Mercurial > repos > guerler > springsuite
view 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 |
parents | 41353488926c |
children | 172398348efd |
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#! /usr/bin/env python3 import argparse import os def main(args): logFile = open(args.log, 'a+') targets = list() targetPath = args.targetpath.rstrip("/") with open(args.targetlist) as file: for line in file: name = line.strip() targets.append(name) print("Loaded %s target names from `%s`." % (len(targets), args.targetlist)) if args.inputlist: inputs = list() inputPath = args.inputpath.rstrip("/") with open(args.inputlist) as file: for line in file: name = line.strip() inputs.append(name) print("Loaded %s input names from `%s`." % (len(inputs), args.inputlist)) else: inputs = targets inputPath = targetPath crossReference = dict() with open(args.crossreference) as file: for line in file: columns = line.split() core = columns[0] partner = columns[-1] if core not in crossReference: crossReference[core] = [] crossReference[core].append(partner) print("Loaded cross reference from `%s`." % args.crossreference) interactions = dict() for targetName in targets: targetFile = "%s/%s" % (targetPath, targetName) matchScores(targetFile=targetFile, targetName=targetName, inputs=inputs, inputPath=inputPath, crossReference=crossReference, idLength=args.idlength, minScore=args.minscore, logFile=logFile, interactions=interactions) if args.inputlist: for inputName in inputs: inputDirectory = inputPath inputFile = "%s/%s" % (inputDirectory, inputName) matchScores(targetFile=inputFile, targetName=inputName, inputs=targets, inputPath=targetPath, crossReference=crossReference, minScore=args.minscore, idLength=args.idlength, logFile=logFile, interactions=interactions) interactions = sorted(interactions.values(), key=lambda item: item["minZ"], reverse=True) with open(args.output, 'w') as output_file: for entry in interactions: output_file.write("%s\t%s\t%s\t%s\n" % (entry["targetName"], entry["inputName"], entry["minZ"], entry["minInfo"])) logFile.close() def matchScores(targetFile, targetName, inputs, inputPath, crossReference, minScore, idLength, logFile, interactions): targetTop, targetHits = getTemplateScores(targetFile, minScore, idLength) if not targetHits: print("No targets found `%s`" % targetFile) else: print("Loaded target scores from `%s`." % targetFile) for inputName in inputs: inputFile = "%s/%s" % (inputPath, inputName) inputTop, inputHits = getTemplateScores(inputFile, minScore, idLength) minZ = 0 minInfo = "" for t in targetHits: if t in crossReference: partners = crossReference[t] for p in partners: if p in inputHits: score = min(targetHits[t], inputHits[p]) if score > minZ: minZ = score minInfo = "%s\t%s\t%s\t%s" % (targetTop, inputTop, t, p) if minZ > minScore: if targetName > inputName: interactionKey = "%s_%s" % (targetName, inputName) else: interactionKey = "%s_%s" % (inputName, targetName) if interactionKey in interactions: if interactions[interactionKey]["minZ"] >= minZ: continue interactions[interactionKey] = dict(targetName=targetName, inputName=inputName, minZ=minZ, minInfo=minInfo) logFile.write("Interaction between %s and %s [min-Z: %s].\n" % (targetName, inputName, minZ)) def getTemplateScores(hhrFile, minScore, idLength): result = dict() topTemplate = None idLength = idLength + 4 if os.path.isfile(hhrFile): with open(hhrFile) as file: for index, line in enumerate(file): if index > 8: if not line.strip(): break templateId = line[4:idLength] templateScore = float(line[57:63]) if templateScore > minScore: if topTemplate is None: topTemplate = templateId result[templateId] = templateScore return topTemplate, result if __name__ == "__main__": parser = argparse.ArgumentParser(description='This script identifies interactions by detecting matching HH-search results.') parser.add_argument('-tl', '--targetlist', help='Text file containing identifiers.', required=True) parser.add_argument('-tp', '--targetpath', help='Directory containing `hhr` files', required=True) parser.add_argument('-il', '--inputlist', help='Text file containing identifiers.', required=False) parser.add_argument('-ip', '--inputpath', help='Directory containing `hhr` files', required=False) parser.add_argument('-c', '--crossreference', help='Cross Reference index file', required=True) parser.add_argument('-o', '--output', help='Output file containing min-Z scores', required=True) parser.add_argument('-l', '--log', help='Log file', required=True) parser.add_argument('-m', '--minscore', help='min-Z score threshold', type=int, default=10) parser.add_argument('-idx', '--idlength', help='Length of identifier in reference', type=int, default=6) args = parser.parse_args() main(args)