comparison read2mut.py @ 90:24f166c1dba7 draft default tip

planemo upload for repository https://github.com/Single-Molecule-Genetics/VariantAnalyzerGalaxy/tree/master/tools/variant_analyzer commit ee4a8e6cf290e6c8a4d55f9cd2839d60ab3b11c8-dirty

89:1a5974404d4f

from __future__ import division

import argparse
import csv
import itertools
import json
import operator
import os
import re
import sys

                                        half1_mate1 = array1_half2
                                        half2_mate1 = array1_half
                                        half1_mate2 = array2_half2
                                        half2_mate2 = array2_half
                                    # calculate HD of "a" in the tag to all "a's" or "b" in the tag to all "b's"
                                    dist = np.array([sum(itertools.map(operator.ne, half1_mate1, c)) for c in half1_mate2])
                                    min_index = np.where(dist == dist.min())  # get index of min HD
                                    # get all "b's" of the tag or all "a's" of the tag with minimum HD
                                    min_tag_half2 = half2_mate2[min_index]
                                    min_tag_array2 = array2[min_index]  # get whole tag with min HD
                                    min_value = dist.min()
                                    # calculate HD of "b" to all "b's" or "a" to all "a's"
                                    dist_second_half = np.array([sum(itertools.map(operator.ne, half2_mate1, e))
                                                                 for e in min_tag_half2])
                                    dist2 = dist_second_half.max()
                                    max_index = np.where(dist_second_half == dist_second_half.max())[0]  # get index of max HD
                                    max_tag = min_tag_array2[max_index]
                                    # tags which have identical parts:

90:24f166c1dba7

from __future__ import division

import argparse
import csv
import json
import operator
import os
import re
import sys

                                        half1_mate1 = array1_half2
                                        half2_mate1 = array1_half
                                        half1_mate2 = array2_half2
                                        half2_mate2 = array2_half
                                    # calculate HD of "a" in the tag to all "a's" or "b" in the tag to all "b's"
                                    dist = np.array([sum(map(operator.ne, half1_mate1, c)) for c in half1_mate2])
                                    min_index = np.where(dist == dist.min())  # get index of min HD
                                    # get all "b's" of the tag or all "a's" of the tag with minimum HD
                                    min_tag_half2 = half2_mate2[min_index]
                                    min_tag_array2 = array2[min_index]  # get whole tag with min HD
                                    min_value = dist.min()
                                    # calculate HD of "b" to all "b's" or "a" to all "a's"
                                    dist_second_half = np.array([sum(map(operator.ne, half2_mate1, e))
                                                                 for e in min_tag_half2])
                                    dist2 = dist_second_half.max()
                                    max_index = np.where(dist_second_half == dist_second_half.max())[0]  # get index of max HD
                                    max_tag = min_tag_array2[max_index]
                                    # tags which have identical parts: