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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


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

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