fsa2xml

name	fsa2xml
description	Use when converting FASTA sequence records into XML for downstream EDirect or XML-based sequence processing.
disable-model-invocation	true
user-invocable	true

fsa2xml

Quick Start

• Command: fsa2xml < sequences.fasta > sequences.xml
• Local executable: /home/vimalinx/miniforge3/envs/bio/bin/fsa2xml
• Reference: See references/help.md for full usage details

When To Use This Tool

• Wrap FASTA records in XML so they can be inspected or transformed with xtract.
• Preserve sequence IDs, optional titles, sequence length, and sequence text in a structured form.
• Bridge plain-text FASTA inputs into XML-centric EDirect workflows.

Common Patterns

# 1) Convert FASTA records into XML
fsa2xml < sequences.fasta > sequences.xml

# 2) Convert and inspect record-level fields immediately
fsa2xml < sequences.fasta | xtract -pattern FASTA -element ID Title Length Seq

Recommended Workflow

1. Start with one-record-per-header FASTA input.
2. Run fsa2xml via stdin redirection or as part of a pipe.
3. Confirm that the emitted XML contains the expected <FASTA> blocks and sequence metadata.
4. Hand the XML off to xtract, xml2json, or other XML-side tools only after that quick inspection.

Guardrails

• This is a thin wrapper around transmute -f2x, so transmute must also be on PATH.
• The current build does not expose a real --help or --version response.
• The emitted XML is record-oriented: each FASTA entry becomes its own <FASTA> block rather than a single enclosing document.
• Prefer stdin or pipes over relying on undocumented positional-file behavior.