Pma2apa

pma2apa

Quick Start

• Command: efetch -db pubmed -id <PMID> -format xml | pma2apa
• Local executable: /home/vimalinx/miniforge3/envs/bio/bin/pma2apa
• Primary modes: default one-line citation text, -xml for structured XML, -ascii for accent-normalized output

When To Use This Tool

• Turn PubMed XML records into APA-style citation strings inside shell pipelines.
• Keep an intermediate XML representation of parsed citation fields when downstream xtract steps need structure.
• Normalize accented characters to ASCII before exporting to plain-text systems.
• Stay inside EDirect tooling after efetch -format xml instead of post-processing citations elsewhere.

Common Patterns

# 1) Default APA citation line, prefixed by PMID
efetch -db pubmed -id 19212835 -format xml | pma2apa

# 2) Keep structured APA XML instead of flattening to one line
efetch -db pubmed -id 19212835 -format xml | pma2apa -xml

# 3) Force accent-normalized ASCII output
efetch -db pubmed -id 19212835 -format xml | pma2apa -ascii

Recommended Workflow

1. Fetch PubmedArticle XML with efetch -db pubmed -format xml.
2. Decide whether you need flat citation text or the structured XML intermediate.
3. Add -ascii only when the downstream consumer cannot handle accented characters.
4. Check the emitted title, journal, pages, and DOI fields before storing or reusing the citation.

Guardrails

• The tool reads PubmedArticle XML from stdin; it does not fetch PubMed records by itself.
• There is no built-in --help or --version; unknown arguments fail with Unrecognized argument ....
• Accepted mode switches are the bare or dashed forms xml/-xml, apa/-apa, and ascii/-ascii.
• Default text mode emits a single tab-delimited line that starts with the PMID and then the formatted citation.
• -xml keeps the <APASet><APAFormat>...</APAFormat></APASet> intermediate instead of flattening to text.
• The wrapper depends on EDirect helpers such as transmute and xtract being available on PATH.