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.
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- |
Print usage message |
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-b |
File is Binary |
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-c |
File is Compressed |
-i filename
Single Input file (standard input by default) when not using -p
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-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
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-t N |
Limit to the given Taxon ID (per http://www.ncbi.nlm.nih.gov/Taxonomy/) | ||
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-x |
Extract .ags to text .agc (format previously distributed) | ||
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-y |
Combine .agc to text .ags (for testing) | ||
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-z |
Combine .agc to binary .ags, then gzip |
AUTHOR
The National Center for Biotechnology Information.
SEE ALSO
asn2all(1), asn2asn(1), asn2xml(1), asndhuff(1), /usr/share/doc/ncbi-tools-bin/gene2xml.txt.gz, /usr/share/doc/libncbi6t64/ncbixml.txt.gz