1 | # converter for ldreduced rgenetics datatype |
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2 | # used for grr and eigenstrat - shellfish if we get around to it |
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3 | # |
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4 | |
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5 | import os,sys,tempfile,subprocess,time |
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6 | |
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7 | from galaxy import eggs |
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8 | |
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9 | prog="pbed_ldreduced_converter.py" |
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10 | |
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11 | galhtmlprefix = """<?xml version="1.0" encoding="utf-8" ?> |
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12 | <!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN" "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd"> |
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13 | <html xmlns="http://www.w3.org/1999/xhtml" xml:lang="en" lang="en"> |
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14 | <head> |
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15 | <meta http-equiv="Content-Type" content="text/html; charset=utf-8" /> |
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16 | <meta name="generator" content="Galaxy %s tool output - see http://g2.trac.bx.psu.edu/" /> |
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17 | <title></title> |
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18 | <link rel="stylesheet" href="/static/style/base.css" type="text/css" /> |
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19 | </head> |
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20 | <body> |
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21 | <div class="document"> |
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22 | """ |
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23 | |
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24 | plinke = 'plink' |
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25 | |
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26 | |
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27 | def timenow(): |
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28 | """return current time as a string |
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29 | """ |
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30 | return time.strftime('%d/%m/%Y %H:%M:%S', time.localtime(time.time())) |
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31 | |
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32 | |
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33 | def pruneLD(plinktasks=[],cd='./',vclbase = []): |
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34 | """ |
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35 | """ |
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36 | fplog,plog = tempfile.mkstemp() |
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37 | alog = [] |
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38 | alog.append('## Rgenetics: http://rgenetics.org Galaxy Tools rgQC.py Plink pruneLD runner\n') |
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39 | for task in plinktasks: # each is a list |
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40 | vcl = vclbase + task |
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41 | sto = file(plog,'w') |
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42 | x = subprocess.Popen(' '.join(vcl),shell=True,stdout=sto,stderr=sto,cwd=cd) |
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43 | retval = x.wait() |
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44 | sto.close() |
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45 | try: |
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46 | lplog = file(plog,'r').readlines() |
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47 | lplog = [x for x in lplog if x.find('Pruning SNP') == -1] |
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48 | alog += lplog |
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49 | alog.append('\n') |
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50 | os.unlink(plog) # no longer needed |
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51 | except: |
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52 | alog.append('### %s Strange - no std out from plink when running command line\n%s\n' % (timenow(),' '.join(vcl))) |
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53 | return alog |
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54 | |
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55 | |
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56 | def makeLDreduced(basename,infpath=None,outfpath=None,plinke='plink',forcerebuild=False,returnFname=False, |
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57 | winsize="60", winmove="40", r2thresh="0.1" ): |
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58 | """ not there so make and leave in output dir for post job hook to copy back into input extra files path for next time |
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59 | """ |
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60 | ldr = basename # we store ld reduced and thinned data |
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61 | ldreduced = os.path.join(outfpath,ldr) # note where this is going |
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62 | outbase = os.path.join(outfpath,basename) |
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63 | inbase = os.path.join(infpath) |
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64 | loglines = [] |
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65 | ldbedname = '%s.bed' % ldreduced |
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66 | bedname = '%s.bed' % basename |
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67 | ldbedfn = os.path.join(infpath,ldbedname) |
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68 | bedfn = os.path.join(infpath,bedname) |
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69 | bmap = os.path.join(infpath,'%s.bim' % basename) |
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70 | plinktasks = [] |
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71 | vclbase = [plinke,'--noweb'] |
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72 | plinktasks += [['--bfile',inbase,'--indep-pairwise %s %s %s' % (winsize,winmove,r2thresh),'--out %s' % outbase], |
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73 | ['--bfile',inbase,'--extract %s.prune.in --make-bed --out %s' % (outbase, outbase)]] |
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74 | vclbase = [plinke,'--noweb'] |
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75 | loglines = pruneLD(plinktasks=plinktasks,cd=outfpath,vclbase = vclbase) |
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76 | |
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77 | def main(): |
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78 | """ |
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79 | need to work with rgenetics composite datatypes |
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80 | so in and out are html files with data in extrafiles path |
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81 | <command interpreter="python"> |
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82 | pbed_ldreduced_converter.py '$input1.extra_files_path/$input1.metadata.base_name' '$winsize' '$winmove' '$r2thresh' |
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83 | '$output1' '$output1.files_path' 'plink' |
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84 | </command> |
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85 | """ |
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86 | nparm = 7 |
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87 | if len(sys.argv) < nparm: |
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88 | sys.stderr.write('## %s called with %s - needs %d parameters \n' % (prog,sys.argv,nparm)) |
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89 | sys.exit(1) |
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90 | inpedfilepath = sys.argv[1] |
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91 | base_name = os.path.split(inpedfilepath)[-1] |
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92 | winsize = sys.argv[2] |
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93 | winmove = sys.argv[3] |
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94 | r2thresh = sys.argv[4] |
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95 | outhtmlname = sys.argv[5] |
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96 | outfilepath = sys.argv[6] |
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97 | try: |
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98 | os.makedirs(outfilepath) |
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99 | except: |
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100 | pass |
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101 | plink = sys.argv[7] |
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102 | makeLDreduced(base_name,infpath=inpedfilepath,outfpath=outfilepath,plinke=plink,forcerebuild=False,returnFname=False, |
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103 | winsize=winsize,winmove=winmove,r2thresh=r2thresh) |
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104 | f = file(outhtmlname,'w') |
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105 | f.write(galhtmlprefix % prog) |
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106 | flist = os.listdir(outfilepath) |
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107 | s1 = '## Rgenetics: http://rgenetics.org Galaxy Tools %s %s' % (prog,timenow()) # becomes info |
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108 | s2 = 'Input %s, winsize=%s, winmove=%s, r2thresh=%s' % (base_name,winsize,winmove,r2thresh) |
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109 | print '%s %s' % (s1,s2) |
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110 | f.write('<div>%s\n%s\n<ol>' % (s1,s2)) |
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111 | for i, data in enumerate( flist ): |
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112 | f.write('<li><a href="%s">%s</a></li>\n' % (os.path.split(data)[-1],os.path.split(data)[-1])) |
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113 | f.write("</div></body></html>") |
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114 | f.close() |
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115 | |
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116 | |
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117 | if __name__ == "__main__": |
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118 | main() |
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119 | |
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