updated requirements.txt and fixed issue with pipeline to convert bio…#19
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darefalola wants to merge 1 commit intomainfrom
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updated requirements.txt and fixed issue with pipeline to convert bio…#19darefalola wants to merge 1 commit intomainfrom
darefalola wants to merge 1 commit intomainfrom
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…python objects to ints
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The pipeline is trying to int()-cast a Biopython position that was turned into its string repr. Instead of a plain number, exon['exon_end'] contains 'ExactPosition(10742191)', so int('ExactPosition(10742191)') blows up with the error below:
ValueError: invalid literal for int() with base 10: 'ExactPosition(10742191)This error also shows up in the database handler as it tries to insert ExactPosition(10742191) into the database directly for columns that have be dimensioned as Integers.
This PR fixes this error in these two places.
This PR also updates the requirements.txt to update some package versions.