Mercurial > repos > yufei-luo > s_mart

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

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Uploaded
author m-zytnicki
date Tue, 30 Apr 2013 14:33:21 -0400
parents 94ab73e8a190
children
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30:5677346472b5 31:0ab839023fe4
64 sys.exit("Do not understand '%s' file format." % (self.format)) 64 sys.exit("Do not understand '%s' file format." % (self.format))
65 65
66 66
67 def setOutputFileName(self, fileName): 67 def setOutputFileName(self, fileName):
68 if options.format == "fasta": 68 if options.format == "fasta":
69 self.writer = FastaWriter(fileName, self.verbosity) 69 self.writer = FastaWriter("%s.mfa" % (fileName), self.verbosity)
70 elif options.format == "fastq": 70 elif options.format == "fastq":
71 self.writer = FastqWriter(fileName, self.verbosity) 71 self.writer = FastqWriter("%s.mfq" % (fileName), self.verbosity)
72 72
73 73
74 def parse(self): 74 def parse(self):
75 progress = Progress(self.parser.getNbSequences(), "Reading sequences in %s" % (options.inputFileName), options.verbosity) 75 progress = Progress(self.parser.getNbSequences(), "Reading sequences in %s" % (options.inputFileName), options.verbosity)
76 for sequence in self.parser.getIterator(): 76 for sequence in self.parser.getIterator():
89 89
90 # parse command line 90 # parse command line
91 description = "Remove Empty Sequences v1.0.2: Remove all the empty sequences in a list. [Category: Personal]" 91 description = "Remove Empty Sequences v1.0.2: Remove all the empty sequences in a list. [Category: Personal]"
92 92
93 parser = OptionParser(description = description) 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]") 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]") 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]") 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]") 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]") 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]") 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]") 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() 101 (options, args) = parser.parse_args()
102 102
103 if options.log: 103 if options.log:
104 logHandle = open("%s.log" % options.outputFileName, "w") 104 logHandle = open("%s.log" % options.outputFileName, "w")
105 105