comparison repmatch_gff3_util.py @ 5:53cbf79396d7 draft

Uploaded

4:1cea96c461a2

pyplot.rc('ytick.major', size=10.00)
pyplot.rc('lines', linewidth=4.00)
pyplot.rc('axes', linewidth=3.00)
pyplot.rc('font', family='Bitstream Vera Sans', size=32.0)

PLOT_FORMATS = ['png', 'pdf', 'svg']
COLORS = 'krb'


class Replicate(object):

def gff_row(cname, start, end, score, source, type='.', strand='.', phase='.', attrs={}):
    return (cname, source, type, start, end, score, strand, phase, gff_attrs(attrs))


def get_temporary_plot_path(plot_format):
    """
    Return the path to a temporary file with a valid image format
    file extension that can be used with bioformats.
    """
    tmp_dir = tempfile.mkdtemp(prefix='tmp-repmatch-')
    fd, name = tempfile.mkstemp(suffix='.%s' % plot_format, dir=tmp_dir)
    os.close(fd)
    return name


def process_files(dataset_paths, galaxy_hids, method, distance, step, replicates, up_limit, low_limit, output_files,
                  plot_format, output_summary, output_orphan, output_detail, output_key, output_histogram):
    output_histogram_file = output_files in ["all"] and method in ["all"]
    if len(dataset_paths) < 2:
        return
    if method == 'all':
        match_methods = METHODS.keys()

                                     step,
                                     replicates,
                                     up_limit,
                                     low_limit,
                                     output_files,
                                     plot_format,
                                     output_summary,
                                     output_orphan,
                                     output_detail,
                                     output_key,
                                     output_histogram)
    if output_histogram_file:
        tmp_histogram_path = get_temporary_plot_path(plot_format)
        frequency_histogram([stat['distribution'] for stat in [statistics]],
                            tmp_histogram_path,
                            METHODS.keys())
        shutil.move(tmp_histogram_path, output_histogram)


def perform_process(dataset_paths, galaxy_hids, method, distance, step, num_required, up_limit, low_limit, output_files,
                    plot_format, output_summary, output_orphan, output_detail, output_key, output_histogram):
    output_detail_file = output_files in ["all"] and output_detail is not None
    output_key_file = output_files in ["all"] and output_key is not None
    output_orphan_file = output_files in ["all", "simple_orphan"] and output_orphan is not None
    output_histogram_file = output_files in ["all"] and output_histogram is not None
    replicates = []

                                    orphan.midpoint+1,
                                    orphan.value,
                                    orphan.distance,
                                    orphan.replicate.id))
    if output_histogram_file:
        tmp_histogram_path = get_temporary_plot_path(plot_format)
        frequency_histogram([freq], tmp_histogram_path)
        shutil.move(tmp_histogram_path, output_histogram)
    return {'distribution': freq}

5:53cbf79396d7

pyplot.rc('ytick.major', size=10.00)
pyplot.rc('lines', linewidth=4.00)
pyplot.rc('axes', linewidth=3.00)
pyplot.rc('font', family='Bitstream Vera Sans', size=32.0)

COLORS = 'krb'


class Replicate(object):

def gff_row(cname, start, end, score, source, type='.', strand='.', phase='.', attrs={}):
    return (cname, source, type, start, end, score, strand, phase, gff_attrs(attrs))


def get_temporary_plot_path():
    """
    Return the path to a temporary file with a valid image format
    file extension that can be used with bioformats.
    """
    tmp_dir = tempfile.mkdtemp(prefix='tmp-repmatch-')
    fd, name = tempfile.mkstemp(suffix='.pdf', dir=tmp_dir)
    os.close(fd)
    return name


def process_files(dataset_paths, galaxy_hids, method, distance, step, replicates, up_limit, low_limit, output_files,
                  output_summary, output_orphan, output_detail, output_key, output_histogram):
    output_histogram_file = output_files in ["all"] and method in ["all"]
    if len(dataset_paths) < 2:
        return
    if method == 'all':
        match_methods = METHODS.keys()

                                     step,
                                     replicates,
                                     up_limit,
                                     low_limit,
                                     output_files,
                                     output_summary,
                                     output_orphan,
                                     output_detail,
                                     output_key,
                                     output_histogram)
    if output_histogram_file:
        tmp_histogram_path = get_temporary_plot_path()
        frequency_histogram([stat['distribution'] for stat in [statistics]],
                            tmp_histogram_path,
                            METHODS.keys())
        shutil.move(tmp_histogram_path, output_histogram)


def perform_process(dataset_paths, galaxy_hids, method, distance, step, num_required, up_limit, low_limit, output_files,
                    output_summary, output_orphan, output_detail, output_key, output_histogram):
    output_detail_file = output_files in ["all"] and output_detail is not None
    output_key_file = output_files in ["all"] and output_key is not None
    output_orphan_file = output_files in ["all", "simple_orphan"] and output_orphan is not None
    output_histogram_file = output_files in ["all"] and output_histogram is not None
    replicates = []

                                    orphan.midpoint+1,
                                    orphan.value,
                                    orphan.distance,
                                    orphan.replicate.id))
    if output_histogram_file:
        tmp_histogram_path = get_temporary_plot_path()
        frequency_histogram([freq], tmp_histogram_path)
        shutil.move(tmp_histogram_path, output_histogram)
    return {'distribution': freq}