def countNexusTrees(nexFileName) :
""" Number of trees in a nexus file."""
nexFile = fileFromName(nexFileName)
c = 0
for l in nexFile:
if l.startswith("tree ") :
c += 1
return c
def countNexusTrees(nexFileName) :
""" Number of trees in a nexus file (cheat: just counts number of lines
beginning with 'tree')."""
nexFile = fileFromName(nexFileName)
c = 0
for l in nexFile:
if l.startswith("tree ") :
c += 1
return c
def getDistanceMatrix(saveName) :
fl = fileFromName(saveName)
labs = [x.strip() for x in next(fl)[2:].split('\t')]
dists = array.array('f',repeat(0.0,nPairs(labs)))
i = 0
for x in fl:
dists[i] = float(x.strip())
i += 1
fl.close()
return dists,labs
def __init__(self, instream) :
self.stream = fileFromName(instream) if isinstance(instream,str) else instream
self._grabLine()
while self.nextline.strip() != '#NEXUS' :
self._grabLine()