How do I install the Tbl2prod skill?

Run npx skillmds add vimalinx/tbl2prod 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.

Is Tbl2prod safe to use?

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This skill is tagged as working with Claude Code, Claude.ai, OpenAI Codex. SKILL.md is an open format, so most agents that read a skills directory can load it too.

Is Tbl2prod free to use?

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

Who published Tbl2prod?

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

Tbl2prod by vimalinx — Agent Skill

Name: Tbl2prod
Rating: 4.666666666666667 (3 reviews)
Author: vimalinx

File contents

tbl2prod

Pipeline helper that reads 8-column variant rows of the form rsid accn ofs del ins cls typ gene, fetches the referenced nucleotide or protein record from NCBI, and emits reference/product peptide sequences for non-genomic variants.

Quick Start

Command: ... | tbl2prod
Local executable: /home/vimalinx/miniforge3/envs/bio/bin/tbl2prod
Typical upstream: ... | spdi2tbl

When To Use This Tool

Translating coding or protein variant rows into actual product sequences
Extending spdi2tbl output with reference and altered peptide strings
Comparing wild-type and mutated products for rsID-derived non-genomic variants
Staying inside the EDirect shell-tool chain for sequence/product derivation

Common Patterns

# Full dbSNP-to-product pipeline
efetch -db snp -id 104894914 -format docsum | snp2hgvs | hgvs2spdi | spdi2tbl | tbl2prod

# Feed a prepared spdi2tbl-style table
cat variants.tsv | tbl2prod

# Save the resulting product table
cat variants.tsv | tbl2prod > products.tsv

Recommended Workflow

Feed tbl2prod the exact 8-column tabular rows produced by spdi2tbl or an equivalent generator.
Expect only coding and protein variants to survive; genomic rows are skipped.
Capture the three-column output and compare the reference (:+) and altered (:ins) definitions as needed.
Use the result for downstream interpretation, not as a generic annotation-file conversion step.

Guardrails

The old autogenerated description was wrong: this script does not read NCBI feature-table .tbl files.
It expects tab-delimited rows shaped like rsid accn ofs del ins cls typ gene; malformed or differently ordered input will misparse silently.
-h and --version are not implemented; with no stdin they simply produce no useful output.
Source inspection shows the script skips Genomic rows entirely, fetches sequence records with efetch -format gp, and uses gbf2xml, xtract, and several transmute transforms internally.
In live testing on rs104894914, the output included both a reference product row such as rs104894914 NM_000513.2:688:T:+ <protein> and an altered product row such as rs104894914 NM_000513.2:688:T:C <protein>.
The final output is sorted and reduced to three columns via sort-table ... | cut -f 1-2,4.

---name: tbl2proddescription: Use when converting `spdi2tbl`-style variant rows into reference and altered product sequences for coding or protein variants.--- # tbl2prod Pipeline helper that reads 8-column variant rows of the form `rsid accn ofs del ins cls typ gene`, fetches the referenced nucleotide or protein record from NCBI, and emits reference/product peptide sequences for non-genomic variants. ## Quick Start - **Command:** `... | tbl2prod` - **Local executable:** `/home/vimalinx/miniforge3/envs/bio/bin/tbl2prod` - **Typical upstream:** `... | spdi2tbl` ## When To Use This Tool - Translating coding or protein variant rows into actual product sequences - Extending `spdi2tbl` output with reference and altered peptide strings - Comparing wild-type and mutated products for rsID-derived non-genomic variants - Staying inside the EDirect shell-tool chain for sequence/product derivation ## Common Patterns ```bash # Full dbSNP-to-product pipeline efetch -db snp -id 104894914 -format docsum | snp2hgvs | hgvs2spdi | spdi2tbl | tbl2prod ``` ```bash # Feed a prepared spdi2tbl-style table cat variants.tsv | tbl2prod ``` ```bash # Save the resulting product table cat variants.tsv | tbl2prod > products.tsv ``` ## Recommended Workflow 1. Feed `tbl2prod` the exact 8-column tabular rows produced by `spdi2tbl` or an equivalent generator. 2. Expect only coding and protein variants to survive; genomic rows are skipped. 3. Capture the three-column output and compare the reference (`:+`) and altered (`:ins`) definitions as needed. 4. Use the result for downstream interpretation, not as a generic annotation-file conversion step. ## Guardrails - The old autogenerated description was wrong: this script does not read NCBI feature-table `.tbl` files. - It expects tab-delimited rows shaped like `rsid accn ofs del ins cls typ gene`; malformed or differently ordered input will misparse silently. - `-h` and `--version` are not implemented; with no stdin they simply produce no useful output. - Source inspection shows the script skips `Genomic` rows entirely, fetches sequence records with `efetch -format gp`, and uses `gbf2xml`, `xtract`, and several `transmute` transforms internally. - In live testing on rs104894914, the output included both a reference product row such as `rs104894914 NM_000513.2:688:T:+ <protein>` and an altered product row such as `rs104894914 NM_000513.2:688:T:C <protein>`. - The final output is sorted and reduced to three columns via `sort-table ... | cut -f 1-2,4`.

Frequently asked questions