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    clj-uniprot

    Clojars

    Oct 20, 2016


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    clj-uniprot

    A parser for Uniprot sequences in XML format.

    Usage

    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 "jason.mulvenna@gmail.com"
                                                           '("P68371"))]
                        (doall (->> (uniprot-seq r)
                                    (map accession))))
    ("P68371")
    clj-uniprot.core>
    

    Sequences can be converted to a fasta string using ‘uniprot->fasta’.

    License

    Copyright © 2016 Jason Mulvenna

    Distributed under the Eclipse Public License either version 1.0 or (at your option) any later version.