comparison cwpair2_util.py @ 5:71188f3f4b76 draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cwpair2 commit cb490a0eee9efc2cd6c98d5bb714b75b5894c56c

4:d843468aeb8f

import sys
import traceback

import matplotlib
matplotlib.use('Agg')
from matplotlib import pyplot  # noqa: E402

# Data outputs
DETAILS = 'D'
MATCHED_PAIRS = 'MP'
ORPHANS = 'O'

def parse_chromosomes(reader):
    # This version of cwpair2 accepts only gff format as input.
    chromosomes = {}
    reader.next()
    for line in reader:
        cname, junk, junk, start, end, value, strand, junk, junk = line
        start = int(start)
        end = int(end)
        value = float(value)

                                output_files)
        statistics.append(stats)
    if output_files == 'all' and method == 'all':
        frequency_plot([s['dist'] for s in statistics],
                       statistics[0]['graph_path'],
                       labels=METHODS.keys())
    return statistics


def perform_process(dataset_path, galaxy_hid, method, threshold, up_distance,
                    down_distance, binsize, output_files):

5:71188f3f4b76

import sys
import traceback

import matplotlib
matplotlib.use('Agg')
from matplotlib import pyplot  # noqa: I202,E402

# Data outputs
DETAILS = 'D'
MATCHED_PAIRS = 'MP'
ORPHANS = 'O'

def parse_chromosomes(reader):
    # This version of cwpair2 accepts only gff format as input.
    chromosomes = {}
    next(reader)
    for line in reader:
        cname, junk, junk, start, end, value, strand, junk, junk = line
        start = int(start)
        end = int(end)
        value = float(value)

                                output_files)
        statistics.append(stats)
    if output_files == 'all' and method == 'all':
        frequency_plot([s['dist'] for s in statistics],
                       statistics[0]['graph_path'],
                       labels=list(METHODS.keys()))
    return statistics


def perform_process(dataset_path, galaxy_hid, method, threshold, up_distance,
                    down_distance, binsize, output_files):