esl-seqrange

name	esl-seqrange
description	Use when splitting an SSI-indexed sequence file into per-process sequence-index ranges for embarrassingly parallel Easel or HMMER jobs.
disable-model-invocation	true
user-invocable	true

esl-seqrange

Quick Start

• Command: esl-seqrange [options] <sqfile> <procidx> <nproc>
• Local executable: /home/vimalinx/miniforge3/envs/bio/bin/esl-seqrange
• Full reference: See references/help.md

When To Use This Tool

• Use esl-seqrange when multiple workers need non-overlapping chunks of the same sequence database.
• It is designed for simple count-balanced partitioning of an SSI-indexed sequence file, returning a start-end sequence-index range for one worker.
• Reach for it when you already have worker IDs and want a quick deterministic split without writing custom indexing code.

Common Patterns

# Build the required SSI index once
esl-sfetch --index sequences.fa

# Get the slice for worker 3 out of 8 total workers
esl-seqrange sequences.fa 3 8

# Force the input format if autodetection is ambiguous
esl-seqrange --informat fasta sequences.fa 1 16

Recommended Workflow

1. Build an SSI index with esl-sfetch --index <sqfile> before trying to partition work.
2. Decide on the total worker count nproc and assign each worker a 1-based procidx.
3. Run esl-seqrange once per worker and capture the returned start-end range.
4. Feed those sequence-index ranges into the downstream worker logic.
5. Aggregate results knowing the split is balanced by number of sequences, not sequence length.

Guardrails

• An SSI index is mandatory even though the short live help does not spell that out clearly; the local man page does.
• Runtime testing shows procidx is 1-based. procidx=0 fails with “minimum allowed value for is 1”.
• Partitioning is based on sequence counts only, so workloads can still be imbalanced if some sequences are much longer than others.
• -h works; --help and --version are rejected by the local executable.