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()