Create GAL export plug-in for array designs

[Johan Vallon-Christersson]

Add functionality to create/download GAL files from array designs (export plugin?).

When performing image analysis using GenePix on files, e.g., *.tif files, from scanned arrays a GAL file is needed.

GAL file format, i.e., GenePix Array List format (*.gal), is defined and described by the GenePix manufacturer: ​http://www.moleculardevices.com/pages/software/gn_genepix_file_formats.html#gal

GAL files are array design specific and can in BASE1 be created and downloaded from array designs. As examples files: a GAL file created by BASE1, ‘10K_RAP_oligo.gal’ (attached), from array design name=‘10K_RAP_oligo’ with the following print map ‘print64_10k_.tam’ (attached).

The BioRobotics TAM format explained is also attached, ‘TAM.txt’.

[Johan Vallon-Christersson]

Example GAL file created in BASE1 from array design ‘10K_RAP_oligo’

[Johan Vallon-Christersson]

TAM file used as print map for array design ‘10K_RAP_oligo’.

[Johan Vallon-Christersson]

TAM format explained

[base]

What's wrong with just downloading the "reporter map" in the "data files" section of the array design page? I guess this is not 100% guaranteed to be the file from which the reporter map was imported, and it's not also guaranteed to be in .GAL format.

Bob.

[Johan Vallon-Christersson]

Replying to base:

What's wrong with just downloading the "reporter map" in the "data files" section of the array design page? I guess this is not 100% guaranteed to be the file from which the reporter map was imported, and it's not also guaranteed to be in .GAL format.

Bob.

In a (our) production setting where arrays are printed and array designs are actual representations of the print process, i.e., a selection of probe plates and a print map that specifies source wells and destination coordinates on arrays, GAL files can not be used as print maps. Rather, the GAL files are needed downstream during image analysis after arrays have been hybridized.

It’s convenient to have BASE produce the GAL files using the information from the array design as users that upload GPR files and associate raw data with the array design are ensured that reporter IDs and coordinates match, and if there are mismatches they then know that something went wrong during their GPR file management (outside of BASE).

[Nicklas Nordborg]

(In [4239]) References #994: Create GAL export plug-in for array designs

Added the exporter and test case. Need to wait for #999 before finalising things.

[Nicklas Nordborg]

(In [4241]) Fixes #994: Create GAL export plug-in for array designs