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
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
After unpacking the installation package, run the setup.py script supplying the "install" command
python setup.py install
The library depends on the availability of the numpy package in the python installation (http://www.numpy.org/)
from IlluminaBeadArrayFiles import GenotypeCalls, BeadPoolManifest, code2genotype
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
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
Class to parse GTC files as produced by Illumina AutoConvert and AutoCall software.
Class to encapsulate a normalization transform for conversion of raw intensity data to normalized intensity data
Class to encapsulate the meta-data collected in the GTC file for a scanner instrument
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.
Represents different strand conventions in manifest
Read information from a binary BPM file
Aggregate information across many samples for a given loci
Read information from a binary EGT file
This library is compatible with Python 2.7 and was tested with Python 2.7.11
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