Python merge_bams Examples

Example #1

            try:
                os.mkdir(
                    os.path.join(env["BASECALLER_RESULTS"],
                                 "unfiltered.untrimmed"))

                basecaller.merge_datasets_basecaller_json(
                    dirs,
                    os.path.join(env["BASECALLER_RESULTS"],
                                 "unfiltered.untrimmed"),
                )

                blockprocessing.merge_bams(
                    dirs,
                    os.path.join(env["BASECALLER_RESULTS"],
                                 "unfiltered.untrimmed"),
                    basecaller_datasets,
                    "picard",
                )
            except Exception:
                print(traceback.format_exc())

            try:
                os.mkdir(
                    os.path.join(env["BASECALLER_RESULTS"],
                                 "unfiltered.trimmed"))

                basecaller.merge_datasets_basecaller_json(
                    dirs,
                    os.path.join(env["BASECALLER_RESULTS"],
                                 "unfiltered.trimmed"))

Example #2

File: MergeTLScript.py Project: vswilliamson/TS

            printtime("ERROR: merging rawtf.basecaller.bam unsuccessful")

        if do_unfiltered_processing:

            basecaller_datasets = blockprocessing.get_datasets_basecaller(env['BASECALLER_RESULTS'])

            try:
                os.mkdir(os.path.join(env['BASECALLER_RESULTS'],'unfiltered.untrimmed'))

                basecaller.merge_datasets_basecaller_json(
                    dirs,
                    os.path.join(env['BASECALLER_RESULTS'],"unfiltered.untrimmed"))

                blockprocessing.merge_bams(
                    dirs,
                    os.path.join(env['BASECALLER_RESULTS'],"unfiltered.untrimmed"),
                    basecaller_datasets,
                    'picard')
            except:
                print traceback.format_exc()


            try:
                os.mkdir(os.path.join(env['BASECALLER_RESULTS'],'unfiltered.trimmed'))

                basecaller.merge_datasets_basecaller_json(
                    dirs,
                    os.path.join(env['BASECALLER_RESULTS'],"unfiltered.trimmed"))

                blockprocessing.merge_bams(
                    dirs,

Example #3

            printtime("ERROR: merging rawtf.basecaller.bam unsuccessful")

        if do_unfiltered_processing:

            basecaller_datasets = blockprocessing.get_datasets_basecaller(env['BASECALLER_RESULTS'])

            try:
                os.mkdir(os.path.join(env['BASECALLER_RESULTS'], 'unfiltered.untrimmed'))

                basecaller.merge_datasets_basecaller_json(
                    dirs,
                    os.path.join(env['BASECALLER_RESULTS'], "unfiltered.untrimmed"))

                blockprocessing.merge_bams(
                    dirs,
                    os.path.join(env['BASECALLER_RESULTS'], "unfiltered.untrimmed"),
                    basecaller_datasets,
                    'picard')
            except:
                print traceback.format_exc()

            try:
                os.mkdir(os.path.join(env['BASECALLER_RESULTS'], 'unfiltered.trimmed'))

                basecaller.merge_datasets_basecaller_json(
                    dirs,
                    os.path.join(env['BASECALLER_RESULTS'], "unfiltered.trimmed"))

                blockprocessing.merge_bams(
                    dirs,
                    os.path.join(env['BASECALLER_RESULTS'], "unfiltered.trimmed"),