python2 script to read an OTU file in mothur format, select a cutoff level, and write the file in qiime format Usage: ./transf.py mothurfile cutoff LICENSE: BSD 2

transf.py

#! /usr/bin/python

# Timothee Poisot
# [email protected]
# released under the BSD 2 license

import sys

def onlyNonEmpty(table):
   N_non_empty = int(table[1][2]) + 3
   table = [l[:N_non_empty] for l in table]
   return table

def revert(otu_file, cutoff):
   output_string = ""
   otu_lines = [l.split() for l in open(otu_file)]
   otu_lines = onlyNonEmpty([otu_lines[i] for i in xrange(len(otu_lines)) if ((i==0) or (otu_lines[i][0] == cutoff))])
   NROW = len(otu_lines)
   NCOL = len(otu_lines[0])
   ## Pivot the table
   for col in xrange(NCOL):
      if (not (col in [0, 2])):
         for row in xrange(NROW):
            to_write = str(otu_lines[row][col])
            if (col > 2) and (row == 0):
               to_write = int(to_write[3:])
            if (col==1) and (row == 0):
               to_write = "#OTU ID"
            output_string += str(to_write)
            if row < (NROW-1):
               output_string += "\t"
         if col < NCOL:
            output_string += "\n"
   ## Write the file
   qiime_file = "qiime_"+cutoff+"_"+otu_file
   of = open(qiime_file, "w")
   of.write(output_string)
   of.close()
   del output_string
   del otu_lines
   print "["+otu_file+"] Cutoff "+cutoff+": "+str(NCOL-3)+" OTUs in "+str(NROW-1)+" samples\n"

if __name__ == "__main__":
   revert(sys.argv[1], str(sys.argv[2]))