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create_vmatch_index
Martin Asser Hansen edited this page Oct 2, 2015
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create_vmatch_index creates a Vmatch index using mkvtree from the Vmatch packaged using sequences found in the stream.
The Vmatch package must be installed in order for create_vmatch_seq to work.
Read more here:
... | create_vmatch_index [options]
[-? | --help] # Print full usage description.
[-x | --no_stream] # Do not emit records.
[-i <string> | --index_name=<string>] # Directory name to contain index files.
[-p <uint> | --prefix_length=<uint>] # Minimum prefix that can be matched - Default=guessed
[-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 Vmatch index from a FASTA file, do:
read_fasta -i <FASTA file(s)> | create_vmatch_index -i ~/my_vmatch_dir/my_vmatch_index -x
You will then get the following files:
~/my_vmatch_dir/my_vmatch_index.al1
~/my_vmatch_dir/my_vmatch_index.bck
~/my_vmatch_dir/my_vmatch_index.des
~/my_vmatch_dir/my_vmatch_index.lcp
~/my_vmatch_dir/my_vmatch_index.llv
~/my_vmatch_dir/my_vmatch_index.prj
~/my_vmatch_dir/my_vmatch_index.sds
~/my_vmatch_dir/my_vmatch_index.suf
~/my_vmatch_dir/my_vmatch_index.tis
And finally to use this new index with vmatch_seq, simply do:
read_fasta -i <FASTA file(s)> | vmatch_seq -i ~/my_vmatch_dir/my_vmatch_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_vmatch_index is part of the Biopieces framework.