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GENE2XML(1)						     NCBI Tools User's Manual						       GENE2XML(1)

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. SEE ALSO
asn2all(1), asn2asn(1), asn2xml(1), asndhuff(1), /usr/share/doc/ncbi-tools-bin/gene2xml.txt.gz, /usr/share/doc/libncbi6/ncbixml.txt.gz NCBI
2005-05-16 GENE2XML(1)

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ASN2ALL(1)						     NCBI Tools User's Manual							ASN2ALL(1)

NAME
asn2all - generate reports from ASN.1 biological data SYNOPSIS
asn2all [-] [-A acc] [-F filename] [-G] [-J n] [-K n] [-M] [-T] [-X] [-a type] [-b] [-c] [-d path] [-f format] [-h] [-i filename] [-k] [-l] [-n policy] [-o filename] [-p path] [-r] [-v filename] [-x ext] DESCRIPTION
asn2all is primarily intended for generating reports from the binary ASN.1 Bioseq-set release files downloaded from the NCBI ftp site (ncbi-asn1 directory). It can produce GenBank and GenPept flatfiles, FASTA sequence files, INSDSet structured XML, TinySeq XML, and Sequin-style 5-column feature tables. The release files (which have the extension .aso.gz) should be uncompressed with gunzip(1), resulting in files with the extension .aso. For example, gbpri1.aso is the first file in the primate division, and the command gunzip gbpri1.aso.gz will result in gbpri1.aso being created. The original gbpri1.aso.gz file is removed after successful decompression. In asn2all, the name of the file to be processed is specified by the -i command line argument. Use -a t to indicate that it is a release file and -b to indicate that it is binary ASN.1. A text ASN.1 file obtained from Entrez can be processed by using -a a instead of -a t -b. Nucleotide and protein records can be processed simultaneously. Use the -o argument to indicate the nucleotide output file, and the -v argument for the protein output file. The -f argument determines the format to be generated, and is documented in more detail (along with other options) in the following sec- tion. OPTIONS
A summary of options is included below. - Print usage message -A accession Accession to fetch; may take the form accession,complexity,flags where complexity should normally be 0 and a flags value of -1 enables fetching of external features -F filename Accession Filter file -G Relaxed Genome Mapping -J n Seq-loc from -K n Seq-loc to -M Seq-loc Minus strand -T Use Threads -X EXtended qualifier output -a type Input ASN.1 type: a Automatic (default) c Catenated z Any e Seq-entry b Bioseq s Bioseq-set m Seq-submit t batch processing (suitable for official releases; autodetects specific type) -b Bioseq-set is Binary -c Bioseq-set is Compressed -d path Path to indexed binary ASN.1 Data -f format Output Format: g GenBank/GenPept (default) m GenBank Master Style f FASTA d CDS FASTA e Gene FASTA t Sequin-style 5-column feature table y TinySet XML (akin to FASTA) s INSDSet XML (akin to GenBank/GenPept) a structurally equivalent text ASN.1 x structurally equivalent XML c cache components -h Display extra Help message -i filename Input file name (standard input by default) -k Enable local fetching -l Lock components in advance -n policy Near FASTA policy: a All n Near only (default) f Far only -o filename Nucleotide Output file name -p path Path to files -r Enable Remote fetching -v filename Protein output file name -x ext File selection suffix when working with entire directories. (default is .aso) EXAMPLES
The command asn2all -i gbpri1.aso -a t -b -f g -o gbpri1.nuc -v gbpri1.prt will generate GenBank and GenPept reports from gbpri1.aso. AUTHOR
The National Center for Biotechnology Information. SEE ALSO
asn2asn(1), asn2ff(1), asn2fsa(1), asn2gb(1), asn2idx(1), asn2xml(1), asndhuff(1), gene2xml(1), gunzip(1). NCBI
2012-06-24 ASN2ALL(1)
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