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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
File is Binary
File is Compressed
Single Input file (standard input by default) when not using -p
Log processing (list files processed when using -p)
Single Output file (standard output by default) when not using -p
Path to Files (if processing an entire directory)
Path for Results when using -p; defaults to the input directory
Limit to the given Taxon ID (per http://www.ncbi.nlm.nih.gov/Taxonomy/)
Extract .ags to text .agc (format previously distributed)
Combine .agc to text .ags (for testing)
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/libncbi6t64/ncbixml.txt.gz

2005-05-16 NCBI