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GENE2XML(1) |
NCBI Tools User's Manual |
GENE2XML(1) |
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.