fasta_util

= Fasta Utility

This is a pretty simple Thor[http://github.com/wycats/thor] application for performing a number of common tasks on fasta files.

So far, supported actions are: fasta_util lengths:: Calculates basic statistics on the lengths of the entries in the file. fasta_util filter:: Applies a variety of filter types to the entries in a fasta file. fasta_util clean:: Reformats each entry, wrapping long lines fasta_util sort:: Sorts the entries in a fasta file according to length.

Detailed help on each of the options can be accessed with

fasta_util help COMMAND

eg:

$ fasta_util help filter

Usage: fasta_util filter FILENAME [options]

Options: -l, [--length-cutoff=N] # Only entries with length >= cutoff will be returned. # Default: 0 -v, [--inverse-match] # Return the inverse of the match after all the other filters have been applied. -d, [--defline-grep=DEFLINE_GREP] # A regular expression, used to search the entry's definition line.

Description: Impose a filter or set of filters on entries in a fasta file where each sequence in the file has to pass all of the filters to be printed.

== Copyright

Copyright (c) 2011 Robert Syme. MIT Licence. See LICENSE.txt for further details.