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gene2xml - convert NCBI Entrez Gene ASN.1 into XML

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
2005-05-16 NCBI