|
9
|
1 """
|
|
|
2 # May 2013 ross added check for bogus gz extension - fastqc gets confused
|
|
|
3 # added sanitizer for user supplied name
|
|
|
4 # removed shell and make cl a sequence for Popen call
|
|
|
5 # ross lazarus August 10 2012 in response to anon insecurity report
|
|
|
6 wrapper for fastqc
|
|
|
7
|
|
|
8 called as
|
|
|
9 <command interpreter="python">
|
|
|
10 rgFastqc.py -i $input_file -d $html_file.files_path -o $html_file -n "$out_prefix"
|
|
|
11 </command>
|
|
|
12
|
|
|
13
|
|
|
14
|
|
|
15 Current release seems overly intolerant of sam/bam header strangeness
|
|
|
16 Author notified...
|
|
|
17
|
|
|
18
|
|
|
19 """
|
|
|
20 import re
|
|
|
21 import os
|
|
|
22 import sys
|
|
|
23 import subprocess
|
|
|
24 import optparse
|
|
|
25 import shutil
|
|
|
26 import tempfile
|
|
|
27 import zipfile
|
|
|
28 import gzip
|
|
|
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
|
|
|
49 class FastQC():
|
|
|
50 """wrapper
|
|
|
51 """
|
|
|
52
|
|
|
53
|
|
|
54 def __init__(self,opts=None):
|
|
|
55 assert opts <> None
|
|
|
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
|
|
|
60
|
|
|
61 def getFileString(self, fpath, outpath):
|
|
|
62 """
|
|
|
63 format a nice file size string
|
|
|
64 """
|
|
|
65 size = ''
|
|
|
66 fp = os.path.join(outpath, fpath)
|
|
|
67 s = fpath
|
|
|
68 if os.path.isfile(fp):
|
|
|
69 n = float(os.path.getsize(fp))
|
|
|
70 if n > 2**20:
|
|
|
71 size = ' (%1.1f MB)' % (n/2**20)
|
|
|
72 elif n > 2**10:
|
|
|
73 size = ' (%1.1f KB)' % (n/2**10)
|
|
|
74 elif n > 0:
|
|
|
75 size = ' (%d B)' % (int(n))
|
|
|
76 s = '%s %s' % (fpath, size)
|
|
|
77 return s
|
|
|
78
|
|
|
79 def run_fastqc(self):
|
|
|
80 """
|
|
|
81 In batch mode fastqc behaves not very nicely - will write to a new folder in
|
|
|
82 the same place as the infile called [infilebasename]_fastqc
|
|
|
83 rlazarus@omics:/data/galaxy/test$ ls FC041_1_sequence_fastqc
|
|
|
84 duplication_levels.png fastqc_icon.png per_base_n_content.png per_sequence_gc_content.png summary.txt
|
|
|
85 error.png fastqc_report.html per_base_quality.png per_sequence_quality.png tick.png
|
|
|
86 fastqc_data.txt per_base_gc_content.png per_base_sequence_content.png sequence_length_distribution.png warning.png
|
|
|
87
|
|
|
88 """
|
|
|
89 serr = ''
|
|
|
90 dummy,tlog = tempfile.mkstemp(prefix='rgFastQC',suffix=".log",dir=self.opts.outputdir)
|
|
|
91 sout = open(tlog, 'w')
|
|
|
92 fastq = os.path.basename(self.opts.input)
|
|
|
93 cl = [self.fastqcexe,'--outdir=%s' % self.opts.outputdir]
|
|
|
94 if self.opts.informat in ['sam','bam']:
|
|
|
95 cl.append('--f=%s' % self.opts.informat)
|
|
|
96 if self.opts.contaminants <> None :
|
|
|
97 cl.append('--contaminants=%s' % self.opts.contaminants)
|
|
|
98 # patch suggested by bwlang https://bitbucket.org/galaxy/galaxy-central/pull-request/30
|
|
|
99 # use a symlink in a temporary directory so that the FastQC report reflects the history input file name
|
|
|
100 # note this exposes a bug in the EBI_SRA download tool which leaves bogus .gz extensions on uncompressed files
|
|
|
101 # which fastqc helpfully tries to uncompress again - hilarity ensues.
|
|
|
102 # patched may 29 2013 until this is fixed properly
|
|
|
103 infname = self.opts.inputfilename
|
|
|
104 linf = infname.lower()
|
|
|
105 trimext = False
|
|
|
106 if ( linf.endswith('.gz') or linf.endswith('.gzip') ):
|
|
|
107 f = gzip.open(self.opts.input)
|
|
|
108 try:
|
|
|
109 testrow = f.readline()
|
|
|
110 except:
|
|
|
111 trimext = True
|
|
|
112 f.close()
|
|
|
113 elif linf.endswith('bz2'):
|
|
|
114 f = bz2.open(self.opts.input,'rb')
|
|
|
115 try:
|
|
|
116 f.readline()
|
|
|
117 except:
|
|
|
118 trimext = True
|
|
|
119 f.close()
|
|
|
120 elif linf.endswith('.zip'):
|
|
|
121 if not zipfile.is_zipfile(self.opts.input):
|
|
|
122 trimext = True
|
|
|
123 if trimext:
|
|
|
124 infname = os.path.splitext(infname)[0]
|
|
|
125 fastqinfilename = re.sub(ur'[^a-zA-Z0-9_\-\.]', '_', os.path.basename(infname))
|
|
|
126 link_name = os.path.join(self.opts.outputdir, fastqinfilename)
|
|
|
127 os.symlink(self.opts.input, link_name)
|
|
|
128 cl.append(link_name)
|
|
|
129 sout.write('# FastQC cl = %s\n' % ' '.join(cl))
|
|
|
130 sout.flush()
|
|
|
131 p = subprocess.Popen(cl, shell=False, stderr=sout, stdout=sout, cwd=self.opts.outputdir)
|
|
|
132 retval = p.wait()
|
|
|
133 sout.close()
|
|
|
134 runlog = open(tlog,'r').readlines()
|
|
|
135 os.unlink(link_name)
|
|
|
136 flist = os.listdir(self.opts.outputdir) # fastqc plays games with its output directory name. eesh
|
|
|
137 odpath = None
|
|
|
138 for f in flist:
|
|
|
139 d = os.path.join(self.opts.outputdir,f)
|
|
|
140 if os.path.isdir(d):
|
|
|
141 if d.endswith('_fastqc'):
|
|
|
142 odpath = d
|
|
|
143 hpath = None
|
|
|
144 if odpath <> None:
|
|
|
145 try:
|
|
|
146 hpath = os.path.join(odpath,'fastqc_report.html')
|
|
|
147 rep = open(hpath,'r').readlines() # for our new html file but we need to insert our stuff after the <body> tag
|
|
|
148 except:
|
|
|
149 pass
|
|
|
150 if hpath == None:
|
|
|
151 serr = '\n'.join(runlog)
|
|
|
152 res = ['## odpath=%s: No output found in %s. Output for the run was:<pre>\n' % (odpath,hpath),]
|
|
|
153 res += runlog
|
|
|
154 res += ['</pre>\n',
|
|
|
155 'Please read the above for clues<br/>\n',
|
|
|
156 'If you selected a sam/bam format file, it might not have headers or they may not start with @HD?<br/>\n',
|
|
|
157 'It is also possible that the log shows that fastqc is not installed?<br/>\n',
|
|
|
158 'If that is the case, please tell the relevant Galaxy administrator that it can be snarfed from<br/>\n',
|
|
|
159 'http://www.bioinformatics.bbsrc.ac.uk/projects/fastqc/<br/>\n',]
|
|
|
160 return res,1,serr
|
|
|
161 self.fix_fastqcimages(odpath)
|
|
|
162 flist = os.listdir(self.opts.outputdir) # these have now been fixed
|
|
|
163 excludefiles = ['tick.png','warning.png','fastqc_icon.png','error.png']
|
|
|
164 flist = [x for x in flist if not x in excludefiles]
|
|
|
165 for i in range(len(rep)): # need to fix links to Icons and Image subdirectories in lastest fastqc code - ugh
|
|
|
166 rep[i] = rep[i].replace('Icons/','')
|
|
|
167 rep[i] = rep[i].replace('Images/','')
|
|
|
168 html = self.fix_fastqc(rep,flist,runlog)
|
|
|
169 return html,retval,serr
|
|
|
170
|
|
|
171
|
|
|
172
|
|
|
173 def fix_fastqc(self,rep=[],flist=[],runlog=[]):
|
|
|
174 """ add some of our stuff to the html
|
|
|
175 """
|
|
|
176 bodyindex = len(rep) -1 # hope they don't change this
|
|
|
177 footrow = bodyindex - 1
|
|
|
178 footer = rep[footrow]
|
|
|
179 rep = rep[:footrow] + rep[footrow+1:]
|
|
|
180 res = ['<div class="module"><h2>Files created by FastQC</h2><table cellspacing="2" cellpadding="2">\n']
|
|
|
181 flist.sort()
|
|
|
182 for i,f in enumerate(flist):
|
|
|
183 if not(os.path.isdir(f)):
|
|
|
184 fn = os.path.split(f)[-1]
|
|
|
185 res.append('<tr><td><a href="%s">%s</a></td></tr>\n' % (fn,self.getFileString(fn, self.opts.outputdir)))
|
|
|
186 res.append('</table>\n')
|
|
|
187 res.append('<a href="http://www.bioinformatics.bbsrc.ac.uk/projects/fastqc/">FastQC documentation and full attribution is here</a><br/><hr/>\n')
|
|
|
188 res.append('FastQC was run by Galaxy using the rgenetics rgFastQC wrapper - see http://rgenetics.org for details and licensing\n</div>')
|
|
|
189 res.append(footer)
|
|
|
190 fixed = rep[:bodyindex] + res + rep[bodyindex:]
|
|
|
191 return fixed # with our additions
|
|
|
192
|
|
|
193
|
|
|
194 def fix_fastqcimages(self,odpath):
|
|
|
195 """ Galaxy wants everything in the same files_dir
|
|
|
196 """
|
|
|
197 icpath = os.path.join(odpath,'Icons')
|
|
|
198 impath = os.path.join(odpath,'Images')
|
|
|
199 for adir in [icpath,impath,odpath]:
|
|
|
200 if os.path.exists(adir):
|
|
|
201 flist = os.listdir(adir) # get all files created
|
|
|
202 for f in flist:
|
|
|
203 if not os.path.isdir(os.path.join(adir,f)):
|
|
|
204 sauce = os.path.join(adir,f)
|
|
|
205 dest = os.path.join(self.opts.outputdir,f)
|
|
|
206 shutil.move(sauce,dest)
|
|
|
207 os.rmdir(adir)
|
|
|
208
|
|
|
209
|
|
|
210 if __name__ == '__main__':
|
|
|
211 op = optparse.OptionParser()
|
|
|
212 op.add_option('-i', '--input', default=None)
|
|
|
213 op.add_option('-j', '--inputfilename', default=None)
|
|
|
214 op.add_option('-o', '--htmloutput', default=None)
|
|
|
215 op.add_option('-d', '--outputdir', default="/tmp/shortread")
|
|
|
216 op.add_option('-f', '--informat', default='fastq')
|
|
|
217 op.add_option('-n', '--namejob', default='rgFastQC')
|
|
|
218 op.add_option('-c', '--contaminants', default=None)
|
|
|
219 op.add_option('-e', '--executable', default='fastqc')
|
|
|
220 opts, args = op.parse_args()
|
|
|
221 assert opts.input <> None
|
|
|
222 if not os.path.exists(opts.outputdir):
|
|
|
223 os.makedirs(opts.outputdir)
|
|
|
224 f = FastQC(opts)
|
|
|
225 html,retval,serr = f.run_fastqc()
|
|
|
226 f = open(opts.htmloutput, 'w')
|
|
|
227 f.write(''.join(html))
|
|
|
228 f.close()
|
|
|
229 if retval <> 0:
|
|
|
230 print >> sys.stderr, serr # indicate failure
|
|
|
231
|
|
|
232
|
|
|
233
|
