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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] [-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 section.


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
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)


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.

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