varity.vcf-to-hgvs
Functions to convert a VCF-style variant into HGVS.
Functions to convert a VCF-style variant into HGVS.
vcf-variant->cdna-hgvscljmultimethod
(vcf-variant->cdna-hgvs variant ref-seq ref-gene)(vcf-variant->cdna-hgvs variant ref-seq ref-gene options)Converts a VCF-style variant (:chr, :pos, :ref, and :alt) into cDNA 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 cDNA HGVS defined in clj-hgvs.
Options:
:tx-margin The length of transcription margin, up to a maximum of 10000, default 5000. :verbose? Print debug information, default false.
Converts a VCF-style variant (:chr, :pos, :ref, and :alt) into cDNA 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 cDNA HGVS defined in clj-hgvs.
Options:
:tx-margin The length of transcription margin, up to a maximum of 10000,
default 5000.
:verbose? Print debug information, default false.vcf-variant->hgvscljmultimethod
(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 :cdna and :protein HGVS defined in clj-hgvs.
Options:
:tx-margin The length of transcription margin, up to a maximum of 10000, default 5000. :verbose? Print debug information, default false.
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 :cdna and :protein HGVS defined in clj-hgvs.
Options:
:tx-margin The length of transcription margin, up to a maximum of 10000,
default 5000.
:verbose? Print debug information, default false.vcf-variant->protein-hgvscljmultimethod
(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:
:verbose? Print debug information, default false.
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: :verbose? Print debug information, default false.
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