---
name: "asn2all"
section: "1"
platform: "linux"
package: "ncbi-tools-bin"
version: "6.1.20170106+dfsg2-6"
release: "Debian 13 (Trixie)"
platforms: ["linux"]
url: "https://new.carta.tech/asn2all"
---

# asn2all(1)

generate reports from ASN.1 biological data

## NAME

asn2all - generate reports from ASN.1 biological data

## SYNOPSIS

**asn2all** \[**-**\] \[**-A** *acc*\] \[**-F** *filename*\] \[**-G**\] \[**-J** *n*\] \[**-K** *n*\] \[**-M**\] \[**-T**\] \[**-X**\] \[**-a** *type*\] \[**-b**\] \[**-c**\] \[**-d** *path*\] \[**-f** *format*\] \[**-h**\] \[**-i** *filename*\] \[**-k**\] \[**-l**\] \[**-n** *policy*\] \[**-o** *filename*\] \[**-p** *path*\] \[**-r**\] \[**-s** *db*\] \[**-v** *filename*\] \[**-x** *ext*\]

## 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)](/gunzip/1.md), 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** *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

  - p

    Piped

  - z

    Any

  - e

    Seq-entry

  - b

    Bioseq

  - s

    Bioseq-set

  - m

    Seq-submit

  - t

    Batch Bioseq-set

  - u

    Batch Seq-submit

- **-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

  - f

    FASTA

  - d

    CDS FASTA

  - e

    Gene FASTA

  - r

    Regenerated Defline

  - 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

- **-s** *db*

  Source database:

  - a

    Any (default)

  - w

    Exclude segmented sequences

- **-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)](/asn2asn/1.md), [**asn2ff**(1)](/asn2ff/1.md), [**asn2fsa**(1)](/asn2fsa/1.md), [**asn2gb**(1)](/asn2gb/1.md), [**asn2idx**(1)](/asn2idx/1.md), [**asn2xml**(1)](/asn2xml/1.md), [**asndhuff**(1)](/asndhuff/1.md), [**gene2xml**(1)](/gene2xml/1.md), [**gunzip**(1)](/gunzip/1.md).