--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/phylogenies/long_branch_finder.py	Tue Mar 11 12:19:13 2014 -0700
@@ -0,0 +1,36 @@
+#!/usr/bin/python -tt
+            
+##usage: ./long_branch_finder.py <tabular treelist file> <number of stdevs as cut-off>  > outfile
+#import modules
+import sys, os, numpy, re
+
+def read(filename):
+  f = open(filename)
+  lines = f.readlines()
+  for eachline in lines:
+    line = eachline.split('\t')
+    gene = line[0]
+    d1 = {}
+    d1[gene] = line[1]   #matches genename with its tree
+    treetips = re.findall('[a-zA-Z0-9]+(?:_[a-zA-Z0-9]+)?\w*:\d+\.\d+', line[1]) #should be more flexible in recognizing speciesnames in trees
+    # treetips = re.findall('[a-zA-Z0-9]+(?:_[a-zA-Z0-9]+)?:\d+\.\d+', line[1])  # makes a list of items like 'spname:bl'
+    #treetips = re.findall('[A-Z][a-z]+_[a-z]+:\d+\.\d+', line[1])  # makes a list of items like 'spname:bl'
+    d2 = {}
+    for i in treetips:
+      spbl = i.split(':')
+      d2.update({spbl[1] : spbl[0]})  #creates link betwn taxon and its BL
+    tipbl = re.findall('\d+\.\d+', str(treetips))
+    std = numpy.std([float(i) for i in tipbl])
+#    numstd = 3*std
+    numstd = int(sys.argv[2])*std
+    for i in tipbl:
+      if float(i) > float(numstd):
+#        print d2[str(i)] + '\t' + gene  + '\t' + i  
+        print d2[str(i)] + '\t' + gene
+  f.close()
+
+def main():
+  read(sys.argv[1])
+
+if __name__ == '__main__':
+  main()