Fasta Utility

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.

Fasta Utility

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