示例#1
0
def main(argv):
    try:
        config, args = bam_config.parse_config(argv)
        if args and args[0].startswith("dry"):
            config.dry_run = True
    except bam_config.ConfigError, error:
        print_err(error)
        return 1
示例#2
0
def main(argv):
    try:
        config, args = bam_config.parse_config(argv)
        if args and args[0].startswith("dry"):
            config.dry_run = True
    except bam_config.ConfigError, error:
        print_err(error)
        return 1
示例#3
0
def main(argv):
    config, args = parse_options(argv)
    if config is None:
        return 1

    # Get default options for bam_pipeline
    bam_config, _ = bam_cfg.parse_config(args)
    makefiles = bam_pipeline.read_makefiles(bam_config, args)
    # Build .fai files for reference .fasta files
    bam_pipeline.index_references(bam_config, makefiles)

    for makefile in makefiles:
        mkfile_fname = makefile["Statistics"]["Filename"]
        bam_config.destination = os.path.dirname(mkfile_fname)
        tasks = bam_pipeline.build_pipeline_full(bam_config,
                                                 makefile,
                                                 return_nodes=False)

        make_dirs(config.destination)
        makefile_name = add_postfix(makefile["Statistics"]["Filename"],
                                    config.postfix)
        makefile_path = reroot_path(config.destination, makefile_name)
        if samefile(makefile["Statistics"]["Filename"], makefile_path):
            sys.stderr.write("ERROR: Would overwrite source makefile at %r\n" %
                             (makefile_path, ))
            sys.stderr.write(
                "       Please set --destination and/or --output-name-postfix\n"
            )
            sys.stderr.write("       before continuing.\n")
            return 1

        print("Writing makefile", makefile_path)

        found_prefix = False
        for prefix in makefile["Prefixes"]:
            if prefix != config.prefix:
                print("%sSkipping %s" % (_INDENTATION, prefix))
            else:
                found_prefix = True

        if not found_prefix:
            sys.stderr.write("\nERROR:\n")
            sys.stderr.write("Could not find prefix %r in %r! Aborting ...\n" %
                             (config.prefix, mkfile_fname))
            return 1

        with open(makefile_path, "w") as makefile_handle:
            bam_mkfile.print_header(dst=makefile_handle)
            makefile_handle.write("\n" * 3)

            for target in tasks:
                target_name = add_postfix(target.name, config.postfix)
                print("%sTarget: %s -> %s" %
                      (_INDENTATION, target.name, target_name))

                makefile_handle.write('%s"%s":\n' %
                                      (_INDENTATION * 0, target_name))
                for prefix in target.prefixes:
                    if prefix.name != config.prefix:
                        continue

                    for sample in prefix.samples:
                        print("%sSample: %s" % (_INDENTATION * 2, sample.name))

                        makefile_handle.write('%s"%s":\n' %
                                              (_INDENTATION * 1, sample.name))

                        for library in sample.libraries:
                            print("%sLibrary: %s" %
                                  (_INDENTATION * 3, library.name))
                            makefile_handle.write(
                                '%s"%s":\n' % (_INDENTATION * 2, library.name))

                            sink_cache = {}
                            destination = os.path.join(target_name, "reads",
                                                       sample.name,
                                                       library.name)

                            for lane in library.lanes:
                                convert_reads(config, destination, lane,
                                              sink_cache)
                            ReadSink.close_all_sinks()

                            for lane_name in sorted(sink_cache):
                                makefile_handle.write(
                                    '%s"%s":\n' %
                                    (_INDENTATION * 3, lane_name))
                                for (reads_type, sink) in sorted(
                                        sink_cache[lane_name].items()):
                                    makefile_handle.write(
                                        '%s%s "%s"\n' %
                                        (_INDENTATION * 4,
                                         ("%s:" % (reads_type, )).ljust(20),
                                         sink.filename))
                                makefile_handle.write("\n")
        print("\tDone ...")
        print()

    return 0
示例#4
0
文件: remap.py 项目: CarlesV/paleomix
def main(argv):
    config, args = parse_options(argv)
    if config is None:
        return 1

    # Get default options for bam_pipeline
    bam_config, _ = bam_cfg.parse_config(args)
    makefiles = bam_pipeline.read_makefiles(bam_config, args)
    # Build .fai files for reference .fasta files
    bam_pipeline.index_references(bam_config, makefiles)

    for makefile in makefiles:
        mkfile_fname = makefile["Statistics"]["Filename"]
        bam_config.destination = os.path.dirname(mkfile_fname)
        tasks = bam_pipeline.build_pipeline_full(bam_config, makefile,
                                                 return_nodes=False)

        make_dirs(config.destination)
        makefile_name = add_postfix(makefile["Statistics"]["Filename"],
                                    config.postfix)
        makefile_path = reroot_path(config.destination, makefile_name)
        if samefile(makefile["Statistics"]["Filename"], makefile_path):
            sys.stderr.write("ERROR: Would overwrite source makefile at %r\n" % (makefile_path,))
            sys.stderr.write("       Please set --destination and/or --output-name-postfix\n")
            sys.stderr.write("       before continuing.\n")
            return 1

        print("Writing makefile", makefile_path)

        found_prefix = False
        for prefix in makefile["Prefixes"]:
            if prefix != config.prefix:
                print("%sSkipping %s" % (_INDENTATION, prefix))
            else:
                found_prefix = True

        if not found_prefix:
            sys.stderr.write("\nERROR:\n")
            sys.stderr.write("Could not find prefix %r in %r! Aborting ...\n"
                             % (config.prefix, mkfile_fname))
            return 1

        with open(makefile_path, "w") as makefile_handle:
            bam_mkfile.print_header(dst=makefile_handle)
            makefile_handle.write("\n" * 3)

            for target in tasks:
                target_name = add_postfix(target.name, config.postfix)
                print("%sTarget: %s -> %s" % (_INDENTATION,
                                              target.name,
                                              target_name))

                makefile_handle.write('%s"%s":\n' % (_INDENTATION * 0,
                                                     target_name))
                for prefix in target.prefixes:
                    if prefix.name != config.prefix:
                        continue

                    for sample in prefix.samples:
                        print("%sSample: %s" % (_INDENTATION * 2, sample.name))

                        makefile_handle.write('%s"%s":\n' % (_INDENTATION * 1,
                                                             sample.name))

                        for library in sample.libraries:
                            print("%sLibrary: %s" % (_INDENTATION * 3,
                                                     library.name))
                            makefile_handle.write('%s"%s":\n'
                                                  % (_INDENTATION * 2,
                                                     library.name))

                            sink_cache = {}
                            destination = os.path.join(target_name,
                                                       "reads",
                                                       sample.name,
                                                       library.name)

                            for lane in library.lanes:
                                convert_reads(config, destination, lane, sink_cache)
                            ReadSink.close_all_sinks()

                            for lane_name in sorted(sink_cache):
                                makefile_handle.write('%s"%s":\n' % (_INDENTATION * 3, lane_name))
                                for (reads_type, sink) in sorted(sink_cache[lane_name].items()):
                                    makefile_handle.write('%s%s "%s"\n'
                                                          % (_INDENTATION * 4,
                                                             ("%s:" % (reads_type,)).ljust(20),
                                                             sink.filename))
                                makefile_handle.write("\n")
        print("\tDone ...")
        print()

    return 0