varity.fusion — varity 0.11.0

NOTE: This algorithm was initially developed at Cancer Precision Medicine Center, Japanese Foundation for Cancer Research and Xcoo re-implemented it with Clojure.

fusion-genes clj

(fusion-genes rg-index
              {[{c1 :chr p1 :pos :as bp1} {c2 :chr p2 :pos :as bp2}]
                 :breakpoints
               is :inserted-seq})

Returns a lazy sequence of annotations of all possible combinations of fusion genes. An annotation is a map containing the following key-values:

• :breakpoints Given breakpoints in the order of 5'-part, 3'-part.
• :genes Candidate genes for each of the :breakpoints.
• :fusion? true iff the genes form a fused transcript.
• :breakpoint-regions Genic regions for each of the :breakpoints.
• :transcript-regions A sequence of regions corresponding to each exon of a resulting transcript. May not be fused or may be nil if no transcription is expected.

fusion-transcripts clj

(fusion-transcripts seq-reader rg-index bp)

Like fusion-genes but returns only in-frame and actually fused genes. An amino acid sequence is added as :transcript for each candidates.

in-frame? clj

(in-frame? transcript-regions)

Checks if the reading frame of given regions are in-frame.

parse-vcf-breakpoints clj

(parse-vcf-breakpoints chr pos ref-base alt-bnd)

Parses a VCF-style breakend string into a map used in varity.fusion.

transcript clj

(transcript seq-reader transcript-regions)

Translates a sequence of regions into an amino acid sequence.

variant->breakpoints clj

(variant->breakpoints {:keys [chr pos ref alt] {:keys [SVTYPE END]} :info})

Converts each allele in a VCF-style variant into a map used in varity.fusion. Returns a lazy sequence of the same length with alleles.