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

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 -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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ASN2GB(1)						     NCBI Tools User's Manual							 ASN2GB(1)

asn2gb - convert ASN.1 biological data to a GenBank-style flat format SYNOPSIS
asn2gb [-] [-A accession] [-F] [-a asn-type] [-b] [-c] [-d] [-f format] [-g N] [-h N] [-i filename] [-j N] [-k N] [-l filename] [-m mode] [-n filename] [-o filename] [-p] [-q filename] [-r] [-s style] [-t N] [-u N] [-y N] DESCRIPTION
asn2gb converts descriptions of biological sequences from NCBI's ASN.1 format to one of several flat-file formats, and is the successor to asn2ff(1). 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 (as with the legacy -F option) -F Fetch remote annotations (equivalent to specifying -A accession,0,-1) -a asn-type ASN.1 Type: [Single record] a Any (autodetected; default) e seq-Entry b Bioseq s bioseq-Set m seq-subMit q Catenated [Release file; components individually processed and freed] t baTch bioseq-set u batch seq-sUbmit -b Input file is binary -c Batch file is compressed -d Seq-loc minus strand -f format Format: b GenBank (default) bp or pb GenBank and GenPept e EMBL p GenPept q nucleotide GBSet (XML) r protein GBSet (XML) t Feature table only x nucleotide INSDSet (XML) y tiny seq (XML) Y FASTA z protein INSDSet (XML) -g N Bit flags (all default to off): 1 HTML 2 XML 4 ContigFeats 8 ContigSrcs 16 FarTransl -h N Lock/Lookup Flags (all default to off): 8 LockProd 16 LookupComp 64 LookupProd -i filename Input file name (default = stdin) -j N Start location (default is 0, beginning of sequence) -k N End location (default is 0, end of sequence) -l filename Log file -m mode Mode: r Release e Entrez s Sequin (default) d Dump -n filename Asn2Flat Executable (default = asn2flat) -o filename Output file name (default = stdout) -p Propagate top descriptors -q filename Ffdiff Executable (default = /netopt/genbank/subtool/bin/ffdiff) -r Enable remote fetching -s style Style: n Normal (default) s Segment m Master c Contig -t N Batch: 1 Report 2 Sequin/Release 3 asn2gb SSEC/nocleanup 4 asn2flat BSEC/nocleanup 5 asn2gb/asn2flat 6 asn2gb NEW dbxref/OLD dbxref 7 oldasn2gb/newasn2gb -u N Custom flags (all default to off): 4 Hide features 1792 Hide references 8192 Hide sources 262144 Hide translations -y N Feature itemID AUTHOR
The National Center for Biotechnology Information. SEE ALSO
asn2all(1), asn2asn(1), asn2ff(1), asn2fsa(1), asn2xml(1), asndhuff(1), insdseqget(1), /usr/share/doc/libncbi6-dev/asn2gb.txt.gz. NCBI
2011-09-02 ASN2GB(1)
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