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Issue 280#296

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lucventurini merged 19 commits intomasterEI-CoreBioinformatics/mikado:masterfrom issue-280EI-CoreBioinformatics/mikado:issue-280Copy head branch name to clipboardMar 10, 2020

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Commits on Mar 2, 2020

• For #280: first tentative to improve the speed of serialise.

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• For #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 sin…

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• Correct commit 4b88696

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• Correct previous commit

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• Correct .travis.yml

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• Correct travis

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Commits on Mar 3, 2020

• Removing another simple queue from ORF, which could have again considerably slowed down serialise.

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• For #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…

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Commits on Mar 4, 2020

• BROKEN; for #280: trying to implement the slow functions using NumPy. Some improvements but currently broken, and it could be better

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• For #280: fixed the previous error.

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• For #280: fastest version of serialise yet. A shame that the new parser from bioPython is so slow

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• For #280: making the merging algorithm much faster, thanks to Stack Overflow

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• Merge branch 'master' into issue-280

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Commits on Mar 5, 2020

• For #280: starting to reorganise code to allow using BLAST tabular - as opposed to only XMLs.

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Commits on Mar 9, 2020

• For #280: progress on definining the functions for parsing tabular blast.

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• Starting to implement the functions necessary to subdivide the work in groups.

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• Stub for the prepare_tab_hit function.

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Commits on Mar 10, 2020

• Fixed merging of master

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• Merge branch 'issue-280' of https://github.com/EI-CoreBioinformatics/mikado into issue-280

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