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)

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)