split_fasta1

Usage

Overview

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

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.