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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] [-s db] [-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 section.

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
              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)

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).