How do I install the Blst2tkns skill?

Run npx skillmds add vimalinx/blst2tkns 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 Blst2tkns safe to use?

This skill has not completed SkillMD's automated safety review yet. Capability flags: reads secrets. SkillMD never runs a skill's scripts for you; review the SKILL.md before installing.

Which AI agents work with Blst2tkns?

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 Blst2tkns free to use?

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

Who published Blst2tkns?

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

Blst2tkns by vimalinx — Agent Skill

Name: Blst2tkns
Rating: 4.2 (5 reviews)
Author: vimalinx

File contents

blst2tkns

EDirect shell wrapper over xtract that reads Seq-align-set_E XML and emits a compact label/value token stream for exon-alignment records.

Quick Start

Command: blst2tkns
Local executable: /home/vimalinx/miniforge3/envs/bio/bin/blst2tkns
Environment prerequisite: add /home/vimalinx/miniforge3/envs/bio/bin to PATH so sibling tools such as xtract are resolvable

When To Use This Tool

Convert Seq-align-set_E XML into a lighter token stream for shell pipelines.
Pull out per-alignment values such as running index, score, start, stop, strand, and nested parts/* content.
Bridge BLAST-derived XML that already lives in an EDirect / xtract workflow into simpler downstream parsing.
Use this only for the expected XML shape; it is not a generic BLAST tabular, plain-text, or FASTA converter.

Common Patterns

# 1) Tokenize an existing Seq-align-set_E XML file
export PATH=/home/vimalinx/miniforge3/envs/bio/bin:$PATH

blst2tkns < seq-align-set.xml > align.tokens.txt

# 2) Inspect the first emitted tokens before scaling up
export PATH=/home/vimalinx/miniforge3/envs/bio/bin:$PATH

blst2tkns < seq-align-set.xml | sed -n '1,30p'

Recommended Workflow

Confirm the upstream XML actually contains Seq-align-set_E records before blaming the wrapper for empty output.
Activate the bio environment or prepend /home/vimalinx/miniforge3/envs/bio/bin to PATH so xtract is available.
Run the wrapper on a small sample and inspect the emitted labels before wiring it into a larger pipeline.
Feed the token stream to your next shell / EDirect stage once the field order matches what you expect.

Guardrails

The script is just a one-line xtract recipe. Without the bio bin directory on PATH, it fails immediately with xtract: command not found.
There is no standalone help path here. With dependencies available, blst2tkns -help still falls through to xtract and errors on missing input.
With xtract available but no XML input, the live failure is No data supplied to xtract from stdin or file.
Source inspection shows it hard-codes emission of index, score, start, stop, strand, nested parts/* tokens, and a terminating end 0 marker. If your XML schema differs, output may be partial or empty.

---name: blst2tknsdescription: Use when turning EDirect-style BLAST XML alignment blocks into a token stream for downstream shell or xtract-based parsing.--- # blst2tkns EDirect shell wrapper over `xtract` that reads `Seq-align-set_E` XML and emits a compact label/value token stream for exon-alignment records. ## Quick Start - **Command:** `blst2tkns` - **Local executable:** `/home/vimalinx/miniforge3/envs/bio/bin/blst2tkns` - **Environment prerequisite:** add `/home/vimalinx/miniforge3/envs/bio/bin` to `PATH` so sibling tools such as `xtract` are resolvable ## When To Use This Tool - Convert `Seq-align-set_E` XML into a lighter token stream for shell pipelines. - Pull out per-alignment values such as running index, score, start, stop, strand, and nested `parts/*` content. - Bridge BLAST-derived XML that already lives in an EDirect / `xtract` workflow into simpler downstream parsing. - Use this only for the expected XML shape; it is not a generic BLAST tabular, plain-text, or FASTA converter. ## Common Patterns ```bash # 1) Tokenize an existing Seq-align-set_E XML file export PATH=/home/vimalinx/miniforge3/envs/bio/bin:$PATH blst2tkns < seq-align-set.xml > align.tokens.txt ``` ```bash # 2) Inspect the first emitted tokens before scaling up export PATH=/home/vimalinx/miniforge3/envs/bio/bin:$PATH blst2tkns < seq-align-set.xml | sed -n '1,30p' ``` ## Recommended Workflow 1. Confirm the upstream XML actually contains `Seq-align-set_E` records before blaming the wrapper for empty output. 2. Activate the bio environment or prepend `/home/vimalinx/miniforge3/envs/bio/bin` to `PATH` so `xtract` is available. 3. Run the wrapper on a small sample and inspect the emitted labels before wiring it into a larger pipeline. 4. Feed the token stream to your next shell / EDirect stage once the field order matches what you expect. ## Guardrails - The script is just a one-line `xtract` recipe. Without the bio bin directory on `PATH`, it fails immediately with `xtract: command not found`. - There is no standalone help path here. With dependencies available, `blst2tkns -help` still falls through to `xtract` and errors on missing input. - With `xtract` available but no XML input, the live failure is `No data supplied to xtract from stdin or file`. - Source inspection shows it hard-codes emission of `index`, `score`, `start`, `stop`, `strand`, nested `parts/*` tokens, and a terminating `end 0` marker. If your XML schema differs, output may be partial or empty.

Frequently asked questions