Use to count the number of singletons present in an QIIME OTU mapping file, write these sequence IDs to an output file.

record_singletons.py

#!/usr/bin/env python

"""Usage: python record_singletons.py X Y
where X is the input OTU mapping file and Y is the output singleton sequence ID file.
"""

from sys import argv

otu_mapping = open(argv[1], "U")
singletons_out = open(argv[2], "w")

count = 0

for line in otu_mapping:
    if len(line.strip()) == 0:
        continue
    curr_line = line.strip().split("\t")
    if len(curr_line) == 2:
        singletons_out.write("%s\n" % curr_line[1])
        count += 1
        
print("Total count of singletons: %d" % count)