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.

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SEE ALSO