Asn2ref

asn2ref

Quick Start

• Command: PATH=/home/vimalinx/miniforge3/envs/bio/bin:$PATH /home/vimalinx/miniforge3/envs/bio/bin/asn2ref < seq_entry.xml
• Local executable: /home/vimalinx/miniforge3/envs/bio/bin/asn2ref
• Full reference: references/help.md

When To Use This Tool

• Extract accession and citation metadata from Seq-entry records.
• Reformat nested article / journal metadata into compact CITATION XML blocks.
• Prepare citation payloads for downstream EDirect tools such as cit2pmid.

Common Patterns

# 1) Convert Seq-entry records into compact citation XML
PATH=/home/vimalinx/miniforge3/envs/bio/bin:$PATH \
  /home/vimalinx/miniforge3/envs/bio/bin/asn2ref \
  < seq_entry.xml

# 2) Pipe the result into downstream citation-matching logic
upstream_seq_entry_command | \
  PATH=/home/vimalinx/miniforge3/envs/bio/bin:$PATH \
  /home/vimalinx/miniforge3/envs/bio/bin/asn2ref

Recommended Workflow

1. Start from Seq-entry content that still contains publication metadata.
2. Run asn2ref as a stdin-driven filter.
3. Inspect the emitted CITATION XML for ACCN, FAUT, LAUT, TITL, JOUR, VOL, ISS, PAGE, and YEAR.
4. Pass the compact citation XML into later citation-matching steps only after confirming the key fields survived extraction.

Guardrails

• This wrapper is just an xtract recipe; it depends on sibling EDirect tools being available on PATH.
• Output is compact XML-like citation data, not human-readable reference text.
• PAGE is normalized to the first page number only.
• There is no dedicated help or version mode.