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).