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Python library to parse file formats related to Illumina bead arrays
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README.md

IlluminaBeadArrayFiles

Library to parse file formats related to Illumina bead arrays. GTC files are produced by the AutoConvert and AutoCall softwares and contain genotyping (and other) information encoded in a binary format. The IlluminaBeadArrayFiles library provides a parser to extract information from these binary files.

Generating GTC files

If you have intensity data files (IDATs) for which GTC files are not currentty available, it is possible to manually generate these files with either the Beeline or AutoConvert software (https://support.illumina.com/array/array_software/beeline/downloads.html). Beeline provides a graphical user interface for the creation of GTC files, while AutoConvert allows GTC files to be generated from the command-line, as shown below

& "C:\Program Files\Illumina\AutoConvert 2.0\AutoConvert.exe" path_to_idat_folder path_to_output_folder manifest_file egt_file

Build instructions

The IlluminaBeadArrayFiles repository supports building a package with the python distutils module (https://docs.python.org/2/distutils/setupscript.html). To build a source distribution, run the included setup.py script supplying the "sdist" command

python setup.py sdist

Installation instructions

After unpacking the installation package, run the setup.py script supplying the "install" command

python setup.py install

Dependencies

The library depends on the availability of the numpy package in the python installation (http://www.numpy.org/)

Example usage

from IlluminaBeadArrayFiles import GenotypeCalls, BeadPoolManifest, code2genotype
import sys
gtc_file = "path_to_genotypes.gtc"
manifest_file = "path_to_manifest.bpm"
names = BeadPoolManifest( manifest_file ).names
genotypes = GenotypeCalls( gtc_file ).get_genotypes()
for (locus, genotype) in zip( names, genotypes ):
  sys.stdout.write( locus + "," + code2genotype[genotype] + "\n" )

Also, see examples/gtc_final_report.py for an additional example of usage.

GTC File Format

The specification for the GTC file format is provided in docs/GTC_File_Format_v5.pdf

Description of classes and objects in exposed in package

For further details on specific class methods, please consult the built-in docstring documentation

code2genotype

Dictionary mapping from genotype byte code (see GTC file format specification) to a string representing the genotype (e.g., "AA")

NC, AA, AB, and BB

Constants representing byte values for associated genotypes

GenotypeCalls

Class to parse GTC files as produced by Illumina AutoConvert and AutoCall software.

NormalizationTransform

Class to encapsulate a normalization transform for conversion of raw intensity data to normalized intensity data

ScannerData

Class to encapsulate the meta-data collected in the GTC file for a scanner instrument

BeadPoolManifest

Class for parsing a binary (BPM) manifest file. This class can be used to recover the in-order list of loci names in a given manifest, which is necessary to associate the genotype information present in the GTC file to a specific locus name.

RefStrand, SourceStrand

Represents different strand conventions in manifest

BeadPoolManifest

Read information from a binary BPM file

LocusAggregate

Aggregate information across many samples for a given loci

ClusterFile

Read information from a binary EGT file

Compatibility

This library is compatible with Python 2.7 and was tested with Python 2.7.11

License

Copyright (c) 2017, Illumina All rights reserved.

Redistribution and use in source and binary forms, with or without modification, are permitted provided that the following conditions are met:

  1. Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer.
  2. Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation and/or other materials provided with the distribution.

THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.

The views and conclusions contained in the software and documentation are those of the authors and should not be interpreted as representing official policies, either expressed or implied, of the FreeBSD Project.

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