def resultfiletopairs(filename, outname):
print "init gene level proteins ..."
proteinsA, proteinsB, orthologs = GeneLevelProtein.initGeneLevelProteins(filename, None, None, False)
print "pairwise orthology mappings ..."
pairwise = Helper.pairwiseOrthologs(orthologs, proteinsA, proteinsB)
Helper.printPairsToFile(pairwise, outname)
def resultfiletopairs(filename, outname):
print "init gene level proteins ..."
proteinsA, proteinsB, orthologs = GeneLevelProtein.initGeneLevelProteins(
filename, None, None, False)
print "pairwise orthology mappings ..."
pairwise = Helper.pairwiseOrthologs(orthologs, proteinsA, proteinsB)
Helper.printPairsToFile(pairwise, outname)
tsvB = rcp.get("Filepaths", "tsvpath") + arg + ".tsv"
taxB = arg
elif opt in ("-w", "--write"):
write = True
else:
ok = False
if ok:
if not write:
"Option -w was not set."
cutoff = rcp.getint("Options","domainlengthcutoff")
#intialising
proteinsA, proteinsB, orthologs, shortA, shortB = GeneLevelProtein.initGeneLevelProteins(fullfile, tsvA, tsvB, True)
domainsA, domainsB, orthologsD = DomainLevelProtein.initDomainLevelProteins(domainfile)
#calc pairwise ortholog mappings
print "pairwise orthology mappings ..."
pairwise = Helper.pairwiseOrthologs(orthologs, proteinsA, proteinsB)
print "pairwise domain orthology mappings ..."
pairwiseDomains = Helper.pairwiseOrthologs(orthologsD, domainsA, domainsB)
#analysing stuff
print "mapping domains to proteins ..."
mapping = mapDomainOrthologsToProteins(pairwiseDomains, domainsA, domainsB)
print "add counters to full sequence orthologs ..."
counters = addMinimumDomainCountToFullOrthologs(pairwise)
print "find proteins where all / not all / not any domains infer orthology ..."
allDomains, notAll, notAny = findProteinsWhereAllDomainsInferOrthology(counters, mapping)
