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comparison smart_toolShed/SMART/Java/Python/removeEmptySequences.py @ 0:e0f8dcca02ed

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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
author yufei-luo
date Thu, 17 Jan 2013 10:52:14 -0500
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-1:000000000000 0:e0f8dcca02ed
1 #! /usr/bin/env python
2 #
3 # Copyright INRA-URGI 2009-2010
4 #
5 # This software is governed by the CeCILL license under French law and
6 # abiding by the rules of distribution of free software. You can use,
7 # modify and/ or redistribute the software under the terms of the CeCILL
8 # license as circulated by CEA, CNRS and INRIA at the following URL
9 # "http://www.cecill.info".
10 #
11 # As a counterpart to the access to the source code and rights to copy,
12 # modify and redistribute granted by the license, users are provided only
13 # with a limited warranty and the software's author, the holder of the
14 # economic rights, and the successive licensors have only limited
15 # liability.
16 #
17 # In this respect, the user's attention is drawn to the risks associated
18 # with loading, using, modifying and/or developing or reproducing the
19 # software by the user in light of its specific status of free software,
20 # that may mean that it is complicated to manipulate, and that also
21 # therefore means that it is reserved for developers and experienced
22 # professionals having in-depth computer knowledge. Users are therefore
23 # encouraged to load and test the software's suitability as regards their
24 # requirements in conditions enabling the security of their systems and/or
25 # data to be ensured and, more generally, to use and operate it in the
26 # same conditions as regards security.
27 #
28 # The fact that you are presently reading this means that you have had
29 # knowledge of the CeCILL license and that you accept its terms.
30 #
31 """
32 Remove empty sequences from a FASTA or FASTQ file
33 """
34
35 import os, random
36 from optparse import OptionParser
37 from commons.core.parsing.FastaParser import *
38 from commons.core.parsing.FastqParser import *
39 from commons.core.writer.FastaWriter import *
40 from commons.core.writer.FastqWriter import *
41 from SMART.Java.Python.misc.Progress import *
42
43
44 class EmptySequenceRemover(object):
45
46 def __init__(self, verbosity = 1):
47 self.verbosity = verbosity
48 self.inputFileName = None
49 self.parser = None
50 self.format = None
51 self.writer = None
52 self.forbiddenNames = {}
53 self.removedNames = {}
54
55
56 def setInputFileName(self, fileName, format):
57 self.inputFileName = fileName
58 self.format = format
59 if options.format == "fasta":
60 self.parser = FastaParser(self.inputFileName, self.verbosity)
61 elif options.format == "fastq":
62 self.parser = FastqParser(self.inputFileName, self.verbosity)
63 else:
64 sys.exit("Do not understand '%s' file format." % (self.format))
65
66
67 def setOutputFileName(self, fileName):
68 if options.format == "fasta":
69 self.writer = FastaWriter("%s.mfa" % (fileName), self.verbosity)
70 elif options.format == "fastq":
71 self.writer = FastqWriter("%s.mfq" % (fileName), self.verbosity)
72
73
74 def parse(self):
75 progress = Progress(self.parser.getNbSequences(), "Reading sequences in %s" % (options.inputFileName), options.verbosity)
76 for sequence in self.parser.getIterator():
77 name = sequence.name.split("/")[0]
78 if name not in self.forbiddenNames:
79 if sequence.sequence == "":
80 self.removedNames[name] = 1
81 else:
82 self.writer.addSequence(sequence)
83 progress.inc()
84 progress.done()
85 self.writer.write()
86
87
88 if __name__ == "__main__":
89
90 # parse command line
91 description = "Remove Empty Sequences v1.0.2: Remove all the empty sequences in a list. [Category: Personal]"
92
93 parser = OptionParser(description = description)
94 parser.add_option("-i", "--input", dest="inputFileName", action="store", type="string", help="input file [compulsory] [format: file in sequence format given by -f]")
95 parser.add_option("-f", "--format", dest="format", action="store", type="string", help="format of the input file [compulsory] [format: sequence file format]")
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]")
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]")
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]")
99 parser.add_option("-v", "--verbosity", dest="verbosity", action="store", default=1, type="int", help="trace level [format: int] [default: 1]")
100 parser.add_option("-l", "--log", dest="log", action="store_true", default=False, help="write a log file [format: bool] [default: false]")
101 (options, args) = parser.parse_args()
102
103 if options.log:
104 logHandle = open("%s.log" % options.outputFileName, "w")
105
106 remover = EmptySequenceRemover(options.verbosity)
107 remover.setInputFileName(options.inputFileName, options.format)
108 remover.setOutputFileName(options.outputFileName)
109 remover.parse()
110 removedNames = remover.removedNames
111 if options.log:
112 for name in removedNames:
113 logHandle.write("Removed '%s' in %s\n" % (name, options.inputFileName))
114 nbSequences = remover.parser.getNbSequences()
115
116 newRemovedNames = {}
117 if options.inputFileName2 != None:
118 remover = EmptySequenceRemover(options.verbosity)
119 remover.setInputFileName(options.inputFileName2, options.format)
120 remover.setOutputFileName(options.outputFileName2)
121 remover.forbiddenNames = removedNames
122 remover.parse()
123 newRemovedNames = remover.removedNames
124 if options.log:
125 for name in newRemovedNames:
126 logHandle.write("Removed '%s' in %s\n" % (name, options.inputFileName2))
127
128 remover = EmptySequenceRemover(options.verbosity)
129 remover.setInputFileName(options.inputFileName, options.format)
130 remover.setOutputFileName(options.outputFileName)
131 remover.forbiddenNames = newRemovedNames
132 remover.parse()
133
134 nbRemoved = len(removedNames.keys()) + len(newRemovedNames.keys())
135 print "%d over %d sequences are empty (%.2f%%)." % (nbRemoved, nbSequences, float(nbRemoved) / nbSequences * 100)