gene2xml(1) convert NCBI Entrez Gene ASN.1 into XML


gene2xml [-] [-b] [-c] [-i filename] [-l] [-o filename] [-p path] [-r path] [-t N] [-x] [-y] [-z]


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.


A summary of options is included below.
Print usage message
File is Binary
File is Compressed
-i filename
Single Input file (standard input by default) when not using -p
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
Extract .ags to text .agc (format previously distributed)
Combine .agc to text .ags (for testing)
Combine .agc to binary .ags, then gzip


The National Center for Biotechnology Information.