Mercurial > repos > bccarstens > demultiplex
diff 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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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/barcode_splitter-bc23f6946bb8/fastx_barcode_splitter_single_galaxy_wrapper.py Mon Jan 16 22:38:10 2012 -0500 @@ -0,0 +1,86 @@ +import sys, os, os.path, tempfile, shutil, re, shlex, subprocess + +def stop_err( msg ): + sys.stderr.write( "%s\n" % msg ) + sys.exit() + +# tranform fastx_barcode_splitter result to html +def results_to_html(results_path,html_path,basepath,print_stdout ): + pat = '%s[/]?([^\t]*)' % basepath + rep = '<a href=\"\\1\">\\1</a>' + txt = open(results_path,'r') + html = open(html_path,'w') + html.write('<html><body><table border=1>\n') + try: + for line in txt: + html.write('<tr><td>%s</td></tr>' % re.sub('\t','</td><td>',re.sub(pat,rep,line))) + if print_stdout: + print >> sys.stdout, '\t'.join(line.split('\t')[:2]) + except Exception, e: + print(str(e)) + pass + html.write('</table></body></html>\n') + html.close() + txt.close() + +def __main__(): + """ + ##params for galaxy wrapper + $output + "$output.id" + "$input.ext" + "$__new_file_path__" + --barcodes='$barcodes' + $BARCODE $input "$input.name" "$output.extra_files_path" + ## params for fastx_barcode_splitter + --mismatches $mismatches --partial $partial $EOL + """ + + output = sys.argv[1] + output_unmatched = sys.argv[2] + file_ext = sys.argv[3] + select_barcode = sys.argv[4].replace('--barcodes=','') + barcodes = os.path.abspath("barcodes") + with open(barcodes, 'w') as f: + f.write("barcode\t%s\n" % (select_barcode)) + + #barcodes = sys.argv[6] + fastx = sys.argv[5] + fastx_name = sys.argv[6] + #extra_files_path = sys.argv[9] + script_args = ' '.join(sys.argv[7:]) + #Sanitize library name, make sure we can create a file with this name + lib_name = re.sub('\W','_',re.sub('\.\W*$','',fastx_name))+'_' + # Check that input datasets exist + if not os.path.isfile(fastx): + stop_err('Error: Input file (%s) not found!' % fastx) + try: + prefix = lib_name + cmd_line = 'zcat -f %s | fastx_barcode_splitter.pl --bcfile %s --prefix %s --suffix %s %s' %(fastx,barcodes,prefix,'.'+file_ext,script_args) + # print >> sys.stderr, cmd_line + # Create file to collect results written to stdout + tmp_dir = tempfile.mkdtemp() + result_path = tempfile.NamedTemporaryFile(dir=tmp_dir, prefix='results_', suffix='.out' ).name + result_file = open( result_path, 'wb' ) + proc = subprocess.Popen( args=cmd_line, shell=True, cwd=tmp_dir, stderr=subprocess.PIPE,stdout=result_file.fileno() ) + returncode = proc.wait() + result_file.close() + stderr = proc.stderr.read() + if returncode != 0: + raise Exception, stderr + # copy results to ouptut + #results_to_html(result_path,output,extra_files_path,True) + # make new datasets for selected barcodes + flist = os.listdir(tmp_dir) + for fname in flist: + if fname.find('_'+barcode+'.'+file_ext) >= 0: + fpath = os.path.join(tmp_dir,fname) + shutil.copy2(fpath, output) + for fname in flist: + if fname.find('_unmatched.' + file_ext) > 0: + fpath = os.path.join(tmp_dir, fname) + shutil.copy2(fpath, output_unmatched) + except Exception, e: + raise Exception, 'Exception caught attempting conversion: ' + str( e ) + +if __name__ == "__main__": __main__()