asn2all - generate reports from ASN.1 biological data

       The National Center for Biotechnology Information.

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  -at
       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 -aa instead of -at-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.

       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.

       asn2all - generate reports from ASN.1 biological data

       A summary of options is included below.

       -      Print usage message

       -Aaccession
              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

       -Ffilename
              Accession Filter file

       -G     Relaxed Genome Mapping

       -Jn   Seq-loc from

       -Kn   Seq-loc to

       -M     Seq-loc Minus strand

       -T     Use Threads

       -X     EXtended qualifier output

       -atype
              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

       -dpath
              Path to indexed binary ASN.1 Data

       -fformat
              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

       -ifilename
              Input file name (standard input by default)

       -k     Enable local fetching

       -l     Lock components in advance

       -npolicy
              Near FASTA policy:
              a      All
              n      Near only (default)
              f      Far only

       -ofilename
              Nucleotide Output file name

       -ppath
              Path to files

       -r     Enable Remote fetching

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

       -vfilename
              Protein output file name

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

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

NCBI                                               2016-09-01                                         ASN2ALL(1)

asn2all  [-]  [-Aacc]  [-Ffilename]  [-G]  [-Jn]  [-Kn]  [-M] [-T] [-X] [-atype] [-b] [-c] [-dpath]
       [-fformat] [-h] [-ifilename] [-k] [-l] [-npolicy] [-ofilename] [-ppath] [-r]  [-sdb]  [-vfilename]
       [-xext]