gene2xml - 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
- -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
The National Center for Biotechnology Information.
asn2all(1),
asn2asn(1),
asn2xml(1),
asndhuff(1),
/usr/share/doc/ncbi-tools-bin/gene2xml.txt.gz,
/usr/share/doc/libncbi6/ncbixml.txt.gz