Esample

esample

Quick Start

• Command: esample -docsum|-article|-book|-protein|-gene|-taxon|-blast|-snp|-hgvs|-bioc|-flatfile|-gff|-gencode
• Local executable: /home/vimalinx/miniforge3/envs/bio/bin/esample
• Full reference: See references/help.md

When To Use This Tool

• Get a representative sample document for xtract, parser, or schema debugging without making a live Entrez request.
• Create fixtures for tests or documentation that need stable example records.
• Learn the structure of a supported output type before switching to real efetch or xfetch data.

Common Patterns

# 1) Prototype an xtract expression against a sample PubMed docsum
esample -docsum | xtract -pattern DocumentSummary -element Id Title

# 2) Save a sample GenBank flatfile or GFF3 record as a fixture
esample -flatfile > example.gb
esample -gff > example.gff3

# 3) Inspect sample genetic code output for parser work
esample -gencode

Recommended Workflow

1. Choose the sample mode that matches the structure you need to inspect.
2. Pipe it into xtract, transmute, or your parser until the transformation is correct.
3. Save the output as a stable fixture if you need repeatable tests.
4. Replace the sample source with real efetch, xfetch, or archived data once the downstream logic is proven.

Guardrails

• esample prints hard-coded example documents; it does not fetch live records from NCBI.
• Output goes to standard output, so redirect to a file if you want to keep the sample.
• Use one mode flag per invocation; this is a selector for canned examples, not a general conversion engine.
• The documented help entry point is -help, not --help.