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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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ASN2FSA(1)						     NCBI Tools User's Manual							ASN2FSA(1)

NAME
asn2fsa - convert biological sequence data from ASN.1 to FASTA SYNOPSIS
asn2fsa [-] [-A acc] [-D] [-E] [-H] [-L filename] [-T] [-a type] [-b] [-c] [-d path] [-e N] [-f path] [-g] [-h filename] [-i filename] [-k] [-l] [-m] [-o filename] [-p path] [-q filename] [-r] [-s] [-u] [-v filename] [-x str] [-z] DESCRIPTION
asn2fsa converts biological sequence data from ASN.1 to FASTA. OPTIONS
A summary of options is included below. - Print usage message -A acc Accession to fetch -D Use Dash for Gap -E Extended Seq-ids -H HTML spans -L filename Log file -T Use Threads -a type Input ASN.1 type: a Automatic (default) 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 ReadDB Database -e N Line length (70 by default; may range from 10 to 120) -f path Path to indexed FASTA data -g Expand delta gaps into Ns -h filename Far component cache output file name -i filename Single input file (standard input by default) -k Local fetching -l Lock components in advance -m Master style for near segmented sequences -o filename Nucleotide Output file name -p path Path to ASN.1 Files -q filename Quality score output file name -r Remote fetching from NCBI -s Far genomic contig for quality scores -u Recurse -v filename Protein output file name -x str File selection substring (.ent by default) [String] -z Print quality score gap as -1 AUTHOR
The National Center for Biotechnology Information. SEE ALSO
asn2all(1), asn2asn(1), asn2ff(1), asn2gb(1), asn2xml(1), asndhuff(1). NCBI
2011-09-02 ASN2FSA(1)
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