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1 import sys, os, os.path, tempfile, shutil, re, shlex, subprocess
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2
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3 def stop_err( msg ):
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4 sys.stderr.write( "%s\n" % msg )
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5 sys.exit()
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6
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7 # tranform fastx_barcode_splitter result to html
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8 def results_to_html(results_path,html_path,basepath,print_stdout ):
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9 pat = '%s[/]?([^\t]*)' % basepath
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10 rep = '<a href=\"\\1\">\\1</a>'
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11 txt = open(results_path,'r')
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12 html = open(html_path,'w')
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13 html.write('<html><body><table border=1>\n')
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14 try:
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15 for line in txt:
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16 html.write('<tr><td>%s</td></tr>' % re.sub('\t','</td><td>',re.sub(pat,rep,line)))
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17 if print_stdout:
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18 print >> sys.stdout, '\t'.join(line.split('\t')[:2])
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19 except Exception, e:
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20 print(str(e))
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21 pass
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22 html.write('</table></body></html>\n')
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23 html.close()
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24 txt.close()
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25
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26 def __main__():
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27 """
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28 ##params for galaxy wrapper
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29 $output
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30 "$output.id"
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31 "$input.ext"
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32 "$__new_file_path__"
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33 --barcodes='$barcodes'
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34 $BARCODE $input "$input.name" "$output.extra_files_path"
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35 ## params for fastx_barcode_splitter
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36 --mismatches $mismatches --partial $partial $EOL
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37 """
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38 output = sys.argv[1]
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39 output_id = sys.argv[2]
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40 file_ext = sys.argv[3]
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41 new_file_path = sys.argv[4]
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42 select_barcodes = sys.argv[5].replace('--barcodes=','')
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43 barcodes = sys.argv[6]
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44 fastx = sys.argv[7]
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45 fastx_name = sys.argv[8]
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46 extra_files_path = sys.argv[9]
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47 script_args = ' '.join(sys.argv[10:])
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48 #Sanitize library name, make sure we can create a file with this name
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49 lib_name = re.sub('\W','_',re.sub('\.\W*$','',fastx_name))+'_'
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50 prefix = os.path.join(extra_files_path,lib_name)
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51 # Check that input datasets exist
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52 if not os.path.isfile(fastx):
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53 stop_err('Error: Input file (%s) not found!' % fastx)
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54 if not os.path.isfile(barcodes):
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55 stop_err('Error: barcode file (%s) not found!' % barcodes)
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56 try:
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57 # Check that extra_files_path exists
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58 if not os.path.isdir(extra_files_path):
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59 os.makedirs(extra_files_path)
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60 cmd_line = 'zcat -f %s | fastx_barcode_splitter.pl --bcfile %s --prefix %s --suffix %s %s' %(fastx,barcodes,prefix,'.'+file_ext,script_args)
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61 # print >> sys.stderr, cmd_line
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62 # Create file to collect results written to stdout
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63 tmp_dir = tempfile.mkdtemp()
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64 result_path = tempfile.NamedTemporaryFile(dir=tmp_dir, prefix='results_', suffix='.out' ).name
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65 result_file = open( result_path, 'wb' )
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66 proc = subprocess.Popen( args=cmd_line, shell=True, cwd=tmp_dir, stderr=subprocess.PIPE,stdout=result_file.fileno() )
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67 returncode = proc.wait()
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68 result_file.close()
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69 stderr = proc.stderr.read()
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70 if returncode != 0:
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71 raise Exception, stderr
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72 # copy results to ouptut
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73 results_to_html(result_path,output,extra_files_path,True)
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74 # make new datasets for selected barcodes
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75 if select_barcodes != None and len(select_barcodes) > 0:
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76 flist = os.listdir(extra_files_path)
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77 for barcode in select_barcodes.split(','):
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78 for fname in flist:
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79 if fname.find('_'+barcode+'.'+file_ext) >= 0:
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80 fpath = os.path.join(extra_files_path,fname)
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81 # filename pattern required by galaxy
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82 fn = "%s_%s_%s_%s_%s" % ( 'primary', output_id, barcode, 'visible', file_ext )
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83 npath = os.path.join(new_file_path,fn)
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84 try:
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85 os.link(fpath, npath)
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86 except:
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87 shutil.copy2(fpath, npath)
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88 except Exception, e:
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89 raise Exception, 'Exception caught attempting conversion: ' + str( e )
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90
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91 if __name__ == "__main__": __main__()
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