NAME
csv2xml,fsa2xml,gbf2ref,gbf2xml,ini2xml,json2xml,scn2xml,tbl2xml,toml2xml,yaml2xml - XMLify
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
DESCRIPTION
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 .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.
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).
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).