xtract

name	xtract
description	Use when parsing, extracting, or converting XML data from NCBI Entrez or other bioinformatics sources into tab-delimited tables. Use for selecting specific elements, filtering records, and restructuring hierarchical XML into flat formats for downstream analysis.
disable-model-invocation	true
user-invocable	true

xtract

Quick Start

• Command: xtract
• Local executable: /home/vimalinx/miniforge3/envs/bio/bin/xtract
• Full reference: See references/help.md for complete argument list and examples

When To Use This Tool

• Convert Entrez XML into tab-delimited tables.
• Extract selected elements or nested values from efetch, esummary, or elink XML output.
• Filter records conditionally while flattening XML into rows.
• Use this after you already know the XML structure you are parsing.

Common Patterns

# 1) Turn document summaries into a simple two-column table
esearch -db assembly -query 'GCF_000001405.40[accn]' | \
  efetch -format docsum | \
  xtract -pattern DocumentSummary -element Id AssemblyAccession

# 2) Extract PubMed summary IDs and titles
esearch -db pubmed -query 'ebola virus[Title/Abstract]' | \
  efetch -format docsum | \
  xtract -pattern DocumentSummary -element Id Title

# 3) Conditional extraction from linked records
elink -db pubmed -id 20210808 -cmd score | \
  xtract -pattern LinkSet -max Link/Score

Recommended Workflow

1. Feed XML from stdin or -input; xtract is not useful without structured input.
2. Define rows first with -pattern.
3. Add -element fields incrementally before reaching for -group, -block, or -if.
4. Save the exact extraction command alongside the analysis so XML-to-table logic remains reproducible.

Guardrails

• xtract requires XML input from stdin or -input; otherwise it errors immediately.
• -pattern defines row boundaries; choosing the wrong pattern is the fastest way to get nonsense tables.
• Start with a minimal extraction and expand, rather than writing a huge one-liner blind.
• Use -strict when embedded HTML or MathML is polluting the text you want to extract.