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Illumina / BeadArrayFiles

Python library to parse file formats related to Illumina bead arrays
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Obtaining GC and GT scores as columns in gtc_final_report.py #29

Open evilvenom opened 2 years ago

evilvenom commented 2 years ago

Greetings! I had a query if I wanted to change the columns that are printed in the txt file of the output. How do I get two columns, one with GC scores and another with GT scores?

output_handle.write("[Data]\n")delim.join(["SNP Name", "Sample ID", "Chr", "Position", "GC Score", "Allele 1 - Plus", "Allele 2 - Plus", "GT Score"]

Something like this, how do I select the relevant attributes?

jjzieve commented 2 years ago

@evilvenom Would these methods work for you? GT: https://github.com/Illumina/BeadArrayFiles/blob/develop/module/GenotypeCalls.py#L411 GC 10 and 50: https://github.com/Illumina/BeadArrayFiles/blob/develop/module/GenotypeCalls.py#L475 https://github.com/Illumina/BeadArrayFiles/blob/develop/module/GenotypeCalls.py#L482