Xml2tbl

xml2tbl

Quick Start

• Command: cat records.xml | xml2tbl > features.tbl
• Local executable: /home/vimalinx/miniforge3/envs/bio/bin/xml2tbl
• Reference: references/help.md

When To Use This Tool

• Flatten INSDSeq XML feature annotations into a compact tabular view.
• Review feature intervals and qualifiers from NCBI sequence XML without writing a custom xtract command.
• Export a quick human-readable feature table from efetch XML output.

Common Patterns

# 1) Convert INSDSeq XML into a feature table
cat records.xml | xml2tbl > features.tbl

# 2) Pipe efetch-style XML straight into a tabular annotation dump
efetch -db nuccore -id ABC123.1 -format gbc | xml2tbl

Recommended Workflow

1. Start from INSDSeq-style XML, usually from efetch or a previously saved XML stream.
2. Pipe the XML into xml2tbl; the wrapper itself is stdin-driven.
3. Inspect the first >Feature block and a few qualifier lines to confirm the layout.
4. Use the resulting table for review, lightweight filtering, or export into downstream annotation tooling.

Guardrails

• This is a fixed xtract recipe for INSDSeq, not a general XML-to-table 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.
• Output is a feature-centric table beginning with >Feature <accession> lines, followed by interval and qualifier rows; downstream code should expect that layout.