find_genes
Martin Asser Hansen edited this page Oct 2, 2015
·
6 revisions
find_genes locates genes in genomes and draft genomes.
find_genes output records like this:
REC_TYPE: GENE
S_ID: gi|48994873|gb|U00096.2|_4313
S_BEG: 4637612
S_END: 4638328
S_LEN: 717
STRAND: -
SEQ: MQTPHILIVED (...)
SEQ_LEN: 239
---
find_genes currently uses Prodigal as engine, and Prodigal 2.6 must be installed.
Read more here:
... | find_genes [options]
[-? | --help] # Print full usage description.
[-f | --full] # Only report full length genes.
[-p <string> | --procedure=<string>] # Procedure to use: single|meta - Default='single'
[-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.
Here is how you find genes in a genome read in with read_fasta and the result is written to KISS format with write_kiss:
read_fasta -i genome.fna | find_genes | write_kiss -x
Or for a meta-genome use -p meta:
read_fasta -i genome.fna | find_genes -p meta | write_kiss -x
Martin Asser Hansen - Copyright (C) - All rights reserved.
December 2009
GNU General Public License version 2
http://www.gnu.org/copyleft/gpl.html
find_genes is part of the Biopieces framework.