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https://github.com/robsyme/fasta_util

An easy way of performing some common operations on fasta files
https://github.com/robsyme/fasta_util

Last synced: 24 days ago
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An easy way of performing some common operations on fasta files

Host: GitHub
URL: https://github.com/robsyme/fasta_util
Owner: robsyme
License: mit
Created: 2011-02-17T06:59:24.000Z (over 13 years ago)
Default Branch: master
Last Pushed: 2011-11-18T02:42:20.000Z (almost 13 years ago)
Last Synced: 2024-10-03T06:50:27.080Z (about 1 month ago)
Language: Ruby
Homepage:
Size: 117 KB
Stars: 1
Watchers: 3
Forks: 0
Open Issues: 0
Metadata Files:
- Readme: README.rdoc
- License: LICENSE.txt

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README

= 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.