convert NCBI Entrez Gene ASN.1 into XML
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 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
The National Center for Biotechnology Information.