varity.vcf-to-hgvs — varity 0.6.1

Functions to convert a VCF-style variant into HGVS.

select-variant clj

(select-variant var seq-rdr rg)

vcf-variant->coding-dna-hgvs clj multimethod

(vcf-variant->coding-dna-hgvs variant ref-seq ref-gene)

(vcf-variant->coding-dna-hgvs variant ref-seq ref-gene options)

Converts a VCF-style variant (:chr, :pos, :ref, and :alt) into coding DNA HGVS. alt must be a single alternation such as "TG". "TG,T", for example, is not allowed. ref-seq must be a path to reference or an instance which implements cljam.io.protocols/ISequenceReader. ref-gene must be a path to refGene.txt(.gz), ref-gene index, or a ref-gene entity. A returned sequence consists of coding DNA HGVS defined in clj-hgvs.

Options:

:prefer-deletion? Prefer deletion (e.g. "c.7_9del") to repeated sequences (e.g. "c.4_6[1]"), default true for backward compatibility. The default value plans to be changed to false in the next major release.

:prefer-insertion? Prefer insertion (e.g. "c.9_10insAGG") to repeated sequences (e.g. "c.4_6[3]"), default false.

:tx-margin The length of transcription margin, up to a maximum of 10000, default 5000.

:verbose? Print debug information, default false.

vcf-variant->hgvs clj multimethod

(vcf-variant->hgvs variant ref-seq ref-gene)

(vcf-variant->hgvs variant ref-seq ref-gene options)

Converts a VCF-style variant (:chr, :pos, :ref, and :alt) into HGVS. alt must be a single alternation such as "TG". "TG,T", for example, is not allowed. ref-seq must be a path to reference or an instance which implements cljam.io.protocols/ISequenceReader. ref-gene must be a path to refGene.txt(.gz), ref-gene index, or a ref-gene entity. A returned sequence consists of maps, each having :coding-dna and :protein HGVS defined in clj-hgvs.

Options:

:prefer-deletion? Prefer deletion (e.g. "c.7_9del") to repeated sequences (e.g. "c.4_6[1]"), default true for backward compatibility. The default value plans to be changed to false in the next major release.

:prefer-insertion? Prefer insertion (e.g. "c.9_10insAGG") to repeated sequences (e.g. "c.4_6[3]"), default false.

:tx-margin The length of transcription margin, up to a maximum of 10000, default 5000.

:verbose? Print debug information, default false.

vcf-variant->protein-hgvs clj multimethod

(vcf-variant->protein-hgvs variant ref-seq ref-gene)

(vcf-variant->protein-hgvs variant ref-seq ref-gene options)

Converts a VCF-style variant (:chr, :pos, :ref, and :alt) into protein HGVS. alt must be a single alternation such as "TG". "TG,T", for example, is not allowed. ref-seq must be a path to reference or an instance which implements cljam.io.protocols/ISequenceReader. ref-gene must be a path to refGene.txt(.gz), ref-gene index, or a ref-gene entity. A returned sequence consists of protein HGVS defined in clj-hgvs.

Options:

:prefer-deletion? Prefer deletion (e.g. "p.P7_H8del") to repeated sequences (e.g. "p.P5_H6[1]"), default true for backward compatibility. The default value plans to be changed to false in the next major release.

:prefer-insertion? Prefer insertion (e.g. "c.H9_L10insRPH") to repeated sequences (e.g. "c.R4_H6[3]"), default false.

:verbose? Print debug information, default false.