How do I install the Spdi2tbl skill?

Run npx skillmds add vimalinx/spdi2tbl in your terminal (requires Node.js), paste this page's agent-chat prompt into Claude, Cursor, or any MCP-connected agent, or download the SKILL.md file and copy it into your agent's skills directory.

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Is Spdi2tbl free to use?

Yes. Installing skills from SkillMD is free, and the skill stays under its author's original license.

Who published Spdi2tbl?

vimalinx (@vimalinx) published this skill. Their other Agent Skills are listed on their SkillMD profile.

Spdi2tbl by vimalinx — Agent Skill

Name: Spdi2tbl
Rating: 4.5 (4 reviews)
Author: vimalinx

File contents

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

Generate real <SPDI> XML upstream, typically from hgvs2spdi.
Pipe the XML into spdi2tbl.
Inspect the resulting 8-column rows before using them downstream.
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.

---name: spdi2tbldescription: Use when flattening SPDI XML records into sorted, deduplicated tabular rows for downstream variant pipelines.--- # 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 ```bash # Canonical dbSNP pipeline into a flat table efetch -db snp -id 104894914 -format docsum | snp2hgvs | hgvs2spdi | spdi2tbl ``` ```bash # Save flattened SPDI rows for downstream use some_spdi_xml_generator | spdi2tbl > variants.tsv ``` ```bash # 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.

Frequently asked questions