Issue 280 #296
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Issue 280 #296
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…ORFs was that the reading process waas **blocking**, due to using a simple queue with a bare put instead of put_nowait. This single change makes the code finally parallel and provides therefore a massive speed-up.
Removing the evaluation of invalidity causes bugs. It's better to recalculate constantly in this case.
Edited Travis to reflect the changes in master
…erably slowed down `serialise`.
…. Also, now using properties to avoid calculating the invalidity of a BED12 object over and over again. This should lead to some more speed improvements.
… Some improvements but currently broken, and it could be better
…er from bioPython is so slow
…as opposed to only XMLs.
lucventurini
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* For EI-CoreBioinformatics#280: first tentative to improve the speed of serialise. * For EI-CoreBioinformatics#280: the biggest, by far, problem in `mikado serialise` for the ORFs was that the reading process waas **blocking**, due to using a simple queue with a bare put instead of put_nowait. This single change makes the code finally parallel and provides therefore a massive speed-up. * Correct commit 4b88696 Removing the evaluation of invalidity causes bugs. It's better to recalculate constantly in this case. * Correct previous commit * Correct .travis.yml Edited Travis to reflect the changes in master * Correct travis * Removing another simple queue from ORF, which could have again considerably slowed down `serialise`. * For EI-CoreBioinformatics#280: now BED12 objects use numpy arrays rather than simple lists. Also, now using properties to avoid calculating the invalidity of a BED12 object over and over again. This should lead to some more speed improvements. * BROKEN; for EI-CoreBioinformatics#280: trying to implement the slow functions using NumPy. Some improvements but currently broken, and it could be better * For EI-CoreBioinformatics#280: fixed the previous error. * For EI-CoreBioinformatics#280: fastest version of serialise yet. A shame that the new parser from bioPython is so slow * For EI-CoreBioinformatics#280: making the merging algorithm much faster, thanks to Stack Overflow * For EI-CoreBioinformatics#280: starting to reorganise code to allow using BLAST tabular - as opposed to only XMLs. * For EI-CoreBioinformatics#280: progress on definining the functions for parsing tabular blast. * Starting to implement the functions necessary to subdivide the work in groups. * Stub for the prepare_tab_hit function.
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Partial fix for #280: still need to improve the BLAST loading.