ASN2ALL(1) NCBI Tools User's Manual ASN2ALL(1)
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
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 sec-
A summary of options is included below.
- Print usage message
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
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
Input ASN.1 type:
a Automatic (default)
t batch processing (suitable for official releases; autodetects specific type)
-b Bioseq-set is Binary
-c Bioseq-set is Compressed
Path to indexed binary ASN.1 Data
g GenBank/GenPept (default)
m GenBank Master Style
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
Input file name (standard input by default)
-k Enable local fetching
-l Lock components in advance
Near FASTA policy:
n Near only (default)
f Far only
Nucleotide Output file name
Path to files
-r Enable Remote fetching
Protein output file name
-x ext File selection suffix when working with entire directories. (default is .aso)
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).