Mercurial > repos > fubar > fastqc_dev
comparison FastQC/rgFastQC.py @ 3:71899f689406 draft
Uploaded
author | fubar |
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date | Tue, 04 Jun 2013 00:12:12 -0400 |
parents | 57f890a5fa73 |
children | 4d6d32306a4a |
comparison
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2:9995fd1f8daa | 3:71899f689406 |
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35 def __init__(self,opts=None): | 35 def __init__(self,opts=None): |
36 assert opts <> None | 36 assert opts <> None |
37 self.opts = opts | 37 self.opts = opts |
38 | 38 |
39 def getFileString(fpath, outpath): | 39 def getFileString(fpath, outpath): |
40 """ | 40 """ |
41 format a nice file size string | 41 format a nice file size string |
42 """ | 42 """ |
43 size = '' | 43 size = '' |
44 fp = os.path.join(outpath, fpath) | 44 fp = os.path.join(outpath, fpath) |
45 s = fpath | 45 s = fpath |
46 if os.path.isfile(fp): | 46 if os.path.isfile(fp): |
47 n = float(os.path.getsize(fp)) | 47 n = float(os.path.getsize(fp)) |
48 if n > 2**20: | 48 if n > 2**20: |
49 size = ' (%1.1f MB)' % (n/2**20) | 49 size = ' (%1.1f MB)' % (n/2**20) |
50 elif n > 2**10: | 50 elif n > 2**10: |
51 size = ' (%1.1f KB)' % (n/2**10) | 51 size = ' (%1.1f KB)' % (n/2**10) |
158 res = ['<div class="module"><h2>Files created by FastQC</h2><table cellspacing="2" cellpadding="2">\n'] | 158 res = ['<div class="module"><h2>Files created by FastQC</h2><table cellspacing="2" cellpadding="2">\n'] |
159 flist.sort() | 159 flist.sort() |
160 for i,f in enumerate(flist): | 160 for i,f in enumerate(flist): |
161 if not(os.path.isdir(f)): | 161 if not(os.path.isdir(f)): |
162 fn = os.path.split(f)[-1] | 162 fn = os.path.split(f)[-1] |
163 res.append('<tr><td><a href="%s">%s</a></td></tr>\n' % (fn,getFileString(fn, self.opts.outputdir))) | 163 res.append('<tr><td><a href="%s">%s</a></td></tr>\n' % (fn,self.getFileString(fn, self.opts.outputdir))) |
164 res.append('</table>\n') | 164 res.append('</table>\n') |
165 res.append('<a href="http://www.bioinformatics.bbsrc.ac.uk/projects/fastqc/">FastQC documentation and full attribution is here</a><br/><hr/>\n') | 165 res.append('<a href="http://www.bioinformatics.bbsrc.ac.uk/projects/fastqc/">FastQC documentation and full attribution is here</a><br/><hr/>\n') |
166 res.append('FastQC was run by Galaxy using the rgenetics rgFastQC wrapper - see http://rgenetics.org for details and licensing\n</div>') | 166 res.append('FastQC was run by Galaxy using the rgenetics rgFastQC wrapper - see http://rgenetics.org for details and licensing\n</div>') |
167 res.append(footer) | 167 res.append(footer) |
168 fixed = rep[:bodyindex] + res + rep[bodyindex:] | 168 fixed = rep[:bodyindex] + res + rep[bodyindex:] |