How do I install the Esl Mask skill?

Run npx skillmds add vimalinx/esl-mask 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 Esl Mask 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 Esl Mask?

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 Esl Mask free to use?

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

Who published Esl Mask?

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

Esl Mask by vimalinx — Agent Skill

Name: Esl Mask
Rating: 4.5 (4 reviews)
Author: vimalinx

File contents

esl-mask

Quick Start

Command: esl-mask [options] <sqfile> <maskfile>
Local executable: /home/vimalinx/miniforge3/envs/bio/bin/esl-mask
Full reference: See references/help.md for detailed options (run esl-mask -h)

When To Use This Tool

Use esl-mask when you have named sequences plus a coordinate table describing which residues to mask or keep.
It is useful for masking low-confidence intervals, trimming flanks, hiding specific motif regions, or generating region-only views with reverse masking.
Reach for -l to lowercase masked residues instead of replacing them, or -m <c> to mask with a custom character such as N or X.
Use -R when your mask file is not in the exact same order as the sequence file and you have an SSI index available.

Common Patterns

# Mask listed regions with the default X character
esl-mask sequences.fa mask.tsv > masked.fa

# Lowercase the masked residues instead of replacing them
esl-mask -l sequences.fa mask.tsv > masked-lower.fa

# Keep only the listed region and mask everything else
esl-mask -r sequences.fa keep-regions.tsv > region-only.fa

# Random-access masking from an SSI-indexed sequence file, padding each region by 5 nt
esl-mask -R -x 5 -m N sequences.fa mask.tsv > padded.fa

Recommended Workflow

Prepare a supported sequence file such as FASTA, EMBL, GenBank, or another Easel-recognized format.
Build a mask file with at least three whitespace-delimited fields per line: sequence name, 1-based start, and 1-based end.
Decide whether you want normal masking, reverse masking (-r), lowercasing (-l), or a replacement character (-m).
If mask rows are not aligned to the sequence-file order, create an SSI index with esl-sfetch --index and rerun with -R.
Inspect output around interval boundaries, especially if you used -x to extend masked regions.

Guardrails

The mask file uses 1-based inclusive coordinates and ignores blank lines plus # comments.
By default, sequence names must appear in the same order and number in both files; -R is the escape hatch, but it requires an .ssi index.
-r masks everything outside start..end, not the interval itself.
-h works; --help and --version are rejected by the local executable.
-x <n> extends masking by up to n residues on both sides, which can change behavior near sequence ends.

---name: esl-maskdescription: Use when applying coordinate-based masks to named sequences in FASTA or other Easel-supported sequence files.--- # esl-mask ## Quick Start - **Command:** `esl-mask [options] <sqfile> <maskfile>` - **Local executable:** `/home/vimalinx/miniforge3/envs/bio/bin/esl-mask` - **Full reference:** See `references/help.md` for detailed options (run `esl-mask -h`) ## When To Use This Tool - Use `esl-mask` when you have named sequences plus a coordinate table describing which residues to mask or keep. - It is useful for masking low-confidence intervals, trimming flanks, hiding specific motif regions, or generating region-only views with reverse masking. - Reach for `-l` to lowercase masked residues instead of replacing them, or `-m <c>` to mask with a custom character such as `N` or `X`. - Use `-R` when your mask file is not in the exact same order as the sequence file and you have an SSI index available. ## Common Patterns ```bash # Mask listed regions with the default X character esl-mask sequences.fa mask.tsv > masked.fa # Lowercase the masked residues instead of replacing them esl-mask -l sequences.fa mask.tsv > masked-lower.fa # Keep only the listed region and mask everything else esl-mask -r sequences.fa keep-regions.tsv > region-only.fa # Random-access masking from an SSI-indexed sequence file, padding each region by 5 nt esl-mask -R -x 5 -m N sequences.fa mask.tsv > padded.fa ``` ## Recommended Workflow 1. Prepare a supported sequence file such as FASTA, EMBL, GenBank, or another Easel-recognized format. 2. Build a mask file with at least three whitespace-delimited fields per line: sequence name, 1-based start, and 1-based end. 3. Decide whether you want normal masking, reverse masking (`-r`), lowercasing (`-l`), or a replacement character (`-m`). 4. If mask rows are not aligned to the sequence-file order, create an SSI index with `esl-sfetch --index` and rerun with `-R`. 5. Inspect output around interval boundaries, especially if you used `-x` to extend masked regions. ## Guardrails - The mask file uses 1-based inclusive coordinates and ignores blank lines plus `#` comments. - By default, sequence names must appear in the same order and number in both files; `-R` is the escape hatch, but it requires an `.ssi` index. - `-r` masks everything outside `start..end`, not the interval itself. - `-h` works; `--help` and `--version` are rejected by the local executable. - `-x <n>` extends masking by up to `n` residues on both sides, which can change behavior near sequence ends.

Frequently asked questions