tiny-count: shift parameters for overlap selectors#280
Merged
taimontgomery merged 13 commits intomasterfrom Feb 10, 2023
Merged
tiny-count: shift parameters for overlap selectors#280taimontgomery merged 13 commits intomasterfrom
taimontgomery merged 13 commits intomasterfrom
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…eter order isn't switched for 3' anchored, and honestly I'm having second thoughts on whether it makes sense to break the pattern for that selector
…ted overlap selectors. Rather than handling the shift param entirely within the IntervalSelector base class, I instead provide a static method for returning a shifted HTSeq.GenomicInterval. This has two advantages: - Maintains IntervalSelectors' small memory footprint since this approach doesn't require any new attributes for the class. These objects can be very numerous depending on the GFF and ruleset - Keeps the code clean for adding matches to the correct intervals in ReferenceTables. Match tuples need to be inserted in the GenomicArray under the same interval that the overlap selector is expecting. Due to the above, cached selectors in build_interval_selectors() have to be added under an updated key that includes the shifted interval as well. Additionally, illegal shift operations (interval goes to zero length or inverted) are handled. Match tuples holding these overlap selectors are simply dropped.
…ased its complexity. It's a little abstract but hopefully this keeps the code approachable. Also improved explanatory docstrings for these methods.
…ive values in the 5' direction and positive values in the 3' direction regardless of strand
# Conflicts: # tiny/rna/counter/features.py
…uild_interval_selectors()
…rval_selectors, and to presort match tuples as ReferenceFeatures does for faster Stage 2 selection
…rvals with negative start positions aren't supported by ChromVectors in HTSeq's GenomicArrays. Also correcting the definition of a null interval (oops)
…skips the countdown for each test case since we don't really need to wait while running tests
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Tested with zswim8 and ram1 data. Needs more extensive testing once the next round of updates to feature selections are implemented. |
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Overlap selector definitions have been extended to optionally accept 2 numerical parameters that shift the 5' and 3' ends of matching feature intervals. Alignments are then evaluated using this shifted interval in Stage 2 selection. They have the following syntax:
Shifting might produce an illegal interval. When this happens, the offending match (the feature-rule pair) is omitted from Stage 2 and 3 selection, but the feature's other matches remain. Illegal intervals include:
Closes #278