CSV2XML(1)

✨ csv2xml — the XMLify girlies 💖

ok so this is the page for the NCBI Entrez Direct User's Manual crew, and bestie, it's a whole family of little converter tools. Let me introduce you to the squad:

• csv2xml
• fsa2xml
• gbf2ref
• gbf2xml
• ini2xml
• json2xml
• scn2xml
• tbl2xml
• toml2xml
• yaml2xml

collectively known as XMLify. no cap, that's literally what the manpage calls them. 👑

🌈 SYNOPSIS 🌈

csv2xml|scn2xml|tbl2xml [-set tag] [-rec tag] [-skip N] [-header]
[-lower|-upper] [-indent|-flush] columnName1 ...

fsa2xml

gbf2ref

gbf2xml

ini2xml

json2xml [-set tag] [-rec tag]
[-nest flat|recurse|plural|singular|depth|element]

toml2xml

yaml2xml

ok so the tea here is that csv2xml, scn2xml, and tbl2xml all share the same options and they take a list of columnName1 ... arguments. json2xml gets its own special little set of flags (it's giving main character energy, honestly). and the rest of them? they take no options at all. they just are. 💅

💜 DESCRIPTION 💜

So here's the vibe: every single one of these commands is just a lil wrapper that invokes a corresponding mode of transmute(1). They each read a stream of data from standard input, convert it to XML that's suitable for -path navigation, and write the result out to standard output. Periodt.

Let's go one by one, bestie:

• csv2xml — corresponds to transmute -c2x, converting comma-separated values to XML. 🍓
• fsa2xml — corresponds to transmute -f2x, converting FASTA streams to XML. 🧬
• gbf2ref — corresponds to transmute -g2r, converting from GenBank/GenPept flatfile format to Reference Index XML.
• gbf2xml — corresponds to transmute -g2x, converting from GenBank/GenPept flatfile format to INSDSeq XML.
• ini2xml — corresponds to transmute -i2x, converting from .ini configuration file format to XML.
• json2xml — corresponds to transmute -j2x, converting JSON to XML. ✨
• scn2xml — corresponds to transmute -s2x, converting a semicolon-delimited table to XML.
• tbl2xml — corresponds to transmute -t2x, converting a tab-delimited table to XML.
• toml2xml — corresponds to transmute -m2x, converting from TOML format to XML.
• yaml2xml — corresponds to transmute -y2x, converting from YAML format to XML.

and there's also an analogous asn2xml wrapper that corresponds to transmute -a2x (that one converts text ASN.1 to XML, iconic of it). BUT — and this is the plot twist — on Debian systems it gets installed to /usr/lib/ncbi-entrez-direct/bin so it doesn't start beef with the ncbi-tools-bin package's asn2xml(1). two queens can't share the same throne, iykyk. 👑

🎀 OPTIONS 🎀

See transmute(1).

that's it. that's the whole options section. the real menu lives over at transmute(1), so go read that one too, bestie. 🫶

🌸 SEE ALSO 🌸

• asn2ref(1)
• download-flatfile(1)
• gbf2facds(1)
• gbf2fsa(1)
• gbf2info(1)
• gbf2tbl(1)
• gene2range(1)
• gff2xml(1)
• jsonl2xml(1)
• ref2pmid(1)
• refseq-nm-cds(1)
• transmute(1)
• xml2fsa(1)
• xml2tbl(1)
• xtract(1)

ok that's the whole page, bestie!! 💖 this one's brought to you by NCBI, dated 2025-05-26 — mwah, go XMLify something gorgeous ✨🦋