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 suffix.
A summary of options is included below.
− |
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
−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/) |
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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 |
The National Center for Biotechnology Information.
asn2all(1), asn2asn(1), asn2xml(1), asndhuff(1), /usr/share/doc/ncbi-tools-bin/gene2xml.txt.gz, /usr/share/doc/libncbi6/ncbixml.txt.gz