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https://github.com/sjackman/fastascripts

Manipulate FASTA files
https://github.com/sjackman/fastascripts

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Manipulate FASTA files

Host: GitHub
URL: https://github.com/sjackman/fastascripts
Owner: sjackman
Created: 2012-12-11T16:46:56.000Z (about 12 years ago)
Default Branch: master
Last Pushed: 2014-08-26T22:25:17.000Z (over 10 years ago)
Last Synced: 2024-05-01T19:40:49.934Z (8 months ago)
Language: Perl
Size: 174 KB
Stars: 30
Watchers: 6
Forks: 10
Open Issues: 0
Metadata Files:
- Readme: README.md

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README

        fastascripts – Manipulate FASTA files

=====================================

These scripts were never meant to see the light of day. I apologize for the

distasteful code.

Utilities

=========

* `facanon`

	Output the lexicographically smaller of the sequence and its reverse complement

* `facat`

	Concatenate FASTA files and add a prefix to the identifier

* `fachain`

	Merge overlapping sequences

* `faclean`

	Reformat and optionally remove short contigs from a FASTA file

* `facmp`

	Compare pairs of sequences

* `facstont`

	Convert colour-space sequence to nucleotides

* `fadecimate`

	Randomly keep 1 in every N pairs of reads

* `faget`

	Select sequences from a FASTA file by identifier

* `fagrep`

	Search a FASTA file using a regular expression

* `fakmer`

	Generate tiled k-mers

* `falength`

	Print the lengths of sequences

* `falint`

	Check the syntax of a FASTA file

* `famd5`

	Calculate a MD5 digest for a FASTA file

* `famd5seq`

	Calculate a MD5 digest for each sequence

* `fanttocs`

	Convert nucleotides to colour-space sequence

* `farand`

	Generate a FASTA file with random sequence

* `farc`

	Reverse and complement the sequences

* `farenumber`

	Renumber the sequences

* `faseperate-mates`

	Separate paired reads into two files

* `fasplit-read`

	Split a read into two at the midpoint

* `fastqtofa`

	Convert a FASTQ file to FASTA format

* `fatoagp`

	Convert FASTA scaffolds to FASTA contigs and an AGP file

* `fatofastq`

	 Convert a FASTA file to a FASTQ file

* `fatoseq`

	Remove FASTA headers

* `faunamb`

	Convert IUPAC-IUB ambiguity codes to ACGT

* `faunscaffold`

	Break scaffolds into contigs at Ns

License

================================================================================

Copyright 2013 Shaun Jackman

### [ISC License][]

Permission to use, copy, modify, and/or distribute this software for any

purpose with or without fee is hereby granted, provided that the above

copyright notice and this permission notice appear in all copies.

[ISC License]: http://opensource.org/licenses/ISC