clj-biosequence.uniprot — clj-biosequence 0.5.2

->uniprotCitation clj

(->uniprotCitation src)

Positional factory function for class clj_biosequence.uniprot.uniprotCitation.

->uniprotComment clj

(->uniprotComment src)

Positional factory function for class clj_biosequence.uniprot.uniprotComment.

->uniprotConnection clj

(->uniprotConnection acc-list retype email alphabet)

Positional factory function for class clj_biosequence.uniprot.uniprotConnection.

->uniprotDbRef clj

(->uniprotDbRef src)

Positional factory function for class clj_biosequence.uniprot.uniprotDbRef.

->uniprotFeature clj

(->uniprotFeature src)

Positional factory function for class clj_biosequence.uniprot.uniprotFeature.

->uniprotFile clj

(->uniprotFile file opts alphabet)

Positional factory function for class clj_biosequence.uniprot.uniprotFile.

->uniprotGene clj

(->uniprotGene src)

Positional factory function for class clj_biosequence.uniprot.uniprotGene.

->uniprotInterval clj

(->uniprotInterval src)

Positional factory function for class clj_biosequence.uniprot.uniprotInterval.

->uniprotProtein clj

(->uniprotProtein src alphabet)

Positional factory function for class clj_biosequence.uniprot.uniprotProtein.

->uniprotReader clj

(->uniprotReader strm alphabet)

Positional factory function for class clj_biosequence.uniprot.uniprotReader.

->uniprotTaxRef clj

(->uniprotTaxRef src)

Positional factory function for class clj_biosequence.uniprot.uniprotTaxRef.

init-uniprot-connection clj

(init-uniprot-connection accessions
                         retype
                         email
                         &
                         {:keys [alphabet] :or {alphabet :iupacAminoAcids}})

Initialises a connection which can be used with bs-reader to open a lazy list of uniprotProteins from the Uniprot servers.

init-uniprot-file clj

(init-uniprot-file path
                   &
                   {:keys [alphabet opts]
                    :or {alphabet :iupacAminoAcids opts ()}})

Initialises a uniprotXmlFile object for use with bs-reader.

map->uniprotCitation clj

(map->uniprotCitation m__7585__auto__)

Factory function for class clj_biosequence.uniprot.uniprotCitation, taking a map of keywords to field values.

map->uniprotComment clj

(map->uniprotComment m__7585__auto__)

Factory function for class clj_biosequence.uniprot.uniprotComment, taking a map of keywords to field values.

map->uniprotConnection clj

(map->uniprotConnection m__7585__auto__)

Factory function for class clj_biosequence.uniprot.uniprotConnection, taking a map of keywords to field values.

map->uniprotDbRef clj

(map->uniprotDbRef m__7585__auto__)

Factory function for class clj_biosequence.uniprot.uniprotDbRef, taking a map of keywords to field values.

map->uniprotFeature clj

(map->uniprotFeature m__7585__auto__)

Factory function for class clj_biosequence.uniprot.uniprotFeature, taking a map of keywords to field values.

map->uniprotFile clj

(map->uniprotFile m__7585__auto__)

Factory function for class clj_biosequence.uniprot.uniprotFile, taking a map of keywords to field values.

map->uniprotGene clj

(map->uniprotGene m__7585__auto__)

Factory function for class clj_biosequence.uniprot.uniprotGene, taking a map of keywords to field values.

map->uniprotInterval clj

(map->uniprotInterval m__7585__auto__)

Factory function for class clj_biosequence.uniprot.uniprotInterval, taking a map of keywords to field values.

map->uniprotProtein clj

(map->uniprotProtein m__7585__auto__)

Factory function for class clj_biosequence.uniprot.uniprotProtein, taking a map of keywords to field values.

map->uniprotReader clj

(map->uniprotReader m__7585__auto__)

Factory function for class clj_biosequence.uniprot.uniprotReader, taking a map of keywords to field values.

map->uniprotTaxRef clj

(map->uniprotTaxRef m__7585__auto__)

Factory function for class clj_biosequence.uniprot.uniprotTaxRef, taking a map of keywords to field values.

uniprot-search clj

(uniprot-search term email)

(uniprot-search term email offset)

Returns a non-lazy list of uniprot accession numbers satisfying the search term. The search term uses the same syntax as the uniprot web interface. For example:

• to get all Schistosoma mansoni proteins in the proteome reference set term would be: 'organism:6183 AND keyword:1185'
• get all Schistosoma mansoni proteins in the proteome set that are intrinsic to the membrane: 'taxonomy:6183 AND keyword:1185 AND go:0031224'
• get all reviewed human entries: 'reviewed:yes AND organism:9606' And so on. Returns an empty list if no matches found. Uniprot requires an email so an email can be supplied using the email argument.