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annotate dotPrep.py @ 0:732267cab191 draft default tip

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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/dotprep commit 6db87bb19217d256b13cd66810043b667d1c7638
author bgruening
date Wed, 03 Dec 2025 16:17:07 +0000
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732267cab191 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/dotprep commit 6db87bb19217d256b13cd66810043b667d1c7638
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1 #! /usr/bin/env python
732267cab191 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/dotprep commit 6db87bb19217d256b13cd66810043b667d1c7638
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3 # Author: Maria Nattestad
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4 # Email: maria.nattestad@gmail.com
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6 import argparse
732267cab191 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/dotprep commit 6db87bb19217d256b13cd66810043b667d1c7638
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7 import gzip
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8 import operator
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9 import re
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10 import time
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13 import numpy as np
732267cab191 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/dotprep commit 6db87bb19217d256b13cd66810043b667d1c7638
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16 def run(args):
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17 filename = args.delta
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18 unique_length = args.unique_length
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19 output_filename = args.out
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20 keep_small_uniques = True
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21 max_overview_alignments = args.overview
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23 header_lines_by_query, lines_by_query = get_query_ref_combinations(filename)
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25 unique_alignments = calculate_uniqueness(
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26 header_lines_by_query, lines_by_query, unique_length, keep_small_uniques
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27 )
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29 reference_lengths, fields_by_query = write_filtered_delta_file(
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30 filename,
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31 output_filename,
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32 unique_alignments,
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33 unique_length,
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34 header_lines_by_query,
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35 )
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37 index_for_dot(reference_lengths, fields_by_query, output_filename, max_overview_alignments)
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40 def scrub(string):
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41 return (
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42 string.replace(",", "_")
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43 .replace("!", "_")
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44 .replace("~", "_")
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45 .replace("#", "_")
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46 )
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49 def get_query_ref_combinations(filename):
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50 print("header from delta file:")
732267cab191 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/dotprep commit 6db87bb19217d256b13cd66810043b667d1c7638
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51 try:
732267cab191 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/dotprep commit 6db87bb19217d256b13cd66810043b667d1c7638
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52 f = gzip.open(filename, "rt")
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53 print(f.readline().strip())
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54 except OSError:
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55 f = open(filename, "r")
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56 print(f.readline().strip())
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57
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58 print(f.readline().strip())
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59 linecounter = 0
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60 current_query_name = ""
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61 current_header = ""
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62 lines_by_query = {}
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63 header_lines_by_query = {}
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64 before = time.time()
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65
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66 for line in f:
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67 if line[0] == ">":
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68 linecounter += 1
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69 current_header = line.strip()
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70 current_query_name = scrub(current_header.split()[1])
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71
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72 if header_lines_by_query.get(current_query_name) is None:
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73 lines_by_query[current_query_name] = []
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74 header_lines_by_query[current_query_name] = []
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75 else:
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76 fields = line.strip().split()
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77 if len(fields) > 4:
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78 query_min = min(int(fields[2]), int(fields[3]))
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79 query_max = max(int(fields[2]), int(fields[3]))
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80 lines_by_query[current_query_name].append((query_min, query_max))
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81 header_lines_by_query[current_query_name].append(current_header)
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82
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83 f.close()
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84 print(
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85 "First read through the file: %d seconds for %d query-reference combinations"
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86 % (time.time() - before, linecounter)
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87 )
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88 return header_lines_by_query, lines_by_query
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89
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90
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91 def calculate_uniqueness(header_lines_by_query, lines_by_query, unique_length, keep_small_uniques):
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92 before = time.time()
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93 unique_alignments = {}
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94 num_queries = len(lines_by_query)
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95 print("Filtering alignments of %d queries" % num_queries)
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96
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97 num_query_step_to_report = max(num_queries / 100, 1)
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98 query_counter = 0
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99
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100 for query in lines_by_query:
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101 unique_alignments[query] = summarize_planesweep(
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102 lines_by_query[query],
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103 unique_length_required=unique_length,
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104 keep_small_uniques=keep_small_uniques,
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105 )
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106 query_counter += 1
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107 if query_counter % num_query_step_to_report == 0:
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108 print("Progress: %d%%" % (query_counter * 100 / num_queries))
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109
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110 print("Progress: 100%")
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111 print(
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112 "Deciding which alignments to keep: %d seconds for %d queries"
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113 % (time.time() - before, num_queries)
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114 )
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115 return unique_alignments
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116
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117
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118 def summarize_planesweep(lines, unique_length_required, keep_small_uniques=False):
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119 unique_alignments = []
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120 if len(lines) == 0:
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121 return []
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122 if len(lines) == 1:
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123 if keep_small_uniques or abs(lines[0][1] - lines[0][0]) >= unique_length_required:
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124 return [0]
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125 return []
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126
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127 starts_and_stops = []
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128 for query_min, query_max in lines:
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129 starts_and_stops.append((query_min, "start"))
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130 starts_and_stops.append((query_max, "stop"))
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131
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132 sorted_starts_and_stops = sorted(starts_and_stops, key=operator.itemgetter(0))
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133 current_coverage = 0
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134 last_position = -1
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135 sorted_unique_intervals_left = []
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136 sorted_unique_intervals_right = []
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137
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138 for pos, change in sorted_starts_and_stops:
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139 if current_coverage == 1:
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140 sorted_unique_intervals_left.append(last_position)
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141 sorted_unique_intervals_right.append(pos)
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142 if change == "start":
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143 current_coverage += 1
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144 else:
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145 current_coverage -= 1
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146 last_position = pos
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147
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148 linecounter = 0
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149 for query_min, query_max in lines:
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150 i = binary_search(query_min, sorted_unique_intervals_left, 0, len(sorted_unique_intervals_left))
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151 exact_match = False
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152 if i < len(sorted_unique_intervals_left):
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153 if (
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154 sorted_unique_intervals_left[i] == query_min
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155 and sorted_unique_intervals_right[i] == query_max
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156 ):
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157 exact_match = True
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158 sum_uniq = 0
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159 while (
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160 i < len(sorted_unique_intervals_left)
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161 and sorted_unique_intervals_left[i] >= query_min
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162 and sorted_unique_intervals_right[i] <= query_max
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163 ):
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164 sum_uniq += sorted_unique_intervals_right[i] - sorted_unique_intervals_left[i]
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165 i += 1
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166 if sum_uniq >= unique_length_required:
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167 unique_alignments.append(linecounter)
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168 elif keep_small_uniques and exact_match:
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169 unique_alignments.append(linecounter)
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170 linecounter += 1
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171
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172 return unique_alignments
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173
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174
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175 def binary_search(query, numbers, left, right):
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176 if left >= right:
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177 return right
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178 mid = int((right + left) / 2)
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179 if query == numbers[mid]:
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180 return mid
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181 if query < numbers[mid]:
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182 return binary_search(query, numbers, left, mid)
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183 return binary_search(query, numbers, mid + 1, right)
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184
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185
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186 def natural_key(string_):
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187 return [int(s) if s.isdigit() else s for s in re.split(r"(\d+)", string_)]
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188
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189
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190 def write_filtered_delta_file(filename, output_filename, unique_alignments, unique_length, header_lines_by_query):
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191 before = time.time()
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192 f_out_delta = gzip.open(
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193 f"{output_filename}.uniqueAnchorFiltered_l{unique_length}.delta.gz",
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194 "wt",
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195 )
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196 try:
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197 f = gzip.open(filename, "rt")
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198 header1 = f.readline()
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199 except OSError:
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200 f = open(filename, "r")
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parents:
diff changeset
201 header1 = f.readline()
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202
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203 f_out_delta.write(header1)
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204 f_out_delta.write(f.readline())
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bgruening
parents:
diff changeset
205 linecounter = 0
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diff changeset
206
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bgruening
parents:
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207 list_of_unique_alignments = []
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bgruening
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208 alignment_counter = {}
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bgruening
parents:
diff changeset
209 keep_printing = False
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parents:
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210 ref_sequences = set()
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bgruening
parents:
diff changeset
211 query_sequences = set()
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bgruening
parents:
diff changeset
212 reference_lengths = []
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diff changeset
213 query_lengths = {}
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bgruening
parents:
diff changeset
214 fields_by_query = {}
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215
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bgruening
parents:
diff changeset
216 for line in f:
732267cab191 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/dotprep commit 6db87bb19217d256b13cd66810043b667d1c7638
bgruening
parents:
diff changeset
217 linecounter += 1
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bgruening
parents:
diff changeset
218 if line[0] == ">":
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bgruening
parents:
diff changeset
219 fields = line.strip().split()
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bgruening
parents:
diff changeset
220 query = scrub(fields[1])
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bgruening
parents:
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221 list_of_unique_alignments = unique_alignments[query]
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222
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parents:
diff changeset
223 header_needed = any(
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parents:
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224 line.strip() == header_lines_by_query[query][index]
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225 for index in list_of_unique_alignments
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parents:
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226 )
732267cab191 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/dotprep commit 6db87bb19217d256b13cd66810043b667d1c7638
bgruening
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227 if header_needed:
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bgruening
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228 f_out_delta.write(line)
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parents:
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229
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bgruening
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230 alignment_counter[query] = alignment_counter.get(query, 0)
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bgruening
parents:
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231 current_reference_name = scrub(fields[0][1:])
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bgruening
parents:
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232 current_query_name = scrub(fields[1])
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bgruening
parents:
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233 current_reference_size = int(fields[2])
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bgruening
parents:
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234 current_query_size = int(fields[3])
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parents:
diff changeset
235
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bgruening
parents:
diff changeset
236 if current_reference_name not in ref_sequences:
732267cab191 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/dotprep commit 6db87bb19217d256b13cd66810043b667d1c7638
bgruening
parents:
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237 reference_lengths.append((current_reference_name, current_reference_size))
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bgruening
parents:
diff changeset
238 ref_sequences.add(current_reference_name)
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bgruening
parents:
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239 if current_query_name not in query_sequences:
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bgruening
parents:
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240 query_lengths[current_query_name] = current_query_size
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bgruening
parents:
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241 query_sequences.add(current_query_name)
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diff changeset
242
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bgruening
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diff changeset
243 else:
732267cab191 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/dotprep commit 6db87bb19217d256b13cd66810043b667d1c7638
bgruening
parents:
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244 fields = line.strip().split()
732267cab191 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/dotprep commit 6db87bb19217d256b13cd66810043b667d1c7638
bgruening
parents:
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245 if len(fields) > 4:
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bgruening
parents:
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246 ref_start = int(fields[0])
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bgruening
parents:
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247 ref_end = int(fields[1])
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bgruening
parents:
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248 query_start = int(fields[2])
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bgruening
parents:
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249 query_end = int(fields[3])
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bgruening
parents:
diff changeset
250 csv_tag = "repetitive"
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bgruening
parents:
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251 if alignment_counter[query] in list_of_unique_alignments:
732267cab191 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/dotprep commit 6db87bb19217d256b13cd66810043b667d1c7638
bgruening
parents:
diff changeset
252 f_out_delta.write(line)
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bgruening
parents:
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253 csv_tag = "unique"
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bgruening
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254 keep_printing = True
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bgruening
parents:
diff changeset
255 else:
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bgruening
parents:
diff changeset
256 keep_printing = False
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parents:
diff changeset
257 record = [
732267cab191 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/dotprep commit 6db87bb19217d256b13cd66810043b667d1c7638
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diff changeset
258 ref_start,
732267cab191 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/dotprep commit 6db87bb19217d256b13cd66810043b667d1c7638
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parents:
diff changeset
259 ref_end,
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parents:
diff changeset
260 query_start,
732267cab191 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/dotprep commit 6db87bb19217d256b13cd66810043b667d1c7638
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parents:
diff changeset
261 query_end,
732267cab191 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/dotprep commit 6db87bb19217d256b13cd66810043b667d1c7638
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parents:
diff changeset
262 current_reference_size,
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parents:
diff changeset
263 current_query_size,
732267cab191 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/dotprep commit 6db87bb19217d256b13cd66810043b667d1c7638
bgruening
parents:
diff changeset
264 current_reference_name,
732267cab191 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/dotprep commit 6db87bb19217d256b13cd66810043b667d1c7638
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parents:
diff changeset
265 current_query_name,
732267cab191 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/dotprep commit 6db87bb19217d256b13cd66810043b667d1c7638
bgruening
parents:
diff changeset
266 csv_tag,
732267cab191 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/dotprep commit 6db87bb19217d256b13cd66810043b667d1c7638
bgruening
parents:
diff changeset
267 ]
732267cab191 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/dotprep commit 6db87bb19217d256b13cd66810043b667d1c7638
bgruening
parents:
diff changeset
268 if fields_by_query.get(current_query_name) is None:
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bgruening
parents:
diff changeset
269 fields_by_query[current_query_name] = []
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bgruening
parents:
diff changeset
270 fields_by_query[current_query_name].append(record)
732267cab191 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/dotprep commit 6db87bb19217d256b13cd66810043b667d1c7638
bgruening
parents:
diff changeset
271 alignment_counter[query] += 1
732267cab191 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/dotprep commit 6db87bb19217d256b13cd66810043b667d1c7638
bgruening
parents:
diff changeset
272 elif keep_printing:
732267cab191 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/dotprep commit 6db87bb19217d256b13cd66810043b667d1c7638
bgruening
parents:
diff changeset
273 f_out_delta.write(line)
732267cab191 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/dotprep commit 6db87bb19217d256b13cd66810043b667d1c7638
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parents:
diff changeset
274
732267cab191 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/dotprep commit 6db87bb19217d256b13cd66810043b667d1c7638
bgruening
parents:
diff changeset
275 f.close()
732267cab191 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/dotprep commit 6db87bb19217d256b13cd66810043b667d1c7638
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parents:
diff changeset
276 f_out_delta.close()
732267cab191 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/dotprep commit 6db87bb19217d256b13cd66810043b667d1c7638
bgruening
parents:
diff changeset
277 print(
732267cab191 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/dotprep commit 6db87bb19217d256b13cd66810043b667d1c7638
bgruening
parents:
diff changeset
278 "Writing filtered delta file and capturing information for coords file: "
732267cab191 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/dotprep commit 6db87bb19217d256b13cd66810043b667d1c7638
bgruening
parents:
diff changeset
279 "%d seconds for %d total lines in file"
732267cab191 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/dotprep commit 6db87bb19217d256b13cd66810043b667d1c7638
bgruening
parents:
diff changeset
280 % (time.time() - before, linecounter)
732267cab191 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/dotprep commit 6db87bb19217d256b13cd66810043b667d1c7638
bgruening
parents:
diff changeset
281 )
732267cab191 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/dotprep commit 6db87bb19217d256b13cd66810043b667d1c7638
bgruening
parents:
diff changeset
282 return reference_lengths, fields_by_query
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bgruening
parents:
diff changeset
283
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parents:
diff changeset
284
732267cab191 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/dotprep commit 6db87bb19217d256b13cd66810043b667d1c7638
bgruening
parents:
diff changeset
285 def index_for_dot(reference_lengths, fields_by_query, output_prefix, max_overview_alignments):
732267cab191 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/dotprep commit 6db87bb19217d256b13cd66810043b667d1c7638
bgruening
parents:
diff changeset
286 reference_lengths.sort(key=lambda x: natural_key(x[0]))
732267cab191 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/dotprep commit 6db87bb19217d256b13cd66810043b667d1c7638
bgruening
parents:
diff changeset
287 cumulative_sum = 0
732267cab191 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/dotprep commit 6db87bb19217d256b13cd66810043b667d1c7638
bgruening
parents:
diff changeset
288 ref_chrom_offsets = {}
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bgruening
parents:
diff changeset
289 queries_by_reference = {}
732267cab191 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/dotprep commit 6db87bb19217d256b13cd66810043b667d1c7638
bgruening
parents:
diff changeset
290
732267cab191 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/dotprep commit 6db87bb19217d256b13cd66810043b667d1c7638
bgruening
parents:
diff changeset
291 for ref_name, ref_length in reference_lengths:
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bgruening
parents:
diff changeset
292 ref_chrom_offsets[ref_name] = cumulative_sum
732267cab191 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/dotprep commit 6db87bb19217d256b13cd66810043b667d1c7638
bgruening
parents:
diff changeset
293 cumulative_sum += ref_length
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bgruening
parents:
diff changeset
294 queries_by_reference[ref_name] = set()
732267cab191 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/dotprep commit 6db87bb19217d256b13cd66810043b667d1c7638
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parents:
diff changeset
295
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parents:
diff changeset
296 flip_by_query = {}
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bgruening
parents:
diff changeset
297 unique_references_by_query = {}
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parents:
diff changeset
298 all_references_by_query = {}
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bgruening
parents:
diff changeset
299 relative_ref_position_by_query = []
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bgruening
parents:
diff changeset
300 ordered_tags = ["unique", "repetitive"]
732267cab191 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/dotprep commit 6db87bb19217d256b13cd66810043b667d1c7638
bgruening
parents:
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301
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302 f_out_coords = open(f"{output_prefix}.coords", "w", encoding="utf-8")
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303 f_out_coords.write("ref_start,ref_end,query_start,query_end,ref\n")
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304
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305 query_byte_positions = {}
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306 query_lengths = {}
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307 all_alignments = []
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308 last_query = ""
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309
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310 for query_name, lines in fields_by_query.items():
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311 sum_forward = 0
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312 sum_reverse = 0
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313 ref_position_scores = []
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314 unique_references_by_query[query_name] = set()
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315 all_references_by_query[query_name] = set()
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316
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bgruening
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317 for fields in lines:
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318 tag = fields[8]
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319 query_lengths[query_name] = int(fields[5])
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320 ref_name = fields[6]
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321 all_references_by_query[query_name].add(ref_name)
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322 if tag == "unique":
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323 query_start = int(fields[2])
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324 query_stop = int(fields[3])
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325 ref_start = int(fields[0])
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326 ref_stop = int(fields[1])
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327 alignment_length = abs(query_stop - query_start)
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328 unique_references_by_query[query_name].add(ref_name)
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329 queries_by_reference[ref_name].add(query_name)
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330 ref_position_scores.append(
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bgruening
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331 ref_chrom_offsets[ref_name] + (ref_start + ref_stop) / 2
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332 )
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bgruening
parents:
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333 if query_stop < query_start:
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bgruening
parents:
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334 sum_reverse += alignment_length
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bgruening
parents:
diff changeset
335 else:
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336 sum_forward += alignment_length
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337
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338 flip = sum_reverse > sum_forward
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parents:
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339 flip_by_query[query_name] = "-" if flip else "+"
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340
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341 for tag in ordered_tags:
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342 query_byte_positions[(last_query, "end")] = f_out_coords.tell()
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bgruening
parents:
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343 query_byte_positions[(query_name, tag)] = f_out_coords.tell()
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344 f_out_coords.write(f"!{query_name}!{tag}\n")
732267cab191 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/dotprep commit 6db87bb19217d256b13cd66810043b667d1c7638
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345 for fields in lines:
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346 if fields[8] == tag:
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347 if flip:
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348 fields[2] = int(fields[5]) - int(fields[2])
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bgruening
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349 fields[3] = int(fields[5]) - int(fields[3])
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350 output_fields = [fields[0], fields[1], fields[2], fields[3], fields[6]]
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351 f_out_coords.write(",".join(str(i) for i in output_fields) + "\n")
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parents:
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352 alignment_length = abs(int(fields[3]) - int(fields[2]))
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353 all_alignments.append((fields, alignment_length))
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354
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355 rel_pos = np.median(ref_position_scores) if ref_position_scores else 0
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diff changeset
356 relative_ref_position_by_query.append((query_name, rel_pos))
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diff changeset
357 last_query = query_name
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diff changeset
358
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diff changeset
359 query_byte_positions[(last_query, "end")] = f_out_coords.tell()
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parents:
diff changeset
360 relative_ref_position_by_query.sort(key=lambda x: x[1])
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parents:
diff changeset
361
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parents:
diff changeset
362 f_out_index = open(f"{output_prefix}.coords.idx", "w", encoding="utf-8")
732267cab191 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/dotprep commit 6db87bb19217d256b13cd66810043b667d1c7638
bgruening
parents:
diff changeset
363 f_out_index.write("#ref\n")
732267cab191 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/dotprep commit 6db87bb19217d256b13cd66810043b667d1c7638
bgruening
parents:
diff changeset
364 f_out_index.write("ref,ref_length,matching_queries\n")
732267cab191 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/dotprep commit 6db87bb19217d256b13cd66810043b667d1c7638
bgruening
parents:
diff changeset
365 for ref_name, ref_length in reference_lengths:
732267cab191 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/dotprep commit 6db87bb19217d256b13cd66810043b667d1c7638
bgruening
parents:
diff changeset
366 f_out_index.write(
732267cab191 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/dotprep commit 6db87bb19217d256b13cd66810043b667d1c7638
bgruening
parents:
diff changeset
367 f"{ref_name},{ref_length},{'~'.join(queries_by_reference[ref_name])}\n"
732267cab191 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/dotprep commit 6db87bb19217d256b13cd66810043b667d1c7638
bgruening
parents:
diff changeset
368 )
732267cab191 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/dotprep commit 6db87bb19217d256b13cd66810043b667d1c7638
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parents:
diff changeset
369
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bgruening
parents:
diff changeset
370 f_out_index.write("#query\n")
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bgruening
parents:
diff changeset
371 f_out_index.write(
732267cab191 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/dotprep commit 6db87bb19217d256b13cd66810043b667d1c7638
bgruening
parents:
diff changeset
372 "query,query_length,orientation,bytePosition_unique,"
732267cab191 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/dotprep commit 6db87bb19217d256b13cd66810043b667d1c7638
bgruening
parents:
diff changeset
373 "bytePosition_repetitive,bytePosition_end,unique_matching_refs,matching_refs\n"
732267cab191 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/dotprep commit 6db87bb19217d256b13cd66810043b667d1c7638
bgruening
parents:
diff changeset
374 )
732267cab191 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/dotprep commit 6db87bb19217d256b13cd66810043b667d1c7638
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parents:
diff changeset
375
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bgruening
parents:
diff changeset
376 for query_name, _ in relative_ref_position_by_query:
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bgruening
parents:
diff changeset
377 f_out_index.write(
732267cab191 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/dotprep commit 6db87bb19217d256b13cd66810043b667d1c7638
bgruening
parents:
diff changeset
378 f"{query_name},{query_lengths[query_name]},{flip_by_query[query_name]},"
732267cab191 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/dotprep commit 6db87bb19217d256b13cd66810043b667d1c7638
bgruening
parents:
diff changeset
379 f"{query_byte_positions[(query_name, 'unique')]},"
732267cab191 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/dotprep commit 6db87bb19217d256b13cd66810043b667d1c7638
bgruening
parents:
diff changeset
380 f"{query_byte_positions[(query_name, 'repetitive')] - query_byte_positions[(query_name, 'unique')]},"
732267cab191 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/dotprep commit 6db87bb19217d256b13cd66810043b667d1c7638
bgruening
parents:
diff changeset
381 f"{query_byte_positions[(query_name, 'end')] - query_byte_positions[(query_name, 'repetitive')]},"
732267cab191 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/dotprep commit 6db87bb19217d256b13cd66810043b667d1c7638
bgruening
parents:
diff changeset
382 f"{'~'.join(unique_references_by_query[query_name])},"
732267cab191 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/dotprep commit 6db87bb19217d256b13cd66810043b667d1c7638
bgruening
parents:
diff changeset
383 f"{'~'.join(all_references_by_query[query_name])}\n"
732267cab191 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/dotprep commit 6db87bb19217d256b13cd66810043b667d1c7638
bgruening
parents:
diff changeset
384 )
732267cab191 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/dotprep commit 6db87bb19217d256b13cd66810043b667d1c7638
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parents:
diff changeset
385
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bgruening
parents:
diff changeset
386 f_out_index.write("#overview\n")
732267cab191 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/dotprep commit 6db87bb19217d256b13cd66810043b667d1c7638
bgruening
parents:
diff changeset
387 f_out_index.write("ref_start,ref_end,query_start,query_end,ref,query,tag\n")
732267cab191 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/dotprep commit 6db87bb19217d256b13cd66810043b667d1c7638
bgruening
parents:
diff changeset
388
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bgruening
parents:
diff changeset
389 num_overview_alignments = min(max_overview_alignments, len(all_alignments))
732267cab191 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/dotprep commit 6db87bb19217d256b13cd66810043b667d1c7638
bgruening
parents:
diff changeset
390 if num_overview_alignments < len(all_alignments):
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bgruening
parents:
diff changeset
391 print(
732267cab191 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/dotprep commit 6db87bb19217d256b13cd66810043b667d1c7638
bgruening
parents:
diff changeset
392 f"Included the longest {max_overview_alignments} alignments in the index "
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bgruening
parents:
diff changeset
393 f"under #overview (change this with the --overview parameter), "
732267cab191 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/dotprep commit 6db87bb19217d256b13cd66810043b667d1c7638
bgruening
parents:
diff changeset
394 f"out of a total of {len(all_alignments)} alignments."
732267cab191 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/dotprep commit 6db87bb19217d256b13cd66810043b667d1c7638
bgruening
parents:
diff changeset
395 )
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parents:
diff changeset
396
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397 all_alignments.sort(key=lambda x: -x[1])
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398 for fields, _ in all_alignments[:num_overview_alignments]:
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399 f_out_index.write(",".join(str(i) for i in fields[:9]) + "\n")
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400
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401 f_out_coords.close()
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402 f_out_index.close()
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403
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404
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405 def main():
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406 parser = argparse.ArgumentParser(
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407 description="Take a delta file, apply Assemblytics unique anchor filtering, "
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408 "and prepare coordinates input files for Dot"
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409 )
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410 parser.add_argument("--delta", help="delta file", dest="delta", type=str, required=True)
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411 parser.add_argument("--out", help="output file", dest="out", type=str, default="output")
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412 parser.add_argument(
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413 "--unique-length",
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414 help="Minimum unique query sequence length required (default: 10000)",
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415 dest="unique_length",
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416 type=int,
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417 default=10000,
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418 )
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419 parser.add_argument(
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420 "--overview",
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421 help="Number of alignments to include in coords.idx overview (default: 1000)",
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422 dest="overview",
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423 type=int,
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424 default=1000,
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425 )
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426 parser.set_defaults(func=run)
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427 args = parser.parse_args()
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428 args.func(args)
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429
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430
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431 if __name__ == "__main__":
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432 main()