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.TH GENE2XML 1 2005-05-16 NCBI "NCBI Tools User's Manual"
.SH NAME
gene2xml \- convert NCBI Entrez Gene ASN.1 into XML
.SH SYNOPSIS
.B gene2xml
[\|\fB\-\fP\|]
[\|\fB\-b\fP\|]
[\|\fB\-c\fP\|]
[\|\fB\-i\fP\ \fIfilename\fP\|]
[\|\fB\-l\fP\|]
[\|\fB\-o\fP\ \fIfilename\fP\|]
[\|\fB\-p\fP\ \fIpath\fP\|]
[\|\fB\-r\fP\ \fIpath\fP\|]
[\|\fB\-t\fP\ \fIN\fP\|]
[\|\fB\-x\fP\|]
[\|\fB\-y\fP\|]
[\|\fB\-z\fP\|]
.SH DESCRIPTION
\fBgene2xml\fP 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 \fB.ags.gz\fP.
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 \fB.xgs\fP as the suffix.
.SH OPTIONS
A summary of options is included below.
.TP
\fB\-\fP
Print usage message
.TP
\fB\-b\fP
File is Binary
.TP
\fB\-c\fP
File is Compressed
.TP
\fB\-i\fP\ \fIfilename\fP
Single Input file (standard input by default) when not using \fB\-p\fP
.TP
\fB\-l\fP
Log processing (list files processed when using \fB\-p\fP)
.TP
\fB\-o\fP\ \fIfilename\fP
Single Output file (standard output by default) when not using \fB\-p\fP
.TP
\fB\-p\fP\ \fIpath\fP
Path to Files (if processing an entire directory)
.TP
\fB\-r\fP\ \fIpath\fP
Path for Results when using \fB\-p\fP; defaults to the input directory
.TP
\fB\-t\fP\ \fIN\fP
Limit to the given Taxon ID (per \fBhttp://www.ncbi.nlm.nih.gov/Taxonomy/\fP)
.TP
\fB\-x\fP
Extract .ags to text .agc (format previously distributed)
.TP
\fB\-y\fP
Combine .agc to text .ags (for testing)
.TP
\fB\-z\fP
Combine .agc to binary .ags, then gzip
.SH AUTHOR
The National Center for Biotechnology Information.
.SH SEE ALSO
.ad l
.BR asn2all (1),
.BR asn2asn (1),
.BR asn2xml (1),
.BR asndhuff (1),
gene2xml.txt,
ncbixml.txt
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