Ds2pme

ds2pme

Quick Start

• Command: efetch -db pubmed -id <PMID> -format docsum | ds2pme
• Local executable: /home/vimalinx/miniforge3/envs/bio/bin/ds2pme
• Primary modes: default ASN.1 text, -xml for intermediate XML

When To Use This Tool

• Convert PubMed DocumentSummary records, rather than full PubmedArticle XML, into Pubmed-entry structures.
• Stay inside a docsum-oriented EDirect workflow when ASN.1 text is the desired downstream format.
• Inspect the intermediate XML before the last flattening step when debugging or archiving conversions.
• Use a lighter-weight alternative to pma2pme when your upstream source is already docsum output.

Common Patterns

# 1) Default Pubmed-entry ASN.1 text
efetch -db pubmed -id 2539356 -format docsum | ds2pme

# 2) Keep the intermediate XML instead of flattening to ASN.1
efetch -db pubmed -id 2539356 -format docsum | ds2pme -xml

# 3) Feed the result into another XML-aware EDirect step
efetch -db pubmed -id 2539356 -format docsum | ds2pme -xml |
xtract -pattern Pubmed-entry -element pmid_

Recommended Workflow

1. Fetch PubMed records as -format docsum.
2. Use plain ds2pme when you need final ASN.1 text, or -xml when you want the structured intermediate.
3. Confirm that identifiers, title, journal, and article IDs look sensible before storing or reusing the output.
4. Switch to pma2pme instead if your upstream source is full PubmedArticle XML rather than docsum output.

Guardrails

• The wrapper expects PubMed DocumentSummary XML on stdin, not full PubmedArticle input.
• There is no built-in --help or --version; unknown arguments fail with Unrecognized argument ....
• Accepted mode switches are xml/-xml and asn/-asn.
• The default mode emits ASN.1 text beginning with Pubmed-entry ::= {.
• -xml stops before the final xtract -pattern Pubmed-entry -element "." flattening step.
• The wrapper depends on EDirect helpers such as transmute and xtract being on PATH.