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FIXME: write description
A parser for Uniprot sequences in XML format.
Import from Clojars:
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@example.com" '("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.