Xml2fsa

xml2fsa

Quick Start

• Command: efetch ... -format gbc | xml2fsa > records.fasta
• Local executable: /home/vimalinx/miniforge3/envs/bio/bin/xml2fsa
• Full reference: See references/help.md for detailed usage

When To Use This Tool

• Convert INSDSeq-style NCBI XML sequence records into FASTA.
• Flatten efetch XML output into headers and plain sequence strings for downstream sequence tools.
• Extract accession/definition-based FASTA entries without writing a custom xtract command.

Common Patterns

# 1) Convert streamed INSDSeq XML into FASTA
cat records.xml | xml2fsa > records.fasta

# 2) Pipe efetch-style XML straight into FASTA output
efetch -db nuccore -id ABC123.1 -format gbc | xml2fsa > ABC123.fasta

Recommended Workflow

1. Start from INSDSeq-style XML, usually streamed from efetch or another NCBI XML source.
2. Pipe that XML into xml2fsa; the wrapper itself is stdin-driven.
3. Inspect the first FASTA header to confirm the accession / definition mapping looks right.
4. Send the resulting FASTA into downstream alignment, indexing, or QC tools.

Guardrails

• The wrapper is a fixed xtract command over INSDSeq; it is not a general XML-to-FASTA converter.
• It does not pass through positional filenames, so stdin / pipes are the reliable invocation path.
• xtract must be available on PATH, and --help / --version just fall through to xtract-style input errors.
• FASTA headers are constructed from the first available accession/id/locus field plus the definition line, so spot-check headers before batch use.