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create_seq_index
Martin Asser Hansen edited this page Oct 2, 2015
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create_seq_index creates a sequence index using sequences in the stream.
Identical sequence names will raise an error.
The resulting index will be:
index_dir/index_name.seq
index_dir/index_name.index
... | create_seq_index [options]
[-? | --help] # Print full usage description.
[-x | --no_stream] # Do not emit records.
[-d <dir> | --directory=<dir>] # Directory to contain 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 a sequence index from a FASTA file, do:
read_fasta -i <FASTA file(s)> | create_seq_index -d ~/my_dir -i my_index -x
You will then get the following files:
~/my_dir/my_index.index
~/my_dir/my_index.seq
Martin Asser Hansen - Copyright (C) - All rights reserved.
September 2009
GNU General Public License version 2
http://www.gnu.org/copyleft/gpl.html
create_seq_index is part of the Biopieces framework.