Mercurial > repos > guerler > springsuite
annotate spring_minz.py @ 33:f115fbf3ac63 draft
"planemo upload commit 90edad77d24453810d6792eaf54ae2ce2ee0913f-dirty"
author | guerler |
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date | Tue, 24 Nov 2020 17:27:22 +0000 |
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1 #! /usr/bin/env python3 |
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2 import argparse |
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3 import os |
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4 |
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5 |
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6 def main(args): |
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7 logFile = open(args.log, 'a+') |
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8 targets = list() |
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9 targetPath = args.targetpath.rstrip("/") |
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10 with open(args.targetlist) as file: |
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11 for line in file: |
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12 name = line.strip() |
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13 targets.append(name) |
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14 print("Loaded %s target names from `%s`." % (len(targets), |
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15 args.targetlist)) |
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16 if args.inputlist: |
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17 inputs = list() |
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18 inputPath = args.inputpath.rstrip("/") |
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19 with open(args.inputlist) as file: |
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20 for line in file: |
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21 name = line.strip() |
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22 inputs.append(name) |
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23 print("Loaded %s input names from `%s`." % (len(inputs), |
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24 args.inputlist)) |
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25 else: |
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26 inputs = targets |
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27 inputPath = targetPath |
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28 crossReference = dict() |
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29 with open(args.crossreference) as file: |
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30 for line in file: |
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31 columns = line.split() |
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32 core = columns[0] |
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33 partner = columns[-1] |
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34 if core not in crossReference: |
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35 crossReference[core] = [] |
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36 crossReference[core].append(partner) |
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37 print("Loaded cross reference from `%s`." % args.crossreference) |
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38 interactions = dict() |
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39 for targetName in targets: |
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40 targetFile = "%s/%s" % (targetPath, targetName) |
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41 matchScores(targetFile=targetFile, |
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42 targetName=targetName, |
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43 inputs=inputs, |
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44 inputPath=inputPath, |
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45 crossReference=crossReference, |
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46 idLength=args.idlength, |
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47 minScore=args.minscore, |
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48 logFile=logFile, |
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49 interactions=interactions) |
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50 if args.inputlist: |
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51 for inputName in inputs: |
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52 inputDirectory = inputPath |
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53 inputFile = "%s/%s" % (inputDirectory, inputName) |
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54 matchScores(targetFile=inputFile, |
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55 targetName=inputName, |
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56 inputs=targets, |
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57 inputPath=targetPath, |
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58 crossReference=crossReference, |
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59 minScore=args.minscore, |
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60 idLength=args.idlength, |
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61 logFile=logFile, |
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62 interactions=interactions) |
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63 interactions = sorted(interactions.values(), key=lambda item: item["minZ"], |
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64 reverse=True) |
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65 with open(args.output, 'w') as output_file: |
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66 for entry in interactions: |
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67 output_file.write("%s\t%s\t%s\t%s\n" % (entry["targetName"], |
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68 entry["inputName"], entry["minZ"], |
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69 entry["minInfo"])) |
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70 logFile.close() |
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71 |
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72 |
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73 def matchScores(targetFile, targetName, inputs, inputPath, crossReference, |
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74 minScore, idLength, logFile, interactions): |
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75 targetTop, targetHits = getTemplateScores(targetFile, minScore, idLength) |
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76 if not targetHits: |
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77 print("No targets found `%s`" % targetFile) |
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78 else: |
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79 print("Loaded target scores from `%s`." % targetFile) |
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80 for inputName in inputs: |
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81 inputFile = "%s/%s" % (inputPath, inputName) |
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82 inputTop, inputHits = getTemplateScores(inputFile, |
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83 minScore, idLength) |
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84 minZ = 0 |
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85 minInfo = "" |
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86 for t in targetHits: |
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87 if t in crossReference: |
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88 partners = crossReference[t] |
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89 for p in partners: |
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90 if p in inputHits: |
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91 score = min(targetHits[t], inputHits[p]) |
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92 if score > minZ: |
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93 minZ = score |
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94 minInfo = "%s\t%s\t%s\t%s" % (targetTop, |
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95 inputTop, t, p) |
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96 if minZ > minScore: |
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97 if targetName > inputName: |
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98 interactionKey = "%s_%s" % (targetName, inputName) |
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99 else: |
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100 interactionKey = "%s_%s" % (inputName, targetName) |
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101 if interactionKey in interactions: |
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102 if interactions[interactionKey]["minZ"] >= minZ: |
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103 continue |
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104 interactions[interactionKey] = dict(targetName=targetName, |
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105 inputName=inputName, |
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106 minZ=minZ, minInfo=minInfo) |
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107 logFile.write("Interaction between %s and %s [min-Z: %s].\n" % |
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108 (targetName, inputName, minZ)) |
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109 |
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110 |
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111 def getTemplateScores(hhrFile, minScore, idLength): |
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112 result = dict() |
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113 topTemplate = None |
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114 idLength = idLength + 4 |
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115 if os.path.isfile(hhrFile): |
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116 with open(hhrFile) as file: |
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117 for index, line in enumerate(file): |
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118 if index > 8: |
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119 if not line.strip(): |
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120 break |
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121 templateId = line[4:idLength] |
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122 templateScore = float(line[57:63]) |
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123 if templateScore > minScore: |
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124 if topTemplate is None: |
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125 topTemplate = templateId |
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126 result[templateId] = templateScore |
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127 return topTemplate, result |
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128 |
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129 |
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130 if __name__ == "__main__": |
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131 parser = argparse.ArgumentParser(description='This script identifies interactions by detecting matching HH-search results.') |
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132 parser.add_argument('-tl', '--targetlist', help='Text file containing identifiers.', required=True) |
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133 parser.add_argument('-tp', '--targetpath', help='Directory containing `hhr` files', required=True) |
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134 parser.add_argument('-il', '--inputlist', help='Text file containing identifiers.', required=False) |
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135 parser.add_argument('-ip', '--inputpath', help='Directory containing `hhr` files', required=False) |
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136 parser.add_argument('-c', '--crossreference', help='Cross Reference index file', required=True) |
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137 parser.add_argument('-o', '--output', help='Output file containing min-Z scores', required=True) |
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138 parser.add_argument('-l', '--log', help='Log file', required=True) |
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139 parser.add_argument('-m', '--minscore', help='min-Z score threshold', type=int, default=10) |
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140 parser.add_argument('-idx', '--idlength', help='Length of identifier in reference', type=int, default=6) |
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141 args = parser.parse_args() |
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142 main(args) |