gbf2xml1
Xmlify
Part of csv2xml(1).
Usage
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
Overview
These commands all simply invoke corresponding transmute(1) modes; each reads a stream of data from standard input, converts it to XML suitable for -path navigation, and writes the result to standard output. Specifically:
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
.iniconfiguration 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.
There is also an analogous asn2xml wrapper corresponding to transmute -a2x (converting text ASN.1 to XML), but Debian systems install it to /usr/lib/ncbi-entrez-direct/bin to avoid conflicting with the ncbi-tools-bin package's asn2xml(1).
Options
See transmute(1).
Releases
4 releases since Debian 10 (Buster); the text changed 3 times.
-a until Debian 11 (Bullseye);
-a2x until Debian 11 (Bullseye);
-aa1to3 until Debian 11 (Bullseye);
-aa3to1 until Debian 11 (Bullseye);
-align until Debian 11 (Bullseye);
-c2x until Debian 11 (Bullseye);
-cdata until Debian 11 (Bullseye);
-cds2prot until Debian 11 (Bullseye);
-code until Debian 11 (Bullseye);
-column until Debian 11 (Bullseye);
-comment until Debian 11 (Bullseye);
-decode64 until Debian 11 (Bullseye);
-decodeURL until Debian 11 (Bullseye);
-decodeXML until Debian 11 (Bullseye);
-delete until Debian 11 (Bullseye);
-diff until Debian 11 (Bullseye);
-doctype until Debian 11 (Bullseye);
-encode64 until Debian 11 (Bullseye);
-encodeURL until Debian 11 (Bullseye);
-encodeXML until Debian 11 (Bullseye);
-every until Debian 11 (Bullseye);
-extract until Debian 11 (Bullseye);
-first until Debian 11 (Bullseye);
-flush until Debian 11 (Bullseye);
-format until Debian 11 (Bullseye);
-frame until Debian 11 (Bullseye);
-g until Debian 11 (Bullseye);
-g2x until Debian 11 (Bullseye);
-h until Debian 11 (Bullseye);
-header until Debian 11 (Bullseye);
-hgvs until Debian 11 (Bullseye);
-indent until Debian 11 (Bullseye);
-insert until Debian 11 (Bullseye);
-j2p until Debian 11 (Bullseye);
-j2x until Debian 11 (Bullseye);
-last until Debian 11 (Bullseye);
-leading until Debian 11 (Bullseye);
-lower until Debian 11 (Bullseye);
-mathml until Debian 11 (Bullseye);
-met until Debian 11 (Bullseye);
-molwt until Debian 11 (Bullseye);
-nest until Debian 11 (Bullseye);
-normalize until Debian 11 (Bullseye);
-offset until Debian 11 (Bullseye);
-part3 until Debian 11 (Bullseye);
-part5 until Debian 11 (Bullseye);
-plainXML until Debian 11 (Bullseye);
-rec until Debian 11 (Bullseye);
-remove until Debian 11 (Bullseye);
-replace until Debian 11 (Bullseye);
-retain until Debian 11 (Bullseye);
-revcomp until Debian 11 (Bullseye);
-script until Debian 11 (Bullseye);
-self until Debian 11 (Bullseye);
-separate until Debian 11 (Bullseye);
-set until Debian 11 (Bullseye);
-skip until Debian 11 (Bullseye);
-stop until Debian 11 (Bullseye);
-t2x until Debian 11 (Bullseye);
-trailing until Debian 11 (Bullseye);
-trim until Debian 11 (Bullseye);
-unicode until Debian 11 (Bullseye);
-upper until Debian 11 (Bullseye);
-x2p until Debian 11 (Bullseye);
-xml until Debian 11 (Bullseye).