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] [-s db] [-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
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.
The command
asn2all -i gbpri1.aso -a t -b -f g -o gbpri1.nuc -v gbpri1.prt
The National Center for Biotechnology Information.
asn2asn(1), asn2ff(1), asn2fsa(1), asn2gb(1), asn2idx(1), asn2xml(1), asndhuff(1), gene2xml(1), gunzip(1).
2016-09-01 | NCBI |