コード例 #1
0
ファイル: PEScript.py プロジェクト: gourneau/TS
        if status == 'corrected':
           bidirectional = True
        else:
           bidirectional = False

        alignment.alignment(
            sff_path,
            fastq_path,
            align_full,
            DIR_BC_FILES,
            libraryName,
            sample,
            chipType,
            site_name,
            flows,
            notes,
            barcodeId,
            aligner_opts_extra,
            mark_duplicates,
            start_time,
            env['ALIGNMENT_RESULTS'],
            bidirectional,
            sam_parsed
            )

        try:
            quality = os.path.join('.',"quality.summary")
            shutil.copy(quality, "../"+status+".quality.summary")
        except:
            printtime("ERROR: %s doesn't exist" % quality)
コード例 #2
0
ファイル: BlockTLScript.py プロジェクト: golharam/TS
                  try:
                      unfiltered_fastq = glob.glob("*." + status + ".fastq")[0]
                  except:
                      printtime("ERROR: unfiltered fastq file not found")
                      unfiltered_fastq = ""

                  alignment.alignment(
                      unfiltered_sff,
                      unfiltered_fastq,
                      env['align_full'],
                      env['DIR_BC_FILES'],
                      env['libraryName'],
                      env['sample'],
                      env['chipType'],
                      env['site_name'],
                      env['flows'],
                      env['notes'],
                      env['barcodeId'],
                      env['aligner_opts_extra'],
                      env['start_time'],
                      env['ALIGNMENT_RESULTS'],
                      bidirectional,
                      env['sam_parsed'])

              os.chdir(top_dir)
          else:
              printtime("Directory unfiltered does not exist")


          alignment.alignment(