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create_blast_index
Martin Asser Hansen edited this page Oct 2, 2015
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create_blast_index creates a BLAST index from sequences found in the stream using formatdb from NCBI's BLAST. The sequence type is determined automagically.
NCBI BLAST/formatdb must be installed in order for create_blast_index to work.
Read more here:
... | create_blast_index [options] -d <my_dir> -i <my_index>
[-? | --help] # Print full usage description.
[-x | --no_stream] # Do not emit records.
[-d <dir> | --directory=<dir>] # Directory to cantain index files.
[-i <string> | --index_name=<string>] # Index name.
[-I <file!> | --stream_in=<file!>] # Read input from stream file - Default=STDIN
[-O <file> | --stream_out=<file>] # Write output to stream file - Default=STDOUT
[-v | --verbose] # Verbose output.
To create the BLAST index from a FASTA file, do:
read_fasta -i <FASTA file(s)> | create_blast_index -d ~/my_blast_dir/ -i my_blast_index -x
Depending on the sequence type you will then get the following files:
For protein sequences:
~/my_blast_dir/my_blast_index.phr
~/my_blast_dir/my_blast_index.pin
~/my_blast_dir/my_blast_index.psq
For nucleotide sequences:
~/my_blast_dir/my_blast_index.nhr
~/my_blast_dir/my_blast_index.nin
~/my_blast_dir/my_blast_index.nsq
And finally to use this new index with blast_seq, simply do:
read_fasta -i <FASTA file(s)> | blast_seq -d ~/my_blast_dir/my_blast_index
Martin Asser Hansen - Copyright (C) - All rights reserved.
August 2007
GNU General Public License version 2
http://www.gnu.org/copyleft/gpl.html
create_blast_index is part of the Biopieces framework.