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