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LEARN ABOUT DEBIAN

asn2all

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)

SCO