Mercurial > repos > bccarstens > demultiplex
comparison barcode_splitter-bc23f6946bb8/fastx_barcode_splitter_single_galaxy_wrapper.py @ 0:2b6d577dd1ab default tip
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| author | bccarstens |
|---|---|
| date | Mon, 16 Jan 2012 22:38:10 -0500 |
| parents | |
| children |
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| -1:000000000000 | 0:2b6d577dd1ab |
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| 1 import sys, os, os.path, tempfile, shutil, re, shlex, subprocess | |
| 2 | |
| 3 def stop_err( msg ): | |
| 4 sys.stderr.write( "%s\n" % msg ) | |
| 5 sys.exit() | |
| 6 | |
| 7 # tranform fastx_barcode_splitter result to html | |
| 8 def results_to_html(results_path,html_path,basepath,print_stdout ): | |
| 9 pat = '%s[/]?([^\t]*)' % basepath | |
| 10 rep = '<a href=\"\\1\">\\1</a>' | |
| 11 txt = open(results_path,'r') | |
| 12 html = open(html_path,'w') | |
| 13 html.write('<html><body><table border=1>\n') | |
| 14 try: | |
| 15 for line in txt: | |
| 16 html.write('<tr><td>%s</td></tr>' % re.sub('\t','</td><td>',re.sub(pat,rep,line))) | |
| 17 if print_stdout: | |
| 18 print >> sys.stdout, '\t'.join(line.split('\t')[:2]) | |
| 19 except Exception, e: | |
| 20 print(str(e)) | |
| 21 pass | |
| 22 html.write('</table></body></html>\n') | |
| 23 html.close() | |
| 24 txt.close() | |
| 25 | |
| 26 def __main__(): | |
| 27 """ | |
| 28 ##params for galaxy wrapper | |
| 29 $output | |
| 30 "$output.id" | |
| 31 "$input.ext" | |
| 32 "$__new_file_path__" | |
| 33 --barcodes='$barcodes' | |
| 34 $BARCODE $input "$input.name" "$output.extra_files_path" | |
| 35 ## params for fastx_barcode_splitter | |
| 36 --mismatches $mismatches --partial $partial $EOL | |
| 37 """ | |
| 38 | |
| 39 output = sys.argv[1] | |
| 40 output_unmatched = sys.argv[2] | |
| 41 file_ext = sys.argv[3] | |
| 42 select_barcode = sys.argv[4].replace('--barcodes=','') | |
| 43 barcodes = os.path.abspath("barcodes") | |
| 44 with open(barcodes, 'w') as f: | |
| 45 f.write("barcode\t%s\n" % (select_barcode)) | |
| 46 | |
| 47 #barcodes = sys.argv[6] | |
| 48 fastx = sys.argv[5] | |
| 49 fastx_name = sys.argv[6] | |
| 50 #extra_files_path = sys.argv[9] | |
| 51 script_args = ' '.join(sys.argv[7:]) | |
| 52 #Sanitize library name, make sure we can create a file with this name | |
| 53 lib_name = re.sub('\W','_',re.sub('\.\W*$','',fastx_name))+'_' | |
| 54 # Check that input datasets exist | |
| 55 if not os.path.isfile(fastx): | |
| 56 stop_err('Error: Input file (%s) not found!' % fastx) | |
| 57 try: | |
| 58 prefix = lib_name | |
| 59 cmd_line = 'zcat -f %s | fastx_barcode_splitter.pl --bcfile %s --prefix %s --suffix %s %s' %(fastx,barcodes,prefix,'.'+file_ext,script_args) | |
| 60 # print >> sys.stderr, cmd_line | |
| 61 # Create file to collect results written to stdout | |
| 62 tmp_dir = tempfile.mkdtemp() | |
| 63 result_path = tempfile.NamedTemporaryFile(dir=tmp_dir, prefix='results_', suffix='.out' ).name | |
| 64 result_file = open( result_path, 'wb' ) | |
| 65 proc = subprocess.Popen( args=cmd_line, shell=True, cwd=tmp_dir, stderr=subprocess.PIPE,stdout=result_file.fileno() ) | |
| 66 returncode = proc.wait() | |
| 67 result_file.close() | |
| 68 stderr = proc.stderr.read() | |
| 69 if returncode != 0: | |
| 70 raise Exception, stderr | |
| 71 # copy results to ouptut | |
| 72 #results_to_html(result_path,output,extra_files_path,True) | |
| 73 # make new datasets for selected barcodes | |
| 74 flist = os.listdir(tmp_dir) | |
| 75 for fname in flist: | |
| 76 if fname.find('_'+barcode+'.'+file_ext) >= 0: | |
| 77 fpath = os.path.join(tmp_dir,fname) | |
| 78 shutil.copy2(fpath, output) | |
| 79 for fname in flist: | |
| 80 if fname.find('_unmatched.' + file_ext) > 0: | |
| 81 fpath = os.path.join(tmp_dir, fname) | |
| 82 shutil.copy2(fpath, output_unmatched) | |
| 83 except Exception, e: | |
| 84 raise Exception, 'Exception caught attempting conversion: ' + str( e ) | |
| 85 | |
| 86 if __name__ == "__main__": __main__() |