comparison genetrack_util.py @ 4:b41a4bb828a3 draft default tip

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genetrack commit 2772547f531819d3f6d892ed041fa39b82e3550f

3:41887967ef14

import subprocess
import sys
import tempfile

import numpy

GFF_EXT = 'gff'
SCIDX_EXT = 'scidx'

    for fn in conversion_functions(in_fmt, out_fmt):
        data = fn(data)
    return data


class ChromosomeManager(object):
    """
    Manages a CSV reader of an index file to only load one chrom at a time
    """

    def __init__(self, reader):

        self.reader = reader
        self.processed_chromosomes = []
        self.current_index = 0
        self.next_valid()

    def next(self):
        self.line = self.reader.next()

    def is_valid(self, line):
        if len(line) not in [4, 5, 9]:
            return False
        try:

    def next_valid(self):
        """
        Advance to the next valid line in the reader
        """
        self.line = self.reader.next()
        s = 0
        while not self.is_valid(self.line):
            self.line = self.reader.next()
            s += 1
        if s > 0:
            # Skip initial line(s) of file
            pass

                    msg = 'Reads in chromosome %s are not sorted by index. (At index %d)' % (cname, self.current_index)
                    stop_err(msg)
                self.current_index = read[0]
                self.add_read(read)
            try:
                self.next()
            except StopIteration:
                self.done = True
                break
        self.processed_chromosomes.append(cname)
        self.current_index = 0

    def normal_func(x):
        return math.exp(-x * x / (2 * sigma2))

    # width is the half of the distribution
    values = map(normal_func, range(-width, width))
    values = numpy.array(values, numpy.float)
    # normalization
    if normalize:
        values = 1.0 / math.sqrt(2 * numpy.pi * sigma2) * values
    return values

4:b41a4bb828a3

import subprocess
import sys
import tempfile

import numpy
from six import Iterator

GFF_EXT = 'gff'
SCIDX_EXT = 'scidx'

    for fn in conversion_functions(in_fmt, out_fmt):
        data = fn(data)
    return data


class ChromosomeManager(Iterator):
    """
    Manages a CSV reader of an index file to only load one chrom at a time
    """

    def __init__(self, reader):

        self.reader = reader
        self.processed_chromosomes = []
        self.current_index = 0
        self.next_valid()

    def __next__(self):
        self.line = next(self.reader)

    def is_valid(self, line):
        if len(line) not in [4, 5, 9]:
            return False
        try:

    def next_valid(self):
        """
        Advance to the next valid line in the reader
        """
        self.line = next(self.reader)
        s = 0
        while not self.is_valid(self.line):
            self.line = next(self.reader)
            s += 1
        if s > 0:
            # Skip initial line(s) of file
            pass

                    msg = 'Reads in chromosome %s are not sorted by index. (At index %d)' % (cname, self.current_index)
                    stop_err(msg)
                self.current_index = read[0]
                self.add_read(read)
            try:
                next(self)
            except StopIteration:
                self.done = True
                break
        self.processed_chromosomes.append(cname)
        self.current_index = 0

    def normal_func(x):
        return math.exp(-x * x / (2 * sigma2))

    # width is the half of the distribution
    values = list(map(normal_func, range(-width, width)))
    values = numpy.array(values, numpy.float)
    # normalization
    if normalize:
        values = 1.0 / math.sqrt(2 * numpy.pi * sigma2) * values
    return values