xenial (1) asn2all.1.gz

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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] [-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
              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).