abi2xml


Table of Contents

1. Introduction
2. Download
3. Installation
3.1. Alternative 1: building from source
3.2. Alternative 2: installing prebuilt binary
4. Usage
5. Related projects
5.1. ABIParser.py
5.2. Biojava - Class ABITrace
5.3. Bioperl - Bio::SeqIO::abi
5.4. Emboss - abiview
5.5. Staden

1. Introduction

abi2xml is a command line utility to convert an abi trace file to an xml file. Abi trace files contain DNA sequence data and are e.g. produced by ABI PRISM TM 377 DNA sequencers. This bioinformatics utility is written in C++ and released under the GPL license.

2. Download

Download the software from the sourceforge project page.

3. Installation

3.1. Alternative 1: building from source

The qt library version 4.1 or later is required for abi2xml. The qt library is available for Linux, Microsoft Windows and Mac OS X and others.

When qt is installed, you just have to unpack the abi2xml sources and run qmake && make && make install

3.2. Alternative 2: installing prebuilt binary

If you are running Windows on a 32-bit (i386) platform you can download the file abi2xml-1.2.zip and unzip it. If your Windows computer lacks zip support you first have to install 7-zip to be able to unzip the file.

4. Usage

[erik@saturn abi2xml-1.2]$ bin/abi2xml --help
abi2xml 1.2

This program parses the binary file format coming from an
ABI PRISM TM 377 DNA Sequencer and writes the information out as
an xml file

Usage: abi2xml [OPTIONS]...

  -h, --help                    Print help and exit
  -V, --version                 Print version and exit
  -i, --input-file=STRING       input abi file
  -o, --output-file=STRING      output xml file
  -I, --input-dir=STRING        input dir with abi files
  -O, --output-dir=STRING       output dir
  -s, --abi-file-suffix=STRING  suffix of abi files ( used with --input-dir )
                                  (default=`abi')
  -a, --int-vector-as-attribute write integer vectors inside attributes ( It
                                  makes file size smaller )
  -e, --input-encoding=STRING   input string encoding.  Available encodings
                                  listed at:
                                  http://doc.trolltech.com/3.0/qtextcodec.html
                                  (default=`Apple Roman')

To convert a single abi file to xml

[erik@saturn abi2xml-1.2]$ bin/abi2xml -i data.abi -o data.xml

To convert a whole directory of abi files to xml

[erik@saturn abi2xml-1.2]$ bin/abi2xml -I dir_with_abi_files -O output_dir

If you want to test abi2xml but you don't have any abi files, you may use the file staden-src-1-6-0/userdata/Sample_671.ab1 found in the staden-src-1-6-0.tar.gz from the Staden project ( see also Section 5.5, “Staden” ).

5. Related projects

5.1. ABIParser.py

ABIParser.py is a python module for parsing ABI files. License: GPL. Programming language: Python.

5.2. Biojava - Class ABITrace

ABITrace java class in biojava. License: LGPL. Programming language: Java.

5.3. Bioperl - Bio::SeqIO::abi

Bio::SeqIO::abi is a perl module in bioperl for parsing ABI files. It doesn't actually parse the abi files but uses the Staden package for that ( see Section 5.5, “Staden” ). License: "You may distribute this module under the same terms as perl itself". Programming language: Perl.

5.4. Emboss - abiview

Emboss includes abiview, an application that parses an abi file and converts the information to vector or bitmap images or to text files. License: GPL. Programming language: C.

5.5. Staden

Staden has capabilities to extract information from abi trace files ( e.g. the program extract_seq ). License: BSD. Programming language: C.


abi2xml is hosted at

SourceForge.net Logo