Hgvs2spdi

hgvs2spdi

Quick Start

• Command: ... | hgvs2spdi [transform.tsv]
• Local executable: /home/vimalinx/miniforge3/envs/bio/bin/hgvs2spdi
• Output: formatted XML with Id, Hgvs, and Spdi fields

When To Use This Tool

• Convert HGVS records produced inside an EDirect pipeline into SPDI coordinates.
• Resolve CDS-relative HGVS notations against transcript-specific coding-start offsets.
• Keep working in XML-based NCBI tooling instead of manually translating coordinates.
• Reuse a cached transform table when you want to avoid repeated live accession lookups.

Common Patterns

# 1) Convert HGVS extracted from dbSNP docsum records
efetch -db snp -id 11549407 -format docsum |
xtract -rec HGVS -pattern DocumentSummary -wrp Id -element Id -rst -hgvs DOCSUM |
hgvs2spdi

# 2) Use a precomputed accession-to-offset transform file
xtract -rec HGVS -pattern DocumentSummary -wrp Id -element Id -rst -hgvs DOCSUM < input.xml |
hgvs2spdi cds_offsets.tsv

# 3) Inspect the resulting SPDI XML
... | hgvs2spdi | xtract -pattern Variant -element Accession,Position,Deleted,Inserted,Spdi

Recommended Workflow

1. Feed the tool HGVS XML, not raw HGVS strings.
2. Decide whether to let the wrapper compute transcript offsets live or to pass an existing accession<TAB>offset table as the optional positional file argument.
3. Inspect the emitted Hgvs and Spdi fields together before downstream storage or querying.
4. Cache transform tables when converting many transcript-relative HGVS records from the same accession set.

Guardrails

• hgvs2spdi reads its HGVS records from stdin; a positional file argument is only for the optional transform table.
• There is no real help path; hgvs2spdi --help with empty stdin exits silently.
• Without a transform file, the wrapper performs live efetch / gbf2xml lookups to derive CDS-start offsets for transcript accessions.
• The transform table is expected to contain Accession<TAB>offset rows suitable for xtract -transform.
• Output is XML, not a bare accession:position:deleted:inserted text line.
• The wrapper depends on sibling EDirect helpers such as xtract, print-columns, gbf2xml, and transmute being on PATH.