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comparison FastQC/rgFastQC.py @ 1:91cb2603b56c draft

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Added getFileSize from rgutils to remove bogus dependency
author fubar
date Mon, 03 Jun 2013 21:34:20 -0400
parents 42251cbdeeac
children
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0:42251cbdeeac 1:91cb2603b56c
22 import sys 22 import sys
23 import subprocess 23 import subprocess
24 import optparse 24 import optparse
25 import shutil 25 import shutil
26 import tempfile 26 import tempfile
27 from rgutils import getFileString
28 import zipfile 27 import zipfile
29 import gzip 28 import gzip
30 29
31 class FastQC(): 30 class FastQC():
32 """wrapper 31 """wrapper
35 34
36 def __init__(self,opts=None): 35 def __init__(self,opts=None):
37 assert opts <> None 36 assert opts <> None
38 self.opts = opts 37 self.opts = opts
39 38
40 39 def getFileString(fpath, outpath):
40 """
41 format a nice file size string
42 """
43 size = ''
44 fp = os.path.join(outpath, fpath)
45 s = fpath
46 if os.path.isfile(fp):
47 n = float(os.path.getsize(fp))
48 if n > 2**20:
49 size = ' (%1.1f MB)' % (n/2**20)
50 elif n > 2**10:
51 size = ' (%1.1f KB)' % (n/2**10)
52 elif n > 0:
53 size = ' (%d B)' % (int(n))
54 s = '%s %s' % (fpath, size)
55 return s
56
41 def run_fastqc(self): 57 def run_fastqc(self):
42 """ 58 """
43 In batch mode fastqc behaves not very nicely - will write to a new folder in 59 In batch mode fastqc behaves not very nicely - will write to a new folder in
44 the same place as the infile called [infilebasename]_fastqc 60 the same place as the infile called [infilebasename]_fastqc
45 rlazarus@omics:/data/galaxy/test$ ls FC041_1_sequence_fastqc 61 rlazarus@omics:/data/galaxy/test$ ls FC041_1_sequence_fastqc