Opened 14 years ago

Closed 14 years ago

#994 closed task (fixed)

Create GAL export plug-in for array designs

Reported by: Johan Vallon-Christersson Owned by: Nicklas Nordborg
Priority: major Milestone: BASE 2.7
Component: coreplugins Version:
Keywords: Cc:

Description

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’.

Attachments (3)

10K_RAP_oligo.gal (482.4 KB) - added by Johan Vallon-Christersson 14 years ago.
Example GAL file created in BASE1 from array design ‘10K_RAP_oligo’
print64_10k_.tam (256.9 KB) - added by Johan Vallon-Christersson 14 years ago.
TAM file used as print map for array design ‘10K_RAP_oligo’.
TAM.txt (1.8 KB) - added by Johan Vallon-Christersson 14 years ago.
TAM format explained

Download all attachments as: .zip

Change History (10)

Changed 14 years ago by Johan Vallon-Christersson

Attachment: 10K_RAP_oligo.gal added

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

Changed 14 years ago by Johan Vallon-Christersson

Attachment: print64_10k_.tam added

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

Changed 14 years ago by Johan Vallon-Christersson

Attachment: TAM.txt added

TAM format explained

comment:1 Changed 14 years ago by 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.

comment:2 in reply to:  1 Changed 14 years ago by 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).

comment:3 Changed 14 years ago by Nicklas Nordborg

Milestone: BASE 2.7
Priority: criticalmajor

comment:4 Changed 14 years ago by Nicklas Nordborg

Owner: changed from everyone to Nicklas Nordborg
Status: newassigned

comment:5 Changed 14 years ago by Nicklas Nordborg

Summary: For array designs, provide downloadable GAL filesCreate GAL export plug-in for array designs
Type: enhancementtask

comment:6 Changed 14 years ago by 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.

comment:7 Changed 14 years ago by Nicklas Nordborg

Resolution: fixed
Status: assignedclosed

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

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