gene2xml1
Convert ncbi entrez gene asn.1 into xml
Usage
gene2xml [-]
[-b]
[-c]
[-i
filename]
[-l]
[-o
filename]
[-p
path]
[-r
path]
[-t
N]
[-x]
[-y]
[-z]
Overview
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
Releases
10 releases since Debian 4.0 (Etch); the text changed 2 times.