man gene2xml (Commandes) - convert NCBI Entrez Gene ASN.1 into XML
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 -> text .agc (format previously distributed)
- -y
- Combine .agc -> text .ags (for testing)
- -z
- Combine .agc -> binary .ags, then gzip
AUTHOR
The National Center for Biotechnology Information.