snp2tbl

name	snp2tbl
description	Use when converting NCBI dbSNP docsum XML into flat tabular rows through the bundled `snp2hgvs | hgvs2spdi | spdi2tbl` pipeline.
disable-model-invocation	true
user-invocable	true

snp2tbl

Thin bash pipeline wrapper. It does not parse SNP XML directly by itself; instead it sends dbSNP docsum XML through snp2hgvs, forwards any CLI arguments to hgvs2spdi, and then flattens the result with spdi2tbl.

Quick Start

• Command: efetch -db snp -id <rsid> -format docsum | snp2tbl
• Local executable: /home/vimalinx/miniforge3/envs/bio/bin/snp2tbl
• Internal pipeline: snp2hgvs | hgvs2spdi "$@" | spdi2tbl

When To Use This Tool

• Turning dbSNP docsum XML into one tabular row per reported variant representation
• Flattening rsID-derived HGVS/SPDI information for downstream filtering or spreadsheets
• Staying inside the Entrez Direct shell-tool ecosystem instead of writing custom XML transforms
• Passing conversion-related flags onward to hgvs2spdi while keeping a one-command wrapper

Common Patterns

# Convert one rsID into tabular rows
efetch -db snp -id 104894914 -format docsum | snp2tbl

# Convert multiple rsIDs in one stream
efetch -db snp -id 104894914,104894915 -format docsum | snp2tbl

# Forward additional arguments to hgvs2spdi
efetch -db snp -id 104894914 -format docsum | snp2tbl <hgvs2spdi-args>

Recommended Workflow

1. Fetch dbSNP records in -format docsum.
2. Pipe them into snp2tbl and inspect the emitted tabular rows.
3. If needed, pass only arguments that hgvs2spdi understands, because this wrapper forwards its own argv there.
4. Capture the resulting table for downstream joins, filtering, or export.

Guardrails

• -h is not a safe help path. In local testing it was forwarded downstream and triggered cat: invalid option -- 'h' plus an xtract no-input error.
• --version is also not implemented as wrapper metadata; with no input it fell through to the same no-data failure class.
• The wrapper depends on snp2hgvs, hgvs2spdi, and spdi2tbl all being available on PATH.
• In live testing on rs104894914, the output contained rows shaped like rs104894914 NC_000023.11 154191715 T C Genomic Substitution OPN1MW.
• Because the first stage is snp2hgvs, this wrapper expects the same dbSNP docsum XML input that snp2hgvs expects; it is not a generic tabularizer for arbitrary SNP XML.