split_fasta(1)
NAME
split_fasta - Split a fasta file according to sequence and character counts
SYNOPSIS
split_fasta query_granularity character_granularity fasta_file
DESCRIPTION
split_fasta is a simple script to split a fasta file according to user provided parameters. The script iterates over the given file, generating a new sub_file called input.i each time the contents of the previous file (input.(i-1)) exceed the number of queries given by query_granularity or the number of characters given by character_granularity.
OPTIONS
EXIT STATUS
On success, returns zero. On failure, returns non-zero.
ENVIRONMENT VARIABLES
EXAMPLES
To split a fasta file smallpks.fa into pieces no larger than 500 queries and with no piece receiving additional sequences if it exceeds 10000 characters we would do:
python split_fasta 500 10000 smallpks.fa
This would generate files input.0, input.1, ..., input.N where N is the number of appropriately constrained files necessary to contain all sequences in smallpks.fa.
COPYRIGHT
The Cooperative Computing Tools are Copyright (C) 2003-2004 Douglas Thain and Copyright (C) 2005-2015 The University of Notre Dame. This software is distributed under the GNU General Public License. See the file COPYING for details.
SEE ALSO
CCTools 7.0.21 FINAL released on