本文整理汇总了Python中Helper.initTsvForOrganism方法的典型用法代码示例。如果您正苦于以下问题：Python Helper.initTsvForOrganism方法的具体用法？Python Helper.initTsvForOrganism怎么用？Python Helper.initTsvForOrganism使用的例子？那么恭喜您, 这里精选的方法代码示例或许可以为您提供帮助。您也可以进一步了解该方法所在类Helper的用法示例。
在下文中一共展示了Helper.initTsvForOrganism方法的3个代码示例，这些例子默认根据受欢迎程度排序。您可以为喜欢或者感觉有用的代码点赞，您的评价将有助于系统推荐出更棒的Python代码示例。
示例1: findProteinsOrthologyOnlyByDomains
# 需要导入模块: import Helper [as 别名]
# 或者: from Helper import initTsvForOrganism [as 别名]
def findProteinsOrthologyOnlyByDomains(proteinsA, proteinsB, pairsDomains, pairsFull, taxidA, taxidB, cutoff):
only = []
other = [] #other contains accession ids of proteins that have no orthology but at least one domain of them has
tsvA = Helper.initTsvForOrganism(taxidA)
tsvB = Helper.initTsvForOrganism(taxidB)
for pair in pairsDomains:
if pair not in pairsFull:
amount = min(len(tsvA[pair.first]), len(tsvB[pair.second]))
if pairsDomains[pair] >= amount:
only.append(pair)
other.append(pair)
return only示例2: float
# 需要导入模块: import Helper [as 别名]
# 或者: from Helper import initTsvForOrganism [as 别名]
# pairfile = filename + ".pairs.txt"
#===========================================================================
pairfile = filename + ".pairs.txt"
resultFileToPairs.resultfiletopairs(filename, pairfile)
header = Helper.readHeaderFromResult(filename)
dAB = float(header.proteinsA - header.inparalogsA) / float(header.proteinsA) * 100.0
dBA = float(header.proteinsB - header.inparalogsB) / float(header.proteinsB) * 100.0
print "distance AB", dAB
print "distance BA", dBA
domainsA = Helper.initTsvForOrganism(taxA)
domainsB = Helper.initTsvForOrganism(taxB)
pairs = Helper.readPairwise(pairfile)
print len(pairs), "pairs"
print len(Helper.unique(pairs)), "unique pairs"
groups = BasicOrthologyGroup.buildGroupsFromPairs(pairs)
print len(groups), "groups"
canrecapture = []
canrecapgroups = []
cannotrecapgroups = []
countsA = []
lengthsA = []
countsB = []示例3: in
# 需要导入模块: import Helper [as 别名]
# 或者: from Helper import initTsvForOrganism [as 别名]
if o in ("-a", "--taxidA"):
taxA = a
elif o in ("-b", "--taxidB"):
taxB = a
elif o in ("-f", "--ffile"):
inputfile = resultpath + a
elif o in ("-o", "--ofile"):
outputname = a
elif o in ("-d", "--dfile"):
dfile = resultpath + a
else:
print "Didn't expect", o, a
print __doc__
sys.exit(2)
tsvA = Helper.initTsvForOrganism(taxA)
tsvB = Helper.initTsvForOrganism(taxB)
allDomains = []
countA = 0
countB = 0
handle = open(inputfile, "r")
for line in handle.readlines():
splitted = line.split()
for entry in tsvA[splitted[0]]:
d = DomainInfo(accession=entry.seqId, start=entry.alignmentStart, end=entry.alignmentEnd)
if d not in allDomains:
allDomains.append(d)
countA += 1
for entry in tsvB[splitted[1]]:
d = DomainInfo(accession=entry.seqId, start=entry.alignmentStart, end=entry.alignmentEnd)