Mercurial > repos > mheinzl > variant_analyzer2

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

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planemo upload for repository https://github.com/Single-Molecule-Genetics/VariantAnalyzerGalaxy/tree/master/tools/variant_analyzer commit ee4a8e6cf290e6c8a4d55f9cd2839d60ab3b11c8-dirty
author mheinzl
date Wed, 26 Apr 2023 18:55:52 +0000
parents 1a5974404d4f
children
comparison
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89:1a5974404d4f 90:24f166c1dba7
22 22
23 from __future__ import division 23 from __future__ import division
24 24
25 import argparse 25 import argparse
26 import csv 26 import csv
27 import itertools
28 import json 27 import json
29 import operator 28 import operator
30 import os 29 import os
31 import re 30 import re
32 import sys 31 import sys
1293 half1_mate1 = array1_half2 1292 half1_mate1 = array1_half2
1294 half2_mate1 = array1_half 1293 half2_mate1 = array1_half
1295 half1_mate2 = array2_half2 1294 half1_mate2 = array2_half2
1296 half2_mate2 = array2_half 1295 half2_mate2 = array2_half
1297 # calculate HD of "a" in the tag to all "a's" or "b" in the tag to all "b's" 1296 # calculate HD of "a" in the tag to all "a's" or "b" in the tag to all "b's"
1298 dist = np.array([sum(itertools.map(operator.ne, half1_mate1, c)) for c in half1_mate2]) 1297 dist = np.array([sum(map(operator.ne, half1_mate1, c)) for c in half1_mate2])
1299 min_index = np.where(dist == dist.min()) # get index of min HD 1298 min_index = np.where(dist == dist.min()) # get index of min HD
1300 # get all "b's" of the tag or all "a's" of the tag with minimum HD 1299 # get all "b's" of the tag or all "a's" of the tag with minimum HD
1301 min_tag_half2 = half2_mate2[min_index] 1300 min_tag_half2 = half2_mate2[min_index]
1302 min_tag_array2 = array2[min_index] # get whole tag with min HD 1301 min_tag_array2 = array2[min_index] # get whole tag with min HD
1303 min_value = dist.min() 1302 min_value = dist.min()
1304 # calculate HD of "b" to all "b's" or "a" to all "a's" 1303 # calculate HD of "b" to all "b's" or "a" to all "a's"
1305 dist_second_half = np.array([sum(itertools.map(operator.ne, half2_mate1, e)) 1304 dist_second_half = np.array([sum(map(operator.ne, half2_mate1, e))
1306 for e in min_tag_half2]) 1305 for e in min_tag_half2])
1307 dist2 = dist_second_half.max() 1306 dist2 = dist_second_half.max()
1308 max_index = np.where(dist_second_half == dist_second_half.max())[0] # get index of max HD 1307 max_index = np.where(dist_second_half == dist_second_half.max())[0] # get index of max HD
1309 max_tag = min_tag_array2[max_index] 1308 max_tag = min_tag_array2[max_index]
1310 # tags which have identical parts: 1309 # tags which have identical parts: