.TH ASN2ALL 1 2016-09-01 NCBI "NCBI Tools User's Manual"
.SH NAME
asn2all \- generate reports from ASN.1 biological data
.SH SYNOPSIS
.B asn2all
[\|\fB\-\fP\|]
[\|\fB\-A\fP\ \fIacc\fP\|]
[\|\fB\-F\fP\ \fIfilename\fP\|]
[\|\fB\-G\fP\|]
[\|\fB\-J\fP\ \fIn\fP\|]
[\|\fB\-K\fP\ \fIn\fP\|]
[\|\fB\-M\fP\|]
[\|\fB\-T\fP\|]
[\|\fB\-X\fP\|]
[\|\fB\-a\fP\ \fItype\fP\|]
[\|\fB\-b\fP\|]
[\|\fB\-c\fP\|]
[\|\fB\-d\fP\ \fIpath\fP\|]
[\|\fB\-f\fP\ \fIformat\fP\|]
[\|\fB\-h\fP\|]
[\|\fB\-i\fP\ \fIfilename\fP\|]
[\|\fB\-k\fP\|]
[\|\fB\-l\fP\|]
[\|\fB\-n\fP\ \fIpolicy\fP\|]
[\|\fB\-o\fP\ \fIfilename\fP\|]
[\|\fB\-p\fP\ \fIpath\fP\|]
[\|\fB\-r\fP\|]
[\|\fB\-s\fP\ \fIdb\fP\|]
[\|\fB\-v\fP\ \fIfilename\fP\|]
[\|\fB\-x\fP\ \fIext\fP\|]
.SH DESCRIPTION
\fBasn2all\fP 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.
.PP
The release files (which have the extension \fB.aso.gz\fP) should be
uncompressed with
.BR gunzip (1),
resulting in files with the extension \fB.aso\fP.
For example, \fBgbpri1.aso\fP is the first file in the primate
division, and the command
.RS
.sp
gunzip gbpri1.aso.gz
.sp
.RE
will result in \fBgbpri1.aso\fP being created.
The original \fBgbpri1.aso.gz\fP file is removed after successful
decompression.
.PP
In \fBasn2all\fP, the name of the file to be processed is specified by
the \fB\-i\fP command line argument.
Use \fB\-a\ t\fP to indicate that it is a release file and \fB\-b\fP to
indicate that it is binary ASN.1.
A text ASN.1 file obtained from Entrez can be processed by using
\fB\-a\ a\fP instead of \fB\-a\ t\ \-b\fP.
.PP
Nucleotide and protein records can be processed simultaneously.
Use the \fB\-o\fP argument to indicate the nucleotide output file, and
the \fB\-v\fP argument for the protein output file.
.PP
The \fB\-f\fP argument determines the format to be generated, and is
documented in more detail (along with other options) in the following
section.
.SH OPTIONS
A summary of options is included below.
.TP
\fB\-\fP
Print usage message
.TP
\fB\-A\fP\ \fIaccession\fP
Accession to fetch; may take the form
.IB accession , complexity , flags
where \fIcomplexity\fP should normally be \fB0\fP and a \fIflags\fP
value of \fB-1\fP enables fetching of external features
.TP
\fB\-F\fP\ \fIfilename\fP
Accession Filter file
.TP
\fB\-G\fP
Relaxed Genome Mapping
.TP
\fB\-J\fP\ \fIn\fP
Seq-loc from
.TP
\fB\-K\fP\ \fIn\fP
Seq-loc to
.TP
\fB\-M\fP
Seq-loc Minus strand
.TP
\fB\-T\fP
Use Threads
.TP
\fB\-X\fP
EXtended qualifier output
.TP
\fB\-a\fP\ \fItype\fP
Input ASN.1 type:
.RS
.PD 0
.IP a
Automatic (default)
.IP c
Catenated
.IP p
Piped
.IP z
Any
.IP e
Seq-entry
.IP b
Bioseq
.IP s
Bioseq-set
.IP m
Seq-submit
.IP t
Batch Bioseq-set
.IP u
Batch Seq-submit
.PD
.RE
.TP
\fB\-b\fP
Bioseq-set is Binary
.TP
\fB\-c\fP
Bioseq-set is Compressed
.TP
\fB\-d\fP\ \fIpath\fP
Path to indexed binary ASN.1 Data
.TP
\fB\-f\fP\ \fIformat\fP
Output Format:
.RS
.PD 0
.IP g
GenBank/GenPept (default)
.IP m
GenBank Master Style
.IP f
FASTA
.IP d
CDS FASTA
.IP e
Gene FASTA
.IP r
Regenerated Defline
.IP t
Sequin-style 5-column feature table
.IP y
TinySet XML (akin to FASTA)
.IP s
INSDSet XML (akin to GenBank/GenPept)
.IP a
structurally equivalent text ASN.1
.IP x
structurally equivalent XML
.IP c
cache components
.PD
.RE
.TP
\fB\-h\fP
Display extra Help message
.TP
\fB\-i\fP\ \fIfilename\fP
Input file name (standard input by default)
.TP
\fB\-k\fP
Enable local fetching
.TP
\fB\-l\fP
Lock components in advance
.TP
\fB\-n\fP\ \fIpolicy\fP
Near FASTA policy:
.RS
.PD 0
.IP a
All
.IP n
Near only (default)
.IP f
Far only
.PD
.RE
.TP
\fB\-o\fP\ \fIfilename\fP
Nucleotide Output file name
.TP
\fB\-p\fP\ \fIpath\fP
Path to files
.TP
\fB\-r\fP
Enable Remote fetching
.TP
\fB\-s\fP\ \fIdb\fP
Source database:
.RS
.PD 0
.IP a
Any (default)
.IP w
Exclude segmented sequences
.PD
.RE
.TP
\fB\-v\fP\ \fIfilename\fP
Protein output file name
.TP
\fB\-x\fP\ \fIext\fP
File selection suffix when working with entire directories.
(default is \fB.aso\fP)
.SH EXAMPLES
The command
.RS
.sp
  asn2all \-i gbpri1.aso \-a t \-b \-f g \-o gbpri1.nuc \-v gbpri1.prt
.sp
.RE
will generate GenBank and GenPept reports from \fBgbpri1.aso\fP.
.SH AUTHOR
The National Center for Biotechnology Information.
.SH SEE ALSO
.BR asn2asn (1),
.BR asn2ff (1),
.BR asn2fsa (1),
.BR asn2gb (1),
.BR asn2idx (1),
.BR asn2xml (1),
.BR asndhuff (1),
.BR gene2xml (1),
.BR gunzip (1).