view tools/ncbi_blast_plus/check_no_duplicates.py @ 11:4c4a0da938ff draft

Uploaded v0.0.22, now wraps BLAST+ 2.2.28 allowing extended tabular output to include the hit descriptions as column 25. Supports $GALAXY_SLOTS. Includes more tests and heavy use of macros.

#!/usr/bin/env python
"""Check for duplicate sequence identifiers in FASTA files.

This is run as a pre-check before makeblastdb, in order to avoid
a regression bug in BLAST+ 2.2.28 which fails to catch this. See:
http://blastedbio.blogspot.co.uk/2012/10/my-ids-not-good-enough-for-ncbi-blast.html

This script takes one or more FASTA filenames as input, and
will return a non-zero error if any duplicate identifiers
are found.
"""
import sys
import os

if "-v" in sys.argv or "--version" in sys.argv:
    print("v0.0.22")
    sys.exit(0)

def stop_err(msg, error=1):
    sys.stderr.write("%s\n" % msg)
    sys.exit(error)


identifiers = set()
files = 0
for filename in sys.argv[1:]:
    if not os.path.isfile(filename):
        stop_err("Missing FASTA file %r" % filename, 2)
    files += 1
    handle = open(filename)
    for line in handle:
        if line.startswith(">"):
            #The split will also take care of the new line character,
            #e.g. ">test\n" and ">test description here\n" both give "test"
            seq_id = line[1:].split(None, 1)[0]
            if seq_id in identifiers:
                handle.close()
                stop_err("Repeated identifiers, e.g. %r" % seq_id, 1)
            identifiers.add(seq_id)
    handle.close()
if not files:
    stop_err("No FASTA files given to check for duplicates", 3)
elif files == 1:
    print("%i sequences" % len(identifiers))
else:
    print("%i sequences in %i FASTA files" % (len(identifiers), files))