spdi2tbl

name	spdi2tbl
description	Use when flattening SPDI XML records into sorted, deduplicated tabular rows for downstream variant pipelines.
disable-model-invocation	true
user-invocable	true

spdi2tbl

Tiny Bash wrapper around xtract plus a final sort-table | cut | uniq cleanup. It reads <SPDI> XML, emits variant rows with rsID, accession, position, deleted/inserted sequence, class, type, and gene, then sorts and deduplicates the result.

Quick Start

• Command: ... | spdi2tbl
• Local executable: /home/vimalinx/miniforge3/envs/bio/bin/spdi2tbl
• Typical upstream: efetch -db snp ... | snp2hgvs | hgvs2spdi

When To Use This Tool

• Flattening SPDI XML into plain tabular rows
• Bridging from hgvs2spdi into shell-friendly TSV output
• Producing deduplicated variant tables for later ranking, filtering, or product-sequence generation
• Normalizing dbSNP-derived variant classes into a stable sort order

Common Patterns

# Canonical dbSNP pipeline into a flat table
efetch -db snp -id 104894914 -format docsum | snp2hgvs | hgvs2spdi | spdi2tbl

# Save flattened SPDI rows for downstream use
some_spdi_xml_generator | spdi2tbl > variants.tsv

# Feed directly into tbl2prod
efetch -db snp -id 104894914 -format docsum | snp2hgvs | hgvs2spdi | spdi2tbl | tbl2prod

Recommended Workflow

1. Generate real <SPDI> XML upstream, typically from hgvs2spdi.
2. Pipe the XML into spdi2tbl.
3. Inspect the resulting 8-column rows before using them downstream.
4. Chain into tbl2prod or other shell filters only after confirming the accession/class mix is what you expect.

Guardrails

• There is no safe local help/version path: both -h and --version fell through to xtract and failed with No data supplied to xtract from stdin or file.
• Source inspection shows the class ordering is explicitly transformed as Genomic=1, Coding=2, Protein=3 before sorting.
• The wrapper depends on sort-table being available on PATH.
• In live testing on rs104894914, the output rows looked like rs104894914 NC_000023.11 154191715 T C Genomic Substitution OPN1MW.
• Final output is deduplicated with uniq after sorting, so repeated equivalent rows are collapsed silently.