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comparison FastQC/rgFastQC.py @ 3:7e6db50c9d47 draft

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Uploaded
author fubar
date Tue, 04 Jun 2013 22:42:51 -0400
parents 68b330b860ee
children
comparison
equal deleted inserted replaced
2:40b80f54e1a7 3:7e6db50c9d47
25 import shutil 25 import shutil
26 import tempfile 26 import tempfile
27 import zipfile 27 import zipfile
28 import gzip 28 import gzip
29 29
30 def pathfind(program):
31 """ toolshed path munging isn't so try to work around june 5 2013
32 """
33 def is_exe(fpath):
34 return os.path.isfile(fpath) and os.access(fpath, os.X_OK)
35
36 fpath, fname = os.path.split(program)
37 if fpath:
38 if is_exe(program):
39 return program
40 else:
41 for path in os.environ["PATH"].split(os.pathsep):
42 path = path.strip('"')
43 exe_file = os.path.join(path, program)
44 if is_exe(exe_file):
45 return exe_file
46
47 return None
48
30 class FastQC(): 49 class FastQC():
31 """wrapper 50 """wrapper
32 """ 51 """
33 52
34 53
35 def __init__(self,opts=None): 54 def __init__(self,opts=None):
36 assert opts <> None 55 assert opts <> None
37 self.opts = opts 56 self.opts = opts
57 fastqcexe = pathfind(opts.executable)
58 assert (fastqcexe != None),'##rgFastQC.py error - cannot find passed fastqc executable %s in path %s' % (opts.executable,os.environ['PATH'])
59 self.fastqcexe = fastqcexe
38 60
39 def getFileString(self, fpath, outpath): 61 def getFileString(self, fpath, outpath):
40 """ 62 """
41 format a nice file size string 63 format a nice file size string
42 """ 64 """
66 """ 88 """
67 serr = '' 89 serr = ''
68 dummy,tlog = tempfile.mkstemp(prefix='rgFastQC',suffix=".log",dir=self.opts.outputdir) 90 dummy,tlog = tempfile.mkstemp(prefix='rgFastQC',suffix=".log",dir=self.opts.outputdir)
69 sout = open(tlog, 'w') 91 sout = open(tlog, 'w')
70 fastq = os.path.basename(self.opts.input) 92 fastq = os.path.basename(self.opts.input)
71 cl = [self.opts.executable,'--outdir=%s' % self.opts.outputdir] 93 cl = [self.fastqcexe,'--outdir=%s' % self.opts.outputdir]
72 if self.opts.informat in ['sam','bam']: 94 if self.opts.informat in ['sam','bam']:
73 cl.append('--f=%s' % self.opts.informat) 95 cl.append('--f=%s' % self.opts.informat)
74 if self.opts.contaminants <> None : 96 if self.opts.contaminants <> None :
75 cl.append('--contaminants=%s' % self.opts.contaminants) 97 cl.append('--contaminants=%s' % self.opts.contaminants)
76 # patch suggested by bwlang https://bitbucket.org/galaxy/galaxy-central/pull-request/30 98 # patch suggested by bwlang https://bitbucket.org/galaxy/galaxy-central/pull-request/30
182 sauce = os.path.join(adir,f) 204 sauce = os.path.join(adir,f)
183 dest = os.path.join(self.opts.outputdir,f) 205 dest = os.path.join(self.opts.outputdir,f)
184 shutil.move(sauce,dest) 206 shutil.move(sauce,dest)
185 os.rmdir(adir) 207 os.rmdir(adir)
186 208
187
188 209
189 if __name__ == '__main__': 210 if __name__ == '__main__':
190 op = optparse.OptionParser() 211 op = optparse.OptionParser()
191 op.add_option('-i', '--input', default=None) 212 op.add_option('-i', '--input', default=None)
192 op.add_option('-j', '--inputfilename', default=None) 213 op.add_option('-j', '--inputfilename', default=None)
196 op.add_option('-n', '--namejob', default='rgFastQC') 217 op.add_option('-n', '--namejob', default='rgFastQC')
197 op.add_option('-c', '--contaminants', default=None) 218 op.add_option('-c', '--contaminants', default=None)
198 op.add_option('-e', '--executable', default='fastqc') 219 op.add_option('-e', '--executable', default='fastqc')
199 opts, args = op.parse_args() 220 opts, args = op.parse_args()
200 assert opts.input <> None 221 assert opts.input <> None
201 assert os.path.isfile(opts.executable),'##rgFastQC.py error - cannot find executable %s' % opts.executable
202 if not os.path.exists(opts.outputdir): 222 if not os.path.exists(opts.outputdir):
203 os.makedirs(opts.outputdir) 223 os.makedirs(opts.outputdir)
204 f = FastQC(opts) 224 f = FastQC(opts)
205 html,retval,serr = f.run_fastqc() 225 html,retval,serr = f.run_fastqc()
206 f = open(opts.htmloutput, 'w') 226 f = open(opts.htmloutput, 'w')