| 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
esearch -db assembly -query 'GCF_000001405.40[accn]' | \
efetch -format docsum | \
xtract -pattern DocumentSummary -element Id AssemblyAccession
esearch -db pubmed -query 'ebola virus[Title/Abstract]' | \
efetch -format docsum | \
xtract -pattern DocumentSummary -element Id Title
elink -db pubmed -id 20210808 -cmd score | \
xtract -pattern LinkSet -max Link/Score
Recommended Workflow
- Feed XML from stdin or
-input; xtract is not useful without structured input.
- Define rows first with
-pattern.
- Add
-element fields incrementally before reaching for -group, -block, or -if.
- 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.
