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@walterst
Created April 3, 2018 08:59
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Use to count the number of singletons present in an QIIME OTU mapping file, write these sequence IDs to an output file.
#!/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)
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