Man page - gene2xml(1)

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ncbi-tools-bin

Manual

GENE2XML

NAME
SYNOPSIS
DESCRIPTION
OPTIONS
AUTHOR
SEE ALSO

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.