clj-biosequence.blast
->blastDB
(->blastDB file alphabet)
Positional factory function for class clj_biosequence.blast.blastDB.
->blastHit
(->blastHit src)
Positional factory function for class clj_biosequence.blast.blastHit.
->blastHsp
(->blastHsp src)
Positional factory function for class clj_biosequence.blast.blastHsp.
->blastIteration
(->blastIteration src)
Positional factory function for class clj_biosequence.blast.blastIteration.
->blastParameters
(->blastParameters src)
Positional factory function for class clj_biosequence.blast.blastParameters.
->blastReader
(->blastReader strm parameters)
Positional factory function for class clj_biosequence.blast.blastReader.
->blastSearch
(->blastSearch file opts)
Positional factory function for class clj_biosequence.blast.blastSearch.
blast
(blast bs program db outfile & {:keys [params], :or {params {}}})
blast-database
(blast-database param)
Returns the database used from a blast parameter record.
blast-evalue
(blast-evalue param)
Returns the evalue used from blast parameter record.
blast-filter
(blast-filter param)
Returns the filter used from a blast parameter record.
blast-matrix
(blast-matrix param)
Returns the matrix used from a blast parameter record.
blast-parameter-value
(blast-parameter-value p key)
Returns the value of a blast parameter from a blastParameters. Key
denotes parameter keys used in the blast xml. All values returned
as strings. Typical keys include:
:Parameters_matrix
:Parameters_expect
:Parameters_include
:Parameters_sc-match
:Parameters_sc-mismatch
:Parameters_gap-open
:Parameters_gap-extend
:Parameters_filter
blast-program
(blast-program param)
Returns the program used from a blast parameter record.
blast-version
(blast-version param)
Returns the blast version from a blast parameter record.
get-hit-value
(get-hit-value this key)
Takes a blastHit object and returns the value corresponding to key.
Keys are the keyword version of the XML nodes in the BLAST xml
output. All values are returned as strings. Typical BLAST Hit
values are:
:Hit_id
:Hit_len
:Hit_accession
:Hit_def
:Hit_num
get-hsp-value
(get-hsp-value this key)
Takes a blastHsp object and returns the value corresponding to key.
Keys are the keyword version of the XML nodes in the BLAST xml
output. All values are returned as strings. Typical BLAST HSP
keys are:
:Hsp_bit-score
:Hsp_score
:Hsp_evalue
:Hsp_query-from
:Hsp_query-to
:Hsp_hit-from
:Hsp_hit-to
:Hsp_positive
:Hsp_identity
:Hsp_gaps
:Hsp_hitgaps
:Hsp_querygaps
:Hsp_qseq
:Hsp_hseq
:Hsp_midline
:Hsp_align-len
:Hsp_query-frame
:Hsp_hit-frame
:Hsp_num
:Hsp_pattern-from
:Hsp_pattern-to
:Hsp_density
hit-accession
(hit-accession hit)
Returns the accession of the Blast hit.
hit-bit-scores
(hit-bit-scores hit)
Takes a blastHit object and returns a list of floats corresponding
to the bit scores of the HSPs composing the hit.
hit-def
(hit-def hit)
Returns the definition line of a Blast hit.
hit-e-values
(hit-e-values hit)
Takes a blastHit object and returns a list of floats corresponding
to the e-values of the HSPs composing the hit.
hit-frames
(hit-frames hit)
Takes a blastHit object and returns a list of frames from each of
the HSPs.
hit-seq
(hit-seq this)
Returns a lazy list of blastHit objects from a blastIteration
object.
hsp-alignment
(hsp-alignment hsp)
Returns the alignment from a HSP as a string.
hsp-seq
(hsp-seq this)
Takes a blastHit object and returns a lazy list of the blastHsp
objects contained in the hit.
init-blast-db
(init-blast-db file alphabet)
Initialises a blastDB object with the path and name of a blast
database (omitting the indexed file extensions).
init-blast-search
(init-blast-search file & opts)
Initialises a blast search with a blast ouput file in xml format.
iteration-query-length
(iteration-query-length iteration)
Takes a blastIteration object and returns the query length.
map->blastDB
(map->blastDB m__5869__auto__)
Factory function for class clj_biosequence.blast.blastDB, taking a map of keywords to field values.
map->blastHit
(map->blastHit m__5869__auto__)
Factory function for class clj_biosequence.blast.blastHit, taking a map of keywords to field values.
map->blastHsp
(map->blastHsp m__5869__auto__)
Factory function for class clj_biosequence.blast.blastHsp, taking a map of keywords to field values.
map->blastIteration
(map->blastIteration m__5869__auto__)
Factory function for class clj_biosequence.blast.blastIteration, taking a map of keywords to field values.
map->blastParameters
(map->blastParameters m__5869__auto__)
Factory function for class clj_biosequence.blast.blastParameters, taking a map of keywords to field values.
map->blastReader
(map->blastReader m__5869__auto__)
Factory function for class clj_biosequence.blast.blastReader, taking a map of keywords to field values.
map->blastSearch
(map->blastSearch m__5869__auto__)
Factory function for class clj_biosequence.blast.blastSearch, taking a map of keywords to field values.
significant-hit-seq
(significant-hit-seq iteration score measure)
Returns a list of blastHit objects from a blastIteration object
that have a bit score equal to or greater than that specified (or
default of 50). Measure argument accepts :bits or :evalue.