Add option to filter probes with poly(A) sequence #22
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This adds polya_filter, which is a filter on probes that contain sequence with long stretches of A bases (or T bases). It might be desirable to avoid such probe sequences, e.g., to not enrich carrier RNA. The definition of such a stretch is given as parameters when initializing a PolyAFilter object. This also adds unit tests for this module.
When this argument is set, design.py uses polya_filter to filter out candidate probes that contain long stretches of A bases (or T bases). The definition of such a stretch is specified as arguments with --filter-polya.
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This adds the
polya_filtermodule, which is a filter on probes that contain sequence with long stretches of A bases (or T bases). It might be desirable to avoid such probe sequences, e.g., to not enrich carrier RNA.This also adds a
--filter-polyaargument todesign.pythat, when set, applies thepolya_filtermodule.The definition of a stretch of A bases (or T bases) given as arguments with
--filter-polya.