How do I install the Gm2ranges skill?

Run npx skillmds add vimalinx/gm2ranges 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 Gm2ranges safe to use?

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

Which AI agents work with Gm2ranges?

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 Gm2ranges free to use?

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

Who published Gm2ranges?

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

Gm2ranges by vimalinx — Agent Skill

Name: Gm2ranges
Rating: 4.666666666666667 (3 reviews)
Author: vimalinx

File contents

gm2ranges

Quick Start

Command: printf 'acc1 score 1|10 5|3 plus|minus\n' | /home/vimalinx/miniforge3/envs/bio/bin/gm2ranges
Local executable: /home/vimalinx/miniforge3/envs/bio/bin/gm2ranges
Full reference: See references/help.md for complete usage details

When To Use This Tool

Turn pipe-delimited start/span/strand alignment summaries into comma-joined genomic ranges.
Prepare interval strings for downstream helpers such as fuse-ranges.
Collapse per-hit dense segment fields into one summarized row with a segment count and an overall strand label.

Common Patterns

# 1) Convert one row of starts/spans/strands into a compact range summary
printf 'acc1 score 1|10 5|3 plus|minus\n' | \
  /home/vimalinx/miniforge3/envs/bio/bin/gm2ranges

# 2) Use in the intended EDirect map pipeline
cat smear.asn | \
  blst2gm | \
  /home/vimalinx/miniforge3/envs/bio/bin/gm2ranges | \
  grep minus | \
  cut -f 2-

Recommended Workflow

Start from rows that already contain accession, score, start-list, span-list, and strand-list columns.
Run gm2ranges as a stdin-to-stdout transformer.
Inspect the emitted segment count, aggregate strand label, and comma-joined range list.
Feed the range list into downstream normalization or fusion steps if you need canonical interval coordinates.

Guardrails

The wrapper expects at least five whitespace-delimited columns; shorter rows are silently skipped.
Minus-strand segments are emitted as descending stop..start strings (for example 12..10), so further normalization is usually needed.
The aggregate strand label becomes mixed when both plus and minus segments appear in the same row.
There is no built-in help or version mode.

---name: gm2rangesdescription: Use when converting BLAST/genomic-map alignment summaries into compact strand-and-range tables for later interval fusion.--- # gm2ranges ## Quick Start - **Command:** `printf 'acc1 score 1|10 5|3 plus|minus\n' | /home/vimalinx/miniforge3/envs/bio/bin/gm2ranges` - **Local executable:** `/home/vimalinx/miniforge3/envs/bio/bin/gm2ranges` - **Full reference:** See [references/help.md](references/help.md) for complete usage details ## When To Use This Tool - Turn pipe-delimited start/span/strand alignment summaries into comma-joined genomic ranges. - Prepare interval strings for downstream helpers such as `fuse-ranges`. - Collapse per-hit dense segment fields into one summarized row with a segment count and an overall strand label. ## Common Patterns ```bash # 1) Convert one row of starts/spans/strands into a compact range summary printf 'acc1 score 1|10 5|3 plus|minus\n' | \ /home/vimalinx/miniforge3/envs/bio/bin/gm2ranges ``` ```bash # 2) Use in the intended EDirect map pipeline cat smear.asn | \ blst2gm | \ /home/vimalinx/miniforge3/envs/bio/bin/gm2ranges | \ grep minus | \ cut -f 2- ``` ## Recommended Workflow 1. Start from rows that already contain accession, score, start-list, span-list, and strand-list columns. 2. Run `gm2ranges` as a stdin-to-stdout transformer. 3. Inspect the emitted segment count, aggregate strand label, and comma-joined range list. 4. Feed the range list into downstream normalization or fusion steps if you need canonical interval coordinates. ## Guardrails - The wrapper expects at least five whitespace-delimited columns; shorter rows are silently skipped. - Minus-strand segments are emitted as descending `stop..start` strings (for example `12..10`), so further normalization is usually needed. - The aggregate strand label becomes `mixed` when both plus and minus segments appear in the same row. - There is no built-in help or version mode.

Frequently asked questions