esl-sfetch

name	esl-sfetch
description	Use when you need to extract specific sequences by name from a sequence file, or index a sequence file for faster lookup.
disable-model-invocation	true
user-invocable	true

esl-sfetch

Quick Start

• Command: esl-sfetch [options] <sqfile> <name> (single sequence) or esl-sfetch [options] -f <sqfile> <namefile> (multiple sequences) or esl-sfetch [options] --index <sqfile> (index file)
• Local executable: /home/vimalinx/miniforge3/envs/bio/bin/esl-sfetch
• Full reference: See references/help.md for complete options and usage details

When To Use This Tool

• Use esl-sfetch when you need random access to one or more named sequences from a sequence file.
• It is especially useful after creating an SSI index on a large FASTA or other Easel-supported sequence file.
• Use -f for batch extraction from a list of identifiers, and -c/-C when you need subsequences rather than whole records.
• Reach for it when plain grep is too brittle and you want indexed, format-aware retrieval.

Common Patterns

# Index a sequence file for fast lookup
esl-sfetch --index sequences.fa

# Fetch one sequence by name
esl-sfetch sequences.fa seq123

# Fetch many sequences listed one-per-line in a file
esl-sfetch -f sequences.fa ids.txt > subset.fa

# Fetch a subsequence range from one record
esl-sfetch -c 23..100 sequences.fa seq123 > subseq.fa

Recommended Workflow

1. Index the sequence file first: esl-sfetch --index <sqfile>
2. Identify the sequence name(s) to extract
3. Fetch sequence(s) using either single name or -f with a name file
4. Verify output matches expected sequences

Guardrails

• Sequence file must exist and be readable before indexing or fetching
• Use -h (not --help) to view available options
• Run --index on large files before fetching to enable fast lookups
• -C changes the expected format of the name file: each line must carry subsequence coordinates, not just an identifier