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) 2005-2019 The University of Notre Dame. This software is distributed under the GNU General Public License. See the file COPYING for details.

SEE ALSO¶

• Cooperative Computing Tools Documentation
• Makeflow User Manual
• makeflow(1) makeflow_monitor(1) makeflow_analyze(1) makeflow_viz(1) makeflow_graph_log(1) starch(1) makeflow_ec2_setup(1) makeflow_ec2_cleanup(1) makeflow_ec2_estimate(1)