clj-biosequence.uniprot
->uniprotCitation
(->uniprotCitation src)
Positional factory function for class clj_biosequence.uniprot.uniprotCitation.
->uniprotConnection
(->uniprotConnection acc-list retype email)
Positional factory function for class clj_biosequence.uniprot.uniprotConnection.
->uniprotDbRef
(->uniprotDbRef src)
Positional factory function for class clj_biosequence.uniprot.uniprotDbRef.
->uniprotFeature
(->uniprotFeature src)
Positional factory function for class clj_biosequence.uniprot.uniprotFeature.
->uniprotFile
(->uniprotFile file opts)
Positional factory function for class clj_biosequence.uniprot.uniprotFile.
->uniprotGene
(->uniprotGene src)
Positional factory function for class clj_biosequence.uniprot.uniprotGene.
->uniprotInterval
(->uniprotInterval src)
Positional factory function for class clj_biosequence.uniprot.uniprotInterval.
->uniprotProtein
(->uniprotProtein src)
Positional factory function for class clj_biosequence.uniprot.uniprotProtein.
->uniprotReader
(->uniprotReader strm)
Positional factory function for class clj_biosequence.uniprot.uniprotReader.
->uniprotTaxRef
(->uniprotTaxRef src)
Positional factory function for class clj_biosequence.uniprot.uniprotTaxRef.
init-uniprot-connection
(init-uniprot-connection accessions retype email)
Initialises a connection which can be used with bs-reader to open a
lazy list of uniprotProteins from the Uniprot servers.
init-uniprot-file
(init-uniprot-file path & opts)
Initialises a uniprotXmlFile object for use with bs-reader.
map->uniprotCitation
(map->uniprotCitation m__5869__auto__)
Factory function for class clj_biosequence.uniprot.uniprotCitation, taking a map of keywords to field values.
map->uniprotConnection
(map->uniprotConnection m__5869__auto__)
Factory function for class clj_biosequence.uniprot.uniprotConnection, taking a map of keywords to field values.
map->uniprotDbRef
(map->uniprotDbRef m__5869__auto__)
Factory function for class clj_biosequence.uniprot.uniprotDbRef, taking a map of keywords to field values.
map->uniprotFeature
(map->uniprotFeature m__5869__auto__)
Factory function for class clj_biosequence.uniprot.uniprotFeature, taking a map of keywords to field values.
map->uniprotFile
(map->uniprotFile m__5869__auto__)
Factory function for class clj_biosequence.uniprot.uniprotFile, taking a map of keywords to field values.
map->uniprotGene
(map->uniprotGene m__5869__auto__)
Factory function for class clj_biosequence.uniprot.uniprotGene, taking a map of keywords to field values.
map->uniprotInterval
(map->uniprotInterval m__5869__auto__)
Factory function for class clj_biosequence.uniprot.uniprotInterval, taking a map of keywords to field values.
map->uniprotProtein
(map->uniprotProtein m__5869__auto__)
Factory function for class clj_biosequence.uniprot.uniprotProtein, taking a map of keywords to field values.
map->uniprotReader
(map->uniprotReader m__5869__auto__)
Factory function for class clj_biosequence.uniprot.uniprotReader, taking a map of keywords to field values.
map->uniprotTaxRef
(map->uniprotTaxRef m__5869__auto__)
Factory function for class clj_biosequence.uniprot.uniprotTaxRef, taking a map of keywords to field values.
uniprot-search
(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.