Parser for sequences in FASTA format.
Import from clojars:
[clj-fasta "0.2.3"]Import into namespace:
(:require [clj-fasta.core :as fa])Takes a buffered reader and returns a lazy list of hashmaps containing the accession, description and sequence of the fasta sequences on the reader. Regular expressions to parse the accession and description from the fasta sequence can be specified (default is accession being text before the first space and the description text after the first space). Ignores all lines prior to the first line that starts with '>'.
user> (with-open [r (reader "/fasta/file.fa")]
(->> (fasta-seq r)
first))
{:accession "TRINITY_DN22_c0_g1_i1", :description
"len=206 path=[638:0-65 639:66-66 640:67-205] [-1, 638, 639, 640, -2]",
:sequence "GCGAGGA..."}
user>A collection of fasta sequences can be sent to file using fasta->file. This function also takes the :append and :func keyword for appending to a file and transforming the sequence before writing. For example:
user> (with-open [r (reader "/fasta/file.fa")]
(fasta->file (fasta-seq r)
"outfile"
:append true
:func #(update-in % [:sequence] clojure.string/lower-case)))
"outfile"
user>Library also works in ClojureScript although there is no fasta->file function or integration with biodb. The fasta-seq function takes a string as its argument and is not lazy.
Copyright © 2016 Jason Mulvenna
Distributed under the Eclipse Public License either version 1.0 or (at your option) any later version.