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       asn2all - generate reports from ASN.1 biological data


       asn2all   [-]   [-A acc]   [-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]


       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


       A summary of options is included below.

       -      Print usage message

       -A acc Accession to fetch

       -T     Use Threads

       -X     EXtended qualifier output

       -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 indexed binary ASN.1 Data

       -f format
              Output Format:
              g      GenBank/GenPept (default)
              f      FASTA
              d      CDS 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)


       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).