Mercurial > repos > kevyin > homer
comparison makeTagDirectory.py @ 23:71e1c2e46752 draft
Uploaded
| author | kevyin |
|---|---|
| date | Wed, 19 Dec 2012 20:21:06 -0500 |
| parents | 74c1fc7bb164 |
| children |
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| 22:a6d9f6e5840f | 23:71e1c2e46752 |
|---|---|
| 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 |