varity.ref-gene — varity 0.4.1

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]})

cds-region clj

(cds-region {:keys [chr cds-start cds-end strand]})

Returns a genomic region of a coding sequence of the given gene. Returns nil if the gene is a non-coding RNA.

cds-seq clj

(cds-seq {:keys [cds-start cds-end] :as ref-gene-record})

Returns a lazy sequence of exons included in a coding region of a ref-gene-record. Note that exons outside of the CDS are removed and partially overlapping ones are cropped in the result. Returns nil if the record is a non-coding RNA.

exon-seq clj

(exon-seq {:keys [chr strand exon-ranges]})

Returns a lazy sequence of regions corresponding to each exon in a gene. The exons are ordered by their index, thus they're reversed in genomic coordinate if the refGene record is on the reverse strand.

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

read-coding-sequence clj

(read-coding-sequence seq-rdr ref-gene-record)

Reads a coding sequence of a ref-gene record ref-gene-record from seq-rdr. Returns nil if the gene is a non-coding RNA.

read-exon-sequence clj

(read-exon-sequence seq-rdr {:keys [strand] :as exon})

Reads a base sequence of an exon from seq-rdr.

read-transcript-sequence clj

(read-transcript-sequence seq-rdr ref-gene-record)

Reads a DNA base sequence of a ref-gene-record from seq-rdr. The sequence contains 5'-UTR, CDS and 3'-UTR.

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

tx-region clj

(tx-region {:keys [chr tx-start tx-end strand]})

Returns a genomic region of the given gene.