clj-biosequence.core — clj-biosequence 0.5.2

->biosequenceIndex clj

(->biosequenceIndex index path)

Positional factory function for class clj_biosequence.core.biosequenceIndex.

->biosequenceIndexReader clj

(->biosequenceIndexReader index strm)

Positional factory function for class clj_biosequence.core.biosequenceIndexReader.

->bzipped clj

(->bzipped file)

Positional factory function for class clj_biosequence.core.bzipped.

->fastaFile clj

(->fastaFile file alphabet opts)

Positional factory function for class clj_biosequence.core.fastaFile.

->fastaReader clj

(->fastaReader strm alphabet)

Positional factory function for class clj_biosequence.core.fastaReader.

->fastaSequence clj

(->fastaSequence acc description alphabet sequence)

Positional factory function for class clj_biosequence.core.fastaSequence.

->fastaString clj

(->fastaString str alphabet)

Positional factory function for class clj_biosequence.core.fastaString.

->gzipped clj

(->gzipped file)

Positional factory function for class clj_biosequence.core.gzipped.

->uncompressed clj

(->uncompressed file)

Positional factory function for class clj_biosequence.core.uncompressed.

->zipped clj

(->zipped file)

Positional factory function for class clj_biosequence.core.zipped.

bioreader clj

(bioreader x & opts)

bioReader clj protocol

make-reader clj

(make-reader x opts)

bioseq->string clj

(bioseq->string bs)

Returns the sequence of a biosequence as a string with newlines every 80 chars.

bioseq-proxy clj

Biosequence clj protocol

alphabet clj

(alphabet this)

Returns the alphabet of a biosequence.

bs-seq clj

(bs-seq this)

Returns the sequence of a biosequence as a vector.

keywords clj

(keywords this)

Returns a collection of keywords.

moltype clj

(moltype this)

Returns the moltype of a biosequence.

protein? clj

(protein? this)

Returns true if a protein and false otherwise.

biosequence->file clj

(biosequence->file bs
                   file
                   &
                   {:keys [append func] :or {append true func fasta-string}})

Takes a collection of biosequences and prints them to file. To append to an existing file use :append true and the :func argument can be used to pass a function that will be used to prepare the printed output, the default is fasta-string which will print the biosequences to the file in fasta format. Returns the file.

biosequenceCitation clj protocol

pstart clj

(pstart this)

Returns the start page of a citation object.

authors clj

(authors this)

Returns the authors from a citation object.

pend clj

(pend this)

Returns the end page of a citation object.

crossrefs clj

(crossrefs this)

Returns crossrefs - DOI, ISBN etc

abstract clj

(abstract this)

Returns the abstract

journal clj

(journal this)

Returns the journal of a citation object.

title clj

(title this)

Returns the title of a citation object.

volume clj

(volume this)

Returns the volume of a citation object.

year clj

(year this)

Returns the year of a citation object.

pubmed clj

(pubmed this)

Returns the pubmed id of a reference if there is one.

biosequenceCitations clj protocol

citation-key clj

(citation-key this)

Returns a citation key from a record.

citations clj

(citations this)

Returns a collection of references in a sequence record.

biosequenceComments clj protocol

comments clj

(comments this)

Returns comments.

filter-comments clj

(filter-comments this value)

Filters comments based on the return value of obj-type.

biosequenceDbRef clj protocol

database-name clj

(database-name this)

Returns the name of the database.

db-properties clj

(db-properties this)

Returns properties of the reference.

object-id clj

(object-id this)

Returns the ID of an database object.

biosequenceDbRefs clj protocol

get-db-refs clj

(get-db-refs this)

Returns db ref records.

biosequenceDescription clj protocol

description clj

(description this)

Returns the description of a biosequence object.

biosequenceEvidence clj protocol

evidence clj

(evidence this)

Returns evidence records.

biosequenceFeature clj protocol

operator clj

(operator this)

Returns an operator for dealing with intervals.

biosequenceFeatures clj protocol

feature-seq clj

(feature-seq this)

Returns a lazy list of features in a sequence.

filter-features clj

(filter-features this name)

Returns a list of features that return 'name' when called using bs/bs-name from biosequenceName protocol.

biosequenceFile clj protocol

bs-path clj

(bs-path this)

Returns the path of the file as string.

biosequenceGene clj protocol

locus clj

(locus this)

Returns the gene locus.

locus-tag clj

(locus-tag this)

Returns a locus tag.

map-location clj

(map-location this)

Returns the map location.

orf clj

(orf this)

ORF associated with the gene.

products clj

(products this)

The products of a gene.

biosequenceGenes clj protocol

genes clj

(genes this)

Returns sub-seq gene records.

biosequenceGoTerm clj protocol

go-component clj

(go-component this)

The GO component, molecular function etc.

go-id clj

(go-id this)

The GO id.

go-term clj

(go-term this)

The GO term.

biosequenceGoTerms clj protocol

gos clj

(gos this)

Returns go term records.

biosequenceID clj protocol

accession clj

(accession this)

Returns the accession of a biosequence object.

accessions clj

(accessions this)

Returns a list of accessions for a biosequence object.

creation-date clj

(creation-date this)

Returns a java date object.

dataset clj

(dataset this)

Returns the dataset.

discontinue-date clj

(discontinue-date this)

Returns a date object.

update-date clj

(update-date this)

Returns a java date object.

version clj

(version this)

Returns the version of the accession nil if none.

biosequenceInterval clj protocol

comp? clj

(comp? this)

Is the interval complementary to the biosequence sequence. Boolean

end clj

(end this)

Returns the end position of an interval as an integer.

point clj

(point this)

Returns a point interval.

start clj

(start this)

Returns the start position of an interval as an integer.

strand clj

(strand this)

Returns '+', '-', '.' or '?' for positive, minus, not stranded or unknwon respectively.

biosequenceIntervals clj protocol

intervals clj

(intervals this)

Returns a list of intervals.

biosequenceIO clj protocol

bs-reader clj

(bs-reader this)

Returns a reader for a file containing biosequences. Use with `with-open'

biosequenceName clj protocol

allergen-names clj

(allergen-names this)

Returns the allergen names.

alternate-names clj

(alternate-names this)

Returns the alternate names.

biotech-names clj

(biotech-names this)

Returns the biotech names.

cd-antigen-names clj

(cd-antigen-names this)

Returns the cd names.

innnames clj

(innnames this)

Returns the innname.

names clj

(names this)

Returns the default names of a record.

submitted-names clj

(submitted-names this)

Returns the submitted names.

biosequenceNameObject clj protocol

obj-description clj

(obj-description this)

obj-heading clj

(obj-heading this)

obj-id clj

(obj-id this)

obj-label clj

(obj-label this)

obj-name clj

(obj-name this)

obj-text clj

(obj-text this)

obj-type clj

(obj-type this)

obj-value clj

(obj-value this)

biosequenceNotes clj protocol

notes clj

(notes this)

Returns notes.

biosequenceParameters clj protocol

parameters clj

(parameters this)

Returns parameters from a reader.

biosequenceProtein clj protocol

activities clj

(activities this)

Returns a lit of activities.

calc-mol-wt clj

(calc-mol-wt this)

The calculated molecular weight.

ecs clj

(ecs this)

Returns list of E.C numbers.

processed clj

(processed this)

Processing of the protein.

biosequenceProteins clj protocol

proteins clj

(proteins this)

Returns protein sub-seq records.

biosequenceReader clj protocol

biosequence-seq clj

(biosequence-seq this)

Returns a lazy sequence of biosequence objects.

get-biosequence clj

(get-biosequence this accession)

Returns the biosequence object with the corresponding accession.

biosequenceStatus clj protocol

status clj

(status this)

Status of an object.

biosequenceSubCellLoc clj protocol

subcell-location clj

(subcell-location this)

subcell-orient clj

(subcell-orient this)

subcell-topol clj

(subcell-topol this)

biosequenceSubCellLocs clj protocol

subcell-locations clj

(subcell-locations this)

biosequenceSummary clj protocol

summary clj

(summary this)

Returns the summary of a sequence.

biosequenceSynonyms clj protocol

synonyms clj

(synonyms this)

Returns a list of synonyms.

biosequenceTaxonomies clj protocol

tax-refs clj

(tax-refs src)

Returns taxonomy records.

biosequenceTaxonomy clj protocol

common-name clj

(common-name this)

Returns the common name.

lineage clj

(lineage this)

Returns a lineage string.

mods clj

(mods this)

Returns a list of modifications to taxonomy.

tax-name clj

(tax-name this)

Returns the taxonomic name.

biosequenceTranslation clj protocol

codon-start clj

(codon-start this)

The start codon.

frame clj

(frame this)

Returns the frame a sequence should be translated in.

trans-table clj

(trans-table this)

Returns the translation table code to be used.

translation clj

(translation this)

Returns the translation of a sequence.

biosequenceUrl clj protocol

anchor clj

(anchor this)

Text to show as highlight

post-text clj

(post-text this)

Text after anchor

pre-text clj

(pre-text this)

Text before anchor.

url clj

(url this)

Returns the url.

biosequenceVariant clj protocol

original clj

(original this)

Returns the original.

variant clj

(variant this)

Returns the variant.

clean-sequences clj

(clean-sequences alphabet coll)

Removes spaces and newlines and checks that all characters are legal characters for the supplied alphabet. Replaces non-valid characters with \X. Only performs cleaning if supplied alphabet is a checked alphabet.

default-biosequence-biosequence clj

Default implementation of Biosequence protocol.

default-biosequence-citation clj

Default implementation of biosequenceCitation protocol.

default-biosequence-citations clj

Default implementation of biosequenceCitations protocol.

default-biosequence-comments clj

Default implementation of biosequenceComments protocol.

default-biosequence-dbref clj

Default implementation of biosequenceDbRef protocol.

default-biosequence-dbrefs clj

Default implementation of biosequenceDbRefs protocol.

default-biosequence-description clj

Default implementation of biosequenceDescription protocol.

default-biosequence-evidence clj

default-biosequence-feature clj

Default implementation of biosequenceFeature protocol.

default-biosequence-features clj

Default implementation of biosequenceFeatures protocol.

default-biosequence-file clj

Default implementation of biosequenceFile protocol.

default-biosequence-gene clj

Default implementation of biosequenceGene protocol.

default-biosequence-genes clj

Default implementation of biosequenceGenes protocol.

default-biosequence-goterm clj

Default implementation of biosequenceGoTerm protocol.

default-biosequence-goterms clj

Default implementation of biosequenceGoTerms protocol.

default-biosequence-id clj

Default implementation of biosequenceID protocol.

default-biosequence-interval clj

Default implementation of biosequenceInterval protocol.

default-biosequence-intervals clj

Default implementation of biosequenceIntervals protocol.

default-biosequence-name clj

Default implementation of biosequenceName protocol.

default-biosequence-nameobject clj

Default implementation of biosequenceNameObject protocol.

default-biosequence-notes clj

Default implementation of biosequenceNotes protocol.

default-biosequence-protein clj

Default implementation of biosequenceProtein protocol.

default-biosequence-proteins clj

Default implementation of biosequenceProteins protocol.

default-biosequence-status clj

Default implementation of biosequenceStatus protocol.

default-biosequence-subcell clj

Default implementation of biosequenceSubCellLoc protocol.

default-biosequence-subcells clj

Default implementation of biosequenceSubCellLocs protocol.

default-biosequence-summary clj

Default implementation of biosequenceSummary protocol.

default-biosequence-synonyms clj

Default implementation of biosequenceSynonyms protocol.

default-biosequence-tax clj

Default implementation of biosequenceTaxonomy protocol.

default-biosequence-taxonomies clj

Default implementation of biosequenceTaxonomies protocol.

default-biosequence-translation clj

Default implementation of biosequenceTranslation protocol.

default-biosequence-url clj

Default implementation of biosequenceUrl protocol.

default-biosequence-variant clj

Default implementation of biosequenceVariant protocol.

default-reader clj

delete-indexed-biosequence clj

(delete-indexed-biosequence index-file)

fasta-string clj

(fasta-string bioseq)

(fasta-string bioseq newlines?)

Returns the biosequence as a fasta formatted string. If newlines? is true then the sequence is formatted into 80 character rows.

fastaReduce clj protocol

fasta-reduce clj

(fasta-reduce this func fold)

Applies a function to sequence data streamed line-by-line and reduces the results using the supplied fold function. Uses the core reducers library so the fold function needs to have an 'identity' value that is returned when the function is called with no arguments.

get-interval-sequence clj

(get-interval-sequence interval bs)

Returns a fasta sequence corresponding to the provided interval.

get-list clj macro

(get-list obj & keys)

Low level macro for retrieving data from xml elements.

get-one clj macro

(get-one obj & keys)

Low level macro for retrieving data from xml elements.

get-req clj

(get-req a)

(get-req a param)

get-text clj macro

(get-text obj & keys)

Low level macro for retrieving data from xml elements.

id-convert clj

(id-convert ids from to email)

Takes a list of accessions and returns a hash-map mapping them to accessions from another database. If nothing found returns an empty hash-map and only returns entries that had a match. Uses the Uniprot id mapping utility and a list of supported databases is supplied at http://www.uniprot.org/faq/28#id_mapping_examples. Some common mappings include:

DB Name Abbreviation Direction UniProtKB AC/ID ACC+ID from UniProtKB AC ACC to EMBL/GenBank/DDBJ EMBL_ID both EMBL/GenBank/DDBJ CDS EMBL both Entrez Gene (GeneID) P_ENTREZGENEID both GI number P_GI both RefSeq Protein P_REFSEQ_AC both RefSeq Nucleotide REFSEQ_NT_ID both WormBase WORMBASE_ID both

There is a 100,000 limit on accessions in a single query imposed by Uniprot.

index-biosequence-collection clj

(index-biosequence-collection collection
                              file
                              &
                              {:keys [func index]
                               :or {func accession index nil}})

index-biosequence-file clj

(index-biosequence-file file
                        &
                        {:keys [func index] :or {func accession index nil}})

index-combine-files clj

(index-combine-files files outpath)

Takes a collection of biosequence files and generates an index combining all the files. If files have parameters only the parameter object from the last file will be retained.

init-biosequence-index clj

(init-biosequence-index path)

init-fasta-file clj

(init-fasta-file path alphabet & opts)

Initialises fasta protein file. Accession numbers and description are processed by splitting the string on the first space, the accession being the first value and description the second. Encoding can be specified using the :encoding keyword, defaults to UTF-8.

init-fasta-reader clj

(init-fasta-reader strm alphabet & {:keys [junk] :or {junk false}})

init-fasta-sequence clj

(init-fasta-sequence accession description alphabet sequence)

(init-fasta-sequence accession description alphabet sequence check-seq)

Returns a new fastaSequence. Currently :iupacNucleicAcids and :iupacAminoAcids are supported alphabets.

init-fasta-string clj

(init-fasta-string str alphabet)

Initialises a fasta string. Accession numbers and description are processed by splitting the string on the first space, the accession being the first value and description the second.

interval-complete? clj

(interval-complete? interval)

Returns the interval if it has a start and end value or a point value, nil otherwise.

is-indexed? clj

(is-indexed? file)

load-biosequence-index clj

(load-biosequence-index path)

make-date clj

(make-date str f)

make-date-format clj

(make-date-format str)

map->biosequenceIndex clj

(map->biosequenceIndex m__7585__auto__)

Factory function for class clj_biosequence.core.biosequenceIndex, taking a map of keywords to field values.

map->biosequenceIndexReader clj

(map->biosequenceIndexReader m__7585__auto__)

Factory function for class clj_biosequence.core.biosequenceIndexReader, taking a map of keywords to field values.

map->bzipped clj

(map->bzipped m__7585__auto__)

Factory function for class clj_biosequence.core.bzipped, taking a map of keywords to field values.

map->fastaFile clj

(map->fastaFile m__7585__auto__)

Factory function for class clj_biosequence.core.fastaFile, taking a map of keywords to field values.

map->fastaReader clj

(map->fastaReader m__7585__auto__)

Factory function for class clj_biosequence.core.fastaReader, taking a map of keywords to field values.

map->fastaSequence clj

(map->fastaSequence m__7585__auto__)

Factory function for class clj_biosequence.core.fastaSequence, taking a map of keywords to field values.

map->fastaString clj

(map->fastaString m__7585__auto__)

Factory function for class clj_biosequence.core.fastaString, taking a map of keywords to field values.

map->gzipped clj

(map->gzipped m__7585__auto__)

Factory function for class clj_biosequence.core.gzipped, taking a map of keywords to field values.

map->uncompressed clj

(map->uncompressed m__7585__auto__)

Factory function for class clj_biosequence.core.uncompressed, taking a map of keywords to field values.

map->zipped clj

(map->zipped m__7585__auto__)

Factory function for class clj_biosequence.core.zipped, taking a map of keywords to field values.

n50 clj

(n50 reader)

Takes anything that can have `biosequence-seq' called on it and returns the N50 of the sequences therein.

normalise-frame clj

(normalise-frame frame)

Takes a frame in the 'minus' format and returns it as a 1-6 frame.

object->file clj

(object->file obj file)

Spits an object to file after making sure print-length is temporarily set to false.

p-key clj

(p-key _)

parse-date clj

(parse-date d)

post-req clj

(post-req a param)

protein-charge clj

(protein-charge p & {:keys [ph disulfides] :or {ph 7 disulfides 0}})

Calculates the theoretical protein charge at the specified pH (default 7). Uses pKa values set out in the protein alphabets from cl-biosequence.alphabet. Considers Lys, His, Arg, Glu, Asp, Tyr and Cys residues only and ignores all other amino acids. The number of disulfides can be specified and 2 times this figure will be deducted from the number of Cys residues used in the calculation. Values used for the pKa of the N-term and C-term are 9.69 and 2.34 respectively.

return-nil clj

reverse-comp clj

(reverse-comp this)

Returns a new fastaSequence with the reverse complement sequence.

reverse-seq clj

(reverse-seq this)

Returns a new fastaSequence with the reverse sequence.

set-bioseq-proxy! clj

(set-bioseq-proxy! params)

six-frame-translation clj

(six-frame-translation nucleotide)

(six-frame-translation nucleotide table)

Returns a lazy list of fastaSequence objects representing translations of a nucleotide biosequence object in six frames.

sub-bioseq clj

(sub-bioseq bs beg)

(sub-bioseq bs beg end)

Returns a new fasta sequence object with the sequence corresponding to 'beg' (inclusive) and 'end' (exclusive) of 'bs'. If no 'end' argument returns from 'start' to the end of the sequence. Unlike vectors assumes NOT a zero based index to correlate with common intervals in annotation files.

translate clj

(translate bs frame & {:keys [table] :or {table (ala/codon-tables 1)}})

Returns a fastaSequence sequence representing the translation of the specified biosequence in the specified frame.