRemover(options.verbosity)
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
119 remover.setInputFileName(options.inputFileName2, options.format)
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
120 remover.setOutputFileName(options.outputFileName2)
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
121 remover.forbiddenNames = removedNames
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
122 remover.parse()
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
123 newRemovedNames = remover.removedNames
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
124 if options.log:
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
125 for name in newRemovedNames:
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
126 logHandle.write("Removed '%s' in %s\n" % (name, options.inputFileName2))
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
127
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
128 remover = EmptySequenceRemover(options.verbosity)
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
129 remover.setInputFileName(options.inputFileName, options.format)
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
130 remover.setOutputFileName(options.outputFileName)
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
131 remover.forbiddenNames = newRemovedNames
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
132 remover.parse()
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
133
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
134 nbRemoved = len(removedNames.keys()) + len(newRemovedNames.keys())
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
135 print "%d over %d sequences are empty (%.2f%%)." % (nbRemoved, nbSequences, float(nbRemoved) / nbSequences * 100)