csv2xml, gbf2ref, gbf2xml, json2xml, scn2xml, tbl2xml - transmute to XML
csv2xml|
scn2xml|
tbl2xml [
-set tag] [
-rec tag] [
-skip N] [
-header] [
-lower|
-upper] [
-indent|
-flush]
columnName1 ...
gbf2ref
gbf2xml
json2xml [
-set tag] [
-rec tag] [
-nest flat|
recurse|
plural|
singular|
depth|
element]
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.
- 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.
- 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.
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).
See
transmute(1).
ref2pmid(1),
transmute(1),
xml2fsa(1),
xml2tbl(1),
xtract(1).