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ASN2ALL(1)		   NCBI	Tools User's Manual		    ASN2ALL(1)

       asn2all - generate reports from ASN.1 biological	data

       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]	[-s db]	[-v filename] [-x ext]

       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	uncom-
       pressed 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 ar-
       gument for the protein output file.

       The -f argument determines the format to	be  generated,	and  is	 docu-
       mented  in more detail (along with other	options) in the	following sec-

       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
	      p	     Piped
	      z	     Any
	      e	     Seq-entry
	      b	     Bioseq
	      s	     Bioseq-set
	      m	     Seq-submit
	      t	     Batch Bioseq-set
	      u	     Batch Seq-submit

       -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
	      r	     Regenerated Defline
	      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

       -s db  Source database:
	      a	     Any (default)
	      w	     Exclude segmented sequences

       -v filename
	      Protein output file name

       -x ext File selection suffix  when  working  with  entire  directories.
	      (default is .aso)

       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.

       The National Center for Biotechnology Information.

       asn2asn(1),  asn2ff(1),	asn2fsa(1), asn2gb(1), asn2idx(1), asn2xml(1),
       asndhuff(1), gene2xml(1), gunzip(1).

NCBI				  2016-09-01			    ASN2ALL(1)


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