esl-mask

name	esl-mask
description	Use when applying coordinate-based masks to named sequences in FASTA or other Easel-supported sequence files.
disable-model-invocation	true
user-invocable	true

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

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.