NAME
asn2all - generate reports from ASN.1 biological data
SYNOPSIS
asn2all [-] [-A acc] [-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 acc Accession to fetch
-T Use Threads
-X EXtended qualifier output
-a type
Input ASN.1 type:
a Automatic (default)
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)
f FASTA
d CDS 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).