GENE2XML(1) NCBI Tools User's Manual GENE2XML(1)
NAME
gene2xml - convert NCBI Entrez Gene ASN.1 into XML
SYNOPSIS
gene2xml [-] [-b] [-c] [-i filename] [-l] [-o filename] [-p path] [-r path] [-t N] [-x] [-y] [-z]
DESCRIPTION
gene2xml is a stand-alone program that converts Entrez Gene ASN.1 into XML. Entrez Gene data are stored as compressed binary Entrezgene-
Set ASN.1 files on the NCBI ftp site, and have the suffix .ags.gz. These are several-fold smaller than compressed XML files, resulting in
a significant savings of disk storage and network bandwidth. Normal processing by gene2xml produces text XML files with the same name but
with .xgs as the suffix.
OPTIONS
A summary of options is included below.
- Print usage message
-b File is Binary
-c File is Compressed
-i filename
Single Input file (standard input by default) when not using -p
-l Log processing (list files processed when using -p)
-o filename
Single Output file (standard output by default) when not using -p
-p path
Path to Files (if processing an entire directory)
-r path
Path for Results when using -p; defaults to the input directory
-t N Limit to the given Taxon ID (per http://www.ncbi.nlm.nih.gov/Taxonomy/)
-x Extract .ags to text .agc (format previously distributed)
-y Combine .agc to text .ags (for testing)
-z Combine .agc to binary .ags, then gzip
AUTHOR
The National Center for Biotechnology Information.
SEE ALSO
asn2all(1), asn2asn(1), asn2xml(1), asndhuff(1), /usr/share/doc/ncbi-tools-bin/gene2xml.txt.gz, /usr/share/doc/libncbi6/ncbixml.txt.gz
NCBI
2005-05-16 GENE2XML(1)
