This is a pretty simple 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 © 2011 Robert Syme. MIT Licence. See LICENSE.txt for further details.