clj-biosequence.genbank — clj-biosequence 0.5.2

->genbankCitation clj

(->genbankCitation src)

Positional factory function for class clj_biosequence.genbank.genbankCitation.

->genbankConnection clj

(->genbankConnection acc-list db retype alphabet opts)

Positional factory function for class clj_biosequence.genbank.genbankConnection.

->genbankDbRef clj

(->genbankDbRef src)

Positional factory function for class clj_biosequence.genbank.genbankDbRef.

->genbankFeature clj

(->genbankFeature src)

Positional factory function for class clj_biosequence.genbank.genbankFeature.

->genbankFile clj

(->genbankFile file opts alphabet)

Positional factory function for class clj_biosequence.genbank.genbankFile.

->genbankInterval clj

(->genbankInterval src)

Positional factory function for class clj_biosequence.genbank.genbankInterval.

->genbankQualifier clj

(->genbankQualifier src)

Positional factory function for class clj_biosequence.genbank.genbankQualifier.

->genbankReader clj

(->genbankReader strm alphabet)

Positional factory function for class clj_biosequence.genbank.genbankReader.

->genbankSequence clj

(->genbankSequence src alphabet)

Positional factory function for class clj_biosequence.genbank.genbankSequence.

->genbankString clj

(->genbankString str opts alphabet)

Positional factory function for class clj_biosequence.genbank.genbankString.

->genbankTaxRef clj

(->genbankTaxRef src)

Positional factory function for class clj_biosequence.genbank.genbankTaxRef.

feature-location clj

(feature-location feature)

Returns the value corresponding to the 'GBFeature_location' element of a genbank feature element.

filter-qualifiers clj

(filter-qualifiers feature qname)

Filter qualifiers in a genbankFeature record using obj-type function.

gb-seq-comment clj

(gb-seq-comment gbseq)

Returns strings from GbSeq_comment xml elements.

genbank-search clj

(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 clj

(get-qualifiers feature name)

Returns qualifier values from a genbankFeature record that have a particular bs-name.

init-genbank-connection clj

(init-genbank-connection accessions db format alphabet & opts)

Initializes a genbankConnection record.

init-genbank-file clj

(init-genbank-file file alphabet & opts)

Initializes a genbankFile record.

init-genbank-string clj

(init-genbank-string str
                     &
                     {:keys [alphabet opts]
                      :or {alphabet :iupacAminoAcids opts ()}})

Initializes a genbankString record.

map->genbankCitation clj

(map->genbankCitation m__7585__auto__)

Factory function for class clj_biosequence.genbank.genbankCitation, taking a map of keywords to field values.

map->genbankConnection clj

(map->genbankConnection m__7585__auto__)

Factory function for class clj_biosequence.genbank.genbankConnection, taking a map of keywords to field values.

map->genbankDbRef clj

(map->genbankDbRef m__7585__auto__)

Factory function for class clj_biosequence.genbank.genbankDbRef, taking a map of keywords to field values.

map->genbankFeature clj

(map->genbankFeature m__7585__auto__)

Factory function for class clj_biosequence.genbank.genbankFeature, taking a map of keywords to field values.

map->genbankFile clj

(map->genbankFile m__7585__auto__)

Factory function for class clj_biosequence.genbank.genbankFile, taking a map of keywords to field values.

map->genbankInterval clj

(map->genbankInterval m__7585__auto__)

Factory function for class clj_biosequence.genbank.genbankInterval, taking a map of keywords to field values.

map->genbankQualifier clj

(map->genbankQualifier m__7585__auto__)

Factory function for class clj_biosequence.genbank.genbankQualifier, taking a map of keywords to field values.

map->genbankReader clj

(map->genbankReader m__7585__auto__)

Factory function for class clj_biosequence.genbank.genbankReader, taking a map of keywords to field values.

map->genbankSequence clj

(map->genbankSequence m__7585__auto__)

Factory function for class clj_biosequence.genbank.genbankSequence, taking a map of keywords to field values.

map->genbankString clj

(map->genbankString m__7585__auto__)

Factory function for class clj_biosequence.genbank.genbankString, taking a map of keywords to field values.

map->genbankTaxRef clj

(map->genbankTaxRef m__7585__auto__)

Factory function for class clj_biosequence.genbank.genbankTaxRef, taking a map of keywords to field values.

qualifiers clj

(qualifiers feature)

Collection of qualifiers in a genbankFeature record.