varity.ref-gene — varity 0.3.8-SNAPSHOT

Handles refGene.txt(.gz) content.

cds->genomic-pos clj

(cds->genomic-pos cds-pos rg)

(cds->genomic-pos cds-pos region {:keys [strand cds-start cds-end exon-ranges]})

cds-coord clj

(cds-coord pos rg)

Converts the genomic position into the cDNA coordinate. The return value is clj-hgvs.coordinate/CDNACoordinate record.

cds-coord->genomic-pos clj

(cds-coord->genomic-pos coord {:keys [strand] :as rg})

Converts the cDNA coordinate into the genomic position. coord must be clj-hgvs.coordinate/CDNACoordinate record.

cds-pos clj

(cds-pos pos {:keys [strand cds-start cds-end exon-ranges]})

in-any-exon? clj

(in-any-exon? chr pos rgidx)

Returns true if chr:pos is located in any ref-gene exon, else false.

in-cds? clj

(in-cds? pos {:keys [cds-start cds-end]})

Returns true if pos is in the coding region, false otherwise.

in-exon? clj

(in-exon? pos {:keys [exon-ranges]})

Returns true if pos is in the exon region, false otherwise.

index clj

(index rgs)

Creates refGene index for search.

load-ref-genes clj

(load-ref-genes f)

Loads f (e.g. refGene.txt(.gz)), returning the all contents as a sequence.

max-tx-margin clj

ref-genes clj

(ref-genes s rgidx)

(ref-genes chr pos rgidx)

(ref-genes chr pos rgidx tx-margin)

Searches refGene entries with ref-seq, gene or (chr, pos) using index, returning results as sequence. See also varity.ref-gene/index.

seek-gene-region clj

(seek-gene-region chr pos rgidx)

(seek-gene-region chr pos rgidx name)

Seeks chr:pos through exon entries in refGene and returns those indices