gene2xml(1) [debian man page]
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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ASN2FF(1) NCBI Tools User's Manual ASN2FF(1) NAME
asn2ff - convert ASN.1 biological data to a flat format (old version) SYNOPSIS
asn2ff [-] [-A X] [-B X] [-C] [-G] [-L F] [-M] [-R] [-V F] [-a filename] [-b] [-d] [-e] [-f b/p/e/s/x/z] [-g] [-h F] [-k F] [-l filename] [-m r/d/s/c/k/l/e/p] [-n F] [-o filename] [-p F] [-q] [-r filename] [-s] [-t] [-v F] [-w] [-y] [-z] DESCRIPTION
asn2ff converts descriptions of biological sequences from NCBI's ASN.1 format to one of several flat-file formats. This program is built around a deprecated interface; please use asn2gb(1) instead. OPTIONS
A summary of options is included below. - Print usage message -A X Show region starting at X (default is 0) -B X Show region ending at X (default is last position) -C Show Bankit comments -G Output is one top bioseq only in genome view -L F Use old (pre-Genbank 127.0) LOCUS line format -M Output is map bioseqs only -R For GenBank Release -V F Don't use VERSION -a filename Filename for ASN.1 input (default is stdin) -b Input asnfile in binary mode -d Use SeqMgr indexing -e Input is a Seq-entry -f b/p/e/s/x/z Output Format: b GenBank (default) p GenPept e EMBL s PseudoEMBL x GenBankSelect z EMBLPEPT -g Show gi numbers -h F Hide sequence -k F Don't use complex sets (phy-set,mut-set, pop-set) -l filename Log errors to filename -m r/d/s/c/k/l/e/p Output mode: r release (default) d dump s Sequin c Chromoscope k dir-sub-debug l dir-sub e revise p partial report -n F Strict gene_binding -o filename Output Filename (default is stdout) -p F Omit new gene features -q Output is one top bioseq only -r filename Output error logfile (default is stderr) -s Input is a Seq-submit -t Show verbose message text -v F Suppress error messages -w Use HTML output format -y Print help format only -z New algorithm for orgnames AUTHOR
The National Center for Biotechnology Information. SEE ALSO
asn2all(1), asn2asn(1), asn2fsa(1), asn2gb(1), asn2xml(1), asndhuff(1). NCBI
2005-05-16 ASN2FF(1)