annotate spring_minz.py @ 29:41353488926c draft

"planemo upload commit 1c0a60f98e36bccb6d6c85ff82a8d737a811b4d5"
author guerler
date Sun, 22 Nov 2020 14:15:24 +0000
parents e34da554d415
children 172398348efd
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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
0
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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)