clj-biosequence.genbank
->genbankCitation
(->genbankCitation src)
Positional factory function for class clj_biosequence.genbank.genbankCitation.
->genbankConnection
(->genbankConnection acc-list db retype)
Positional factory function for class clj_biosequence.genbank.genbankConnection.
->genbankDbRef
(->genbankDbRef src)
Positional factory function for class clj_biosequence.genbank.genbankDbRef.
->genbankFeature
(->genbankFeature src)
Positional factory function for class clj_biosequence.genbank.genbankFeature.
->genbankFile
(->genbankFile file)
Positional factory function for class clj_biosequence.genbank.genbankFile.
->genbankInterval
(->genbankInterval src)
Positional factory function for class clj_biosequence.genbank.genbankInterval.
->genbankQualifier
(->genbankQualifier src)
Positional factory function for class clj_biosequence.genbank.genbankQualifier.
->genbankReader
(->genbankReader strm)
Positional factory function for class clj_biosequence.genbank.genbankReader.
->genbankSequence
(->genbankSequence src)
Positional factory function for class clj_biosequence.genbank.genbankSequence.
->genbankString
(->genbankString str)
Positional factory function for class clj_biosequence.genbank.genbankString.
->genbankTaxRef
(->genbankTaxRef src)
Positional factory function for class clj_biosequence.genbank.genbankTaxRef.
feature-location
(feature-location feature)
Returns the value corresponding to the 'GBFeature_location' element
of a genbank feature element.
filter-qualifiers
(filter-qualifiers feature qname)
Filter qualifiers in a genbankFeature record using obj-type
function.
genbank-search
(genbank-search term db)(genbank-search term db restart key)
Returns a non-lazy list of result ids from NCBI for a particular search term and
database. Search term syntax is the same as is used at the NCBI. For example,
to retreive all Schistosoma mansoni protein sequences the 'db' argument would
be 'protein' and the search term 'txid6183[Organism:noexp]'. Database arguments
are restricted to the following keyword arguments and any other value will cause
an error:
:protein - a collection of sequences from several sources, including
translations from annotated coding regions in GenBank, RefSeq
and TPA, as well as records from SwissProt, PIR, PRF, and PDB.
:nucest - a collection of short single-read transcript sequences from GenBank.
:nuccore - a collection of sequences from several sources, including GenBank,
RefSeq, TPA and PDB.
:nucgss - a collection of unannotated short single-read primarily genomic
sequences from GenBank including random survey sequences clone-end
sequences and exon-trapped sequences.
:popset - a set of DNA sequences that have been collected to analyse the
evolutionary relatedness of a population. The population could
originate from different members of the same species, or from
organisms from different species.
Note that when retrieving popset entries multiple sequences are returned from a
single accession number. Returns an empty list if no matches found.get-qualifiers
(get-qualifiers feature name)
Returns qualifier values from a genbankFeature record that have a
particular bs-name.
init-genbank-connection
(init-genbank-connection accessions db format)
Initializes a genbankConnection record.
init-genbank-file
(init-genbank-file file)
Initializes a genbankFile record.
init-genbank-reader
(init-genbank-reader strm)
Initializes a genbankReader.
init-genbank-string
(init-genbank-string str)
Initializes a genbankString record.
map->genbankCitation
(map->genbankCitation m__5869__auto__)
Factory function for class clj_biosequence.genbank.genbankCitation, taking a map of keywords to field values.
map->genbankConnection
(map->genbankConnection m__5869__auto__)
Factory function for class clj_biosequence.genbank.genbankConnection, taking a map of keywords to field values.
map->genbankDbRef
(map->genbankDbRef m__5869__auto__)
Factory function for class clj_biosequence.genbank.genbankDbRef, taking a map of keywords to field values.
map->genbankFeature
(map->genbankFeature m__5869__auto__)
Factory function for class clj_biosequence.genbank.genbankFeature, taking a map of keywords to field values.
map->genbankFile
(map->genbankFile m__5869__auto__)
Factory function for class clj_biosequence.genbank.genbankFile, taking a map of keywords to field values.
map->genbankInterval
(map->genbankInterval m__5869__auto__)
Factory function for class clj_biosequence.genbank.genbankInterval, taking a map of keywords to field values.
map->genbankQualifier
(map->genbankQualifier m__5869__auto__)
Factory function for class clj_biosequence.genbank.genbankQualifier, taking a map of keywords to field values.
map->genbankReader
(map->genbankReader m__5869__auto__)
Factory function for class clj_biosequence.genbank.genbankReader, taking a map of keywords to field values.
map->genbankSequence
(map->genbankSequence m__5869__auto__)
Factory function for class clj_biosequence.genbank.genbankSequence, taking a map of keywords to field values.
map->genbankString
(map->genbankString m__5869__auto__)
Factory function for class clj_biosequence.genbank.genbankString, taking a map of keywords to field values.
map->genbankTaxRef
(map->genbankTaxRef m__5869__auto__)
Factory function for class clj_biosequence.genbank.genbankTaxRef, taking a map of keywords to field values.
qualifiers
(qualifiers feature)
Collection of qualifiers in a genbankFeature record.