comparison cwpair2_util.py @ 2:abc464ca7260 draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cwpair2 commit 0e7c1b37cf73425c6637b4e196fdeb290e042bc1

1:d4db13c9dd7f

import bisect
import csv
import os
import sys
import traceback
import matplotlib
matplotlib.use('Agg')
from matplotlib import pyplot

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

    def get_bin(self, x):
        """
        Returns the bin in which a data point falls
        """
        return self.start + (x-self.start) // self.binsize * self.binsize + self.binsize/2.0

    def add(self, x):
        x = self.get_bin(x)
        self.dist[x] = self.dist.get(x, 0) + 1

    sys.stderr.write(msg)
    sys.exit(1)


def distance(peak1, peak2):
    return (peak2[1]+peak2[2])/2 - (peak1[1]+peak1[2])/2


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

    for peaks in chromosomes.values():
        for peak in peaks:
            values.append(peak[3])
    values.sort()
    # Get 95% value
    return values[int(len(values)*0.95)]


def filter(chromosomes, threshold=0.05):
    """
    Filters the peaks to those above a threshold. Threshold < 1.0 is interpreted

                dist.add(distance(peak, cpeak))
    return dist


def make_keys(crick):
    return [(data[1] + data[2])//2 for data in crick]


def get_window(crick, peak, up_distance, down_distance, keys=None):
    """
    Returns a window of all crick peaks within a distance of a watson peak.

def match_mode(window, peak, mode):
    if not window:
        return None
    return min(window, key=lambda cpeak: abs(distance(peak, cpeak)-mode))

METHODS = {'mode': match_mode, 'closest': match_closest, 'largest': match_largest}


def frequency_plot(freqs, fname, labels=[], title=''):

                                              cname,
                                              match[1],
                                              match[2],
                                              match[3], '-',
                                              midpoint,
                                              peak[3]+match[3],
                                              d))
                i = bisect.bisect_left(keys, (match[1]+match[2])/2)
                del crick[i]
                del keys[i]
            else:
                if output_orphans:
                    orphan_output.writerow((cname, peak[0], peak[1], peak[2], peak[3]))

2:abc464ca7260

import bisect
import csv
import os
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 get_bin(self, x):
        """
        Returns the bin in which a data point falls
        """
        return self.start + (x - self.start) // self.binsize * self.binsize + self.binsize / 2.0

    def add(self, x):
        x = self.get_bin(x)
        self.dist[x] = self.dist.get(x, 0) + 1

    sys.stderr.write(msg)
    sys.exit(1)


def distance(peak1, peak2):
    return (peak2[1] + peak2[2]) / 2 - (peak1[1] + peak1[2]) / 2


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

    for peaks in chromosomes.values():
        for peak in peaks:
            values.append(peak[3])
    values.sort()
    # Get 95% value
    return values[int(len(values) * 0.95)]


def filter(chromosomes, threshold=0.05):
    """
    Filters the peaks to those above a threshold. Threshold < 1.0 is interpreted

                dist.add(distance(peak, cpeak))
    return dist


def make_keys(crick):
    return [(data[1] + data[2]) // 2 for data in crick]


def get_window(crick, peak, up_distance, down_distance, keys=None):
    """
    Returns a window of all crick peaks within a distance of a watson peak.

def match_mode(window, peak, mode):
    if not window:
        return None
    return min(window, key=lambda cpeak: abs(distance(peak, cpeak) - mode))

METHODS = {'mode': match_mode, 'closest': match_closest, 'largest': match_largest}


def frequency_plot(freqs, fname, labels=[], title=''):

                                              cname,
                                              match[1],
                                              match[2],
                                              match[3], '-',
                                              midpoint,
                                              peak[3] + match[3],
                                              d))
                i = bisect.bisect_left(keys, (match[1] + match[2]) / 2)
                del crick[i]
                del keys[i]
            else:
                if output_orphans:
                    orphan_output.writerow((cname, peak[0], peak[1], peak[2], peak[3]))