|
18
|
1 #! /usr/bin/env python
|
|
|
2
|
|
|
3 import os
|
|
|
4 import sys
|
|
|
5 import getopt
|
|
|
6 from commons.core.checker.CheckerException import CheckerException
|
|
|
7
|
|
|
8 SMART_PATH = "%s/SMART" % os.environ["REPET_PATH"]
|
|
|
9
|
|
|
10 class WrappGetLetterDistribution(object):
|
|
|
11
|
|
|
12 def __init__(self):
|
|
|
13 self._inputFileName = ""
|
|
|
14 self._inputFileFormat = ""
|
|
|
15 self._outputFileName = "tmpOutputFile"
|
|
|
16 self._csv = False
|
|
|
17
|
|
|
18 def help( self ):
|
|
|
19 print
|
|
|
20 print "usage: %s [ options ]" % ( sys.argv[0] )
|
|
|
21 print "options:"
|
|
|
22 print " -h: this help"
|
|
|
23 print " -i: input file"
|
|
|
24 print " -f: 'fasta' or 'fastq'"
|
|
|
25 print " -c: CSV output file"
|
|
|
26 print " -a: first PNG output file"
|
|
|
27 print " -b: second PNG output file"
|
|
|
28 print
|
|
|
29 print "Exemple:"
|
|
|
30 print
|
|
|
31 print "1:\n\tpython WrappGetLetterDistribution.py -i inputFile.fasta -f fasta -c outputFile1.csv -a outputFile2.png -b outputFile3.png"
|
|
|
32 print
|
|
|
33 print "2:\n\tpython WrappGetLetterDistribution.py -i inputFile.fastq -f fastq -c outputFile1.csv -a outputFile2.png -b outputFile3.png"
|
|
|
34 print
|
|
|
35 print
|
|
|
36
|
|
|
37
|
|
|
38 def setAttributesFromCommandLine(self):
|
|
|
39 try:
|
|
|
40 opts, args = getopt.getopt( sys.argv[1:], "hi:f:a:b:c:" )
|
|
|
41 except getopt.GetoptError, err:
|
|
|
42 print str(err); sys.exit(1)
|
|
|
43 for o, a in opts:
|
|
|
44 if o == "-h":
|
|
|
45 self.help()
|
|
|
46 sys.exit(0)
|
|
|
47 if o == "-i":
|
|
|
48 self._inputFileName = a
|
|
|
49 elif o == "-f":
|
|
|
50 self._inputFileFormat = a
|
|
|
51 elif o == "-c":
|
|
|
52 self._outputFileNameCSV = a
|
|
|
53 self._csv = True
|
|
|
54 elif o == "-a":
|
|
|
55 self._outputFileNamePNG = a
|
|
|
56 elif o == "-b":
|
|
|
57 self._outputFileNamePerNtPNG = a
|
|
|
58
|
|
|
59 def checkAttributes(self):
|
|
|
60 lMsg = []
|
|
|
61 if self._inputFileName == "" and not os.path.exists(self._inputFileName):
|
|
|
62 lMsg.append("ERROR: This input file doesn't exist!")
|
|
|
63 if self._inputFileFormat == "":
|
|
|
64 lMsg.append("ERROR: No input file format specified in option!")
|
|
|
65 if self._outputFileNamePNG == "":
|
|
|
66 lMsg.append("ERROR: No output file.png specified in option!")
|
|
|
67 if self._outputFileNamePerNtPNG == "":
|
|
|
68 lMsg.append("ERROR: No output filePerNt.png specified in option!")
|
|
|
69 if self._outputFileNameCSV == "" and self._csv == True :
|
|
|
70 lMsg.append("ERROR: No output file.csv specified in option!")
|
|
|
71
|
|
|
72 print ">>> lMsg " + str(lMsg)
|
|
|
73 if lMsg != []:
|
|
|
74 exp = CheckerException()
|
|
|
75 exp.setMessages(lMsg)
|
|
|
76 raise (exp)
|
|
|
77
|
|
|
78 def _cleanWorkingDir(self, cDir):
|
|
|
79 os.system("rm %s/tmpData* %s/tmpScript*" % (cDir, cDir))
|
|
|
80
|
|
|
81 def wrapp(self):
|
|
|
82 self.checkAttributes()
|
|
|
83 cDir = os.getcwd()
|
|
|
84
|
|
|
85 if self._csv == True:
|
|
|
86 os.system("python %s/Java/Python/getLetterDistribution.py -i %s -f %s -o %s/%s -c" % (SMART_PATH, self._inputFileName, self._inputFileFormat, cDir, self._outputFileName))
|
|
|
87 os.system("mv %s/%s.csv %s" % (cDir, self._outputFileName, self._outputFileNameCSV))
|
|
|
88 os.system("mv %s/%s.png %s" % (cDir, self._outputFileName, self._outputFileNamePNG))
|
|
|
89 os.system("mv %s/%sPerNt.png %s" % (cDir, self._outputFileName, self._outputFileNamePerNtPNG))
|
|
|
90
|
|
|
91 self._cleanWorkingDir(cDir)
|
|
|
92
|
|
|
93 if __name__ == '__main__':
|
|
|
94 launcher = WrappGetLetterDistribution()
|
|
|
95 launcher.setAttributesFromCommandLine()
|
|
|
96 launcher.wrapp()
|
|
|
97
|
