Pma2pme

pma2pme

Quick Start

• Command: efetch -db pubmed -id <PMID> -format xml | pma2pme
• Local executable: /home/vimalinx/miniforge3/envs/bio/bin/pma2pme
• Primary modes: default ASN.1 text, -xml for intermediate XML, -std or -ml for author encoding style

When To Use This Tool

• Convert PubMed XML into Pubmed-entry records for older NCBI / EDirect archival or interchange workflows.
• Choose between Medline-style author strings (-ml, default) and split standard author fields (-std).
• Inspect the intermediate XML structure before the final ASN.1 rendering step.
• Stay in a shell / EDirect pipeline instead of rewriting the transformation in another language.

Common Patterns

# 1) Default Pubmed-entry ASN.1 text
efetch -db pubmed -id 2539356 -format xml | pma2pme

# 2) Use standard split author fields instead of Medline-style names
efetch -db pubmed -id 2539356 -format xml | pma2pme -std

# 3) Keep the intermediate XML instead of flattening to ASN.1
efetch -db pubmed -id 2539356 -format xml | pma2pme -xml

Recommended Workflow

1. Fetch one or more PubmedArticle records as XML with efetch.
2. Pick the author style deliberately: default -ml for Medline-like compact names, or -std for separate last name / initials fields.
3. Use -xml when debugging transformations or when another XML-aware step should consume the record before ASN.1 conversion.
4. Validate the generated identifiers, title, journal block, and author representation before archiving the output.

Guardrails

• The wrapper reads XML from stdin and does not fetch PMIDs on its own.
• There is no built-in --help or --version; unknown arguments fail with Unrecognized argument ....
• Default behavior is -ml plus ASN.1 output; -asn merely reasserts the default final rendering mode.
• -xml skips the last xtract flattening step and returns the intermediate XML record instead of ASN.1 text.
• Accepted author-style flags include std/-std/-STD and ml/-ml/-ML.
• The wrapper depends on EDirect helpers such as transmute and xtract being available on PATH.