|
4
|
1 """
|
|
|
2
|
|
|
3
|
|
|
4 """
|
|
|
5 import re
|
|
|
6 import os
|
|
|
7 import sys
|
|
|
8 import subprocess
|
|
|
9 import optparse
|
|
|
10 import shutil
|
|
|
11 import tempfile
|
|
|
12
|
|
|
13 def getFileString(fpath, outpath):
|
|
|
14 """
|
|
|
15 format a nice file size string
|
|
|
16 """
|
|
|
17 size = ''
|
|
|
18 fp = os.path.join(outpath, fpath)
|
|
|
19 s = '? ?'
|
|
|
20 if os.path.isfile(fp):
|
|
|
21 n = float(os.path.getsize(fp))
|
|
|
22 if n > 2**20:
|
|
|
23 size = ' (%1.1f MB)' % (n/2**20)
|
|
|
24 elif n > 2**10:
|
|
|
25 size = ' (%1.1f KB)' % (n/2**10)
|
|
|
26 elif n > 0:
|
|
|
27 size = ' (%d B)' % (int(n))
|
|
|
28 s = '%s %s' % (fpath, size)
|
|
|
29 return s
|
|
|
30
|
|
|
31 class makeTagDirectory():
|
|
|
32 """wrapper
|
|
|
33 """
|
|
|
34
|
|
|
35 def __init__(self,opts=None, args=None):
|
|
|
36 self.opts = opts
|
|
|
37 self.args = args
|
|
|
38
|
|
|
39 def run_makeTagDirectory(self):
|
|
|
40 """
|
|
|
41 makeTagDirectory <Output Directory Name> [options] <alignment file1> [alignment file 2]
|
|
|
42
|
|
|
43 """
|
|
|
44 if self.opts.format != "bam":
|
|
|
45 cl = [self.opts.executable] + args + ["-format" , self.opts.format]
|
|
|
46 else:
|
|
|
47 cl = [self.opts.executable] + args
|
|
|
48 print cl
|
|
|
49 p = subprocess.Popen(cl)
|
|
|
50 retval = p.wait()
|
|
|
51
|
|
|
52
|
|
|
53 html = self.gen_html(args[0])
|
|
|
54 #html = self.gen_html()
|
|
|
55 return html,retval
|
|
|
56
|
|
|
57 def gen_html(self, dr=os.getcwd()):
|
|
|
58 flist = os.listdir(dr)
|
|
|
59 print flist
|
|
|
60 """ add a list of all files in the tagdirectory
|
|
|
61 """
|
|
|
62 res = ['<div class="module"><h2>Files created by makeTagDirectory</h2><table cellspacing="2" cellpadding="2">\n']
|
|
|
63
|
|
|
64 flist.sort()
|
|
|
65 for i,f in enumerate(flist):
|
|
|
66 if not(os.path.isdir(f)):
|
|
|
67 fn = os.path.split(f)[-1]
|
|
|
68 res.append('<tr><td><a href="%s">%s</a></td></tr>\n' % (fn,getFileString(fn, dr)))
|
|
|
69
|
|
|
70 res.append('</table>\n')
|
|
|
71
|
|
|
72 return res
|
|
|
73
|
|
|
74 if __name__ == '__main__':
|
|
|
75 op = optparse.OptionParser()
|
|
|
76 op.add_option('-e', '--executable', default='makeTagDirectory')
|
|
|
77 op.add_option('-o', '--htmloutput', default=None)
|
|
|
78 op.add_option('-f', '--format', default="sam")
|
|
|
79 opts, args = op.parse_args()
|
|
|
80 #assert os.path.isfile(opts.executable),'## makeTagDirectory.py error - cannot find executable %s' % opts.executable
|
|
|
81
|
|
|
82 #if not os.path.exists(opts.outputdir):
|
|
|
83 #os.makedirs(opts.outputdir)
|
|
|
84 f = makeTagDirectory(opts, args)
|
|
|
85
|
|
|
86 html,retval = f.run_makeTagDirectory()
|
|
|
87 f = open(opts.htmloutput, 'w')
|
|
|
88 f.write(''.join(html))
|
|
|
89 f.close()
|
|
|
90 if retval <> 0:
|
|
|
91 print >> sys.stderr, serr # indicate failure
|
|
|
92
|
|
|
93
|
|
|
94
|
