54320c314f235d369ef86bc9a6f2f5acf2526275,hicexplorer/hicMergeDomains.py,,main,#Any#,382

Before Change

    listOfDomains = []
    ctcfList = None
    if args.ctcfFile is not None:
        log.debug("ctcf: true")
        ctcfList = read_ctcf(args.ctcfFile)
        log.debug("ctcfList {}".format(ctcfList[:10]))

    mergedList = create_list_with_ctcf(args.domainFiles[0], args.minPeak, ctcfList)

After Change

    mergedList = create_list_with_protein(args.domainFiles[0], args.minPeak, proteinList)

    if len(args.domainFiles) > 1:
        for domain in args.domainFiles[1:]:
            listOfDomains.append(create_list_with_protein(domain, args.minPeak, proteinList))
        for domain in listOfDomains:
            mergedList = merge_list(mergedList, domain, pValue)

    mergedListWithId = add_id(mergedList)
    write_in_file(mergedListWithId, args.outputMergedList)
    if len(args.domainFiles) > 1:
        relationList = create_relationsship_list(mergedListWithId, args.percent)

Instances