Mercurial > repos > devteam > ncbi_blast_plus
annotate tools/ncbi_blast_plus/check_no_duplicates.py @ 14:2fe07f50a41e draft
Uploaded v0.1.01 - Requires blastdbd datatype (blast_datatypes v0.0.19). Support for makeprofiledb to create protein domain databases and use them in RPS-BLAST and RPS-TBLASTN. Tools now support GI and SeqID filters, and embed the citations.
author | peterjc |
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date | Mon, 01 Dec 2014 05:59:16 -0500 |
parents | 4c4a0da938ff |
children | 3034ce97dd33 |
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11
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Uploaded v0.0.22, now wraps BLAST+ 2.2.28 allowing extended tabular output to include the hit descriptions as column 25.
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1 #!/usr/bin/env python |
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2 """Check for duplicate sequence identifiers in FASTA files. |
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3 |
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4 This is run as a pre-check before makeblastdb, in order to avoid |
4c4a0da938ff
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peterjc
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5 a regression bug in BLAST+ 2.2.28 which fails to catch this. See: |
4c4a0da938ff
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peterjc
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6 http://blastedbio.blogspot.co.uk/2012/10/my-ids-not-good-enough-for-ncbi-blast.html |
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7 |
4c4a0da938ff
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peterjc
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8 This script takes one or more FASTA filenames as input, and |
4c4a0da938ff
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peterjc
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9 will return a non-zero error if any duplicate identifiers |
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peterjc
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10 are found. |
4c4a0da938ff
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peterjc
parents:
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11 """ |
4c4a0da938ff
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peterjc
parents:
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12 import sys |
4c4a0da938ff
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peterjc
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13 import os |
4c4a0da938ff
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peterjc
parents:
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14 |
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15 if "-v" in sys.argv or "--version" in sys.argv: |
4c4a0da938ff
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16 print("v0.0.22") |
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17 sys.exit(0) |
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18 |
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19 def stop_err(msg, error=1): |
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20 sys.stderr.write("%s\n" % msg) |
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parents:
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21 sys.exit(error) |
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peterjc
parents:
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22 |
4c4a0da938ff
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peterjc
parents:
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23 |
4c4a0da938ff
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24 identifiers = set() |
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25 files = 0 |
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26 for filename in sys.argv[1:]: |
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27 if not os.path.isfile(filename): |
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28 stop_err("Missing FASTA file %r" % filename, 2) |
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29 files += 1 |
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30 handle = open(filename) |
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31 for line in handle: |
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32 if line.startswith(">"): |
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33 #The split will also take care of the new line character, |
4c4a0da938ff
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34 #e.g. ">test\n" and ">test description here\n" both give "test" |
4c4a0da938ff
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35 seq_id = line[1:].split(None, 1)[0] |
4c4a0da938ff
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peterjc
parents:
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36 if seq_id in identifiers: |
4c4a0da938ff
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peterjc
parents:
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37 handle.close() |
4c4a0da938ff
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peterjc
parents:
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38 stop_err("Repeated identifiers, e.g. %r" % seq_id, 1) |
4c4a0da938ff
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peterjc
parents:
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39 identifiers.add(seq_id) |
4c4a0da938ff
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peterjc
parents:
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40 handle.close() |
4c4a0da938ff
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peterjc
parents:
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41 if not files: |
4c4a0da938ff
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peterjc
parents:
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42 stop_err("No FASTA files given to check for duplicates", 3) |
4c4a0da938ff
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peterjc
parents:
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43 elif files == 1: |
4c4a0da938ff
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peterjc
parents:
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44 print("%i sequences" % len(identifiers)) |
4c4a0da938ff
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peterjc
parents:
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45 else: |
4c4a0da938ff
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peterjc
parents:
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46 print("%i sequences in %i FASTA files" % (len(identifiers), files)) |