A parser for Uniprot sequences in XML format.
Import from Clojars:
[clj-uniprot "0.1.9"]Use in your namespace:
(:require [clj-uniprot.core :as up])Open a reader on a file containing Uniprot sequences in XML format and call 'uniprot-seq'. This will return a lazy list of zippers, one for each sequence in the file, that can be used with the usual Clojure XML parsing libraries.
user> (with-open [r (reader "/uniprot/file.xml")]
(doall (->> (uniprot-seq r)
(take 5)
(map accession))))
("Q4U9M9" "P15711" "Q6V4H0" "Q43495" "P13813")
user>Some accessors are defined (accessions, accession, description and tax-name) and 'biosequence' returns the sequence of the protein as a string. Others will be added as I need them.
Uniprot can be searched remotely using 'uniprot-search' which returns a list of accessions matching your search. Sequences can be fetched from Uniprot using 'get-uniprot-sequence'. This returns a buffered reader that can be directly used with 'with-open' and 'uniprot-seq'.
clj-uniprot.core> (with-open [r (get-uniprot-sequences "[email protected]"
'("P68371"))]
(doall (->> (uniprot-seq r)
(map accession))))
("P68371")
clj-uniprot.core>Sequences can be converted to a fasta string using 'uniprot->fasta'.
Copyright © 2016 Jason Mulvenna
Distributed under the Eclipse Public License either version 1.0 or (at your option) any later version.