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), gene2xml.txt, ncbixml.txt