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Dev restruct opt#22

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cbouyio merged 22 commits intodevelopparisepigenetics/great_3d:developfrom dev-restruct-optparisepigenetics/great_3d:dev-restruct-optCopy head branch name to clipboardJan 26, 2024

+420-371

Commits

Commits on Jan 22, 2024

• Correct some whitespaces.

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• Remove uncessecary impots to the main and add thw timing decorator.

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• Change the imports for the new code break into two major great3d parts.

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• Remove the old monolithic file of transcriptome3d.

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• Introduce the new package structure with two seperate modules to conduct clasulation and visualisation seperately

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• Implementation of new correlation calculation function. 3times more efficient, but UNTESTED.

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Commits on Jan 23, 2024

• Some syntactic fixes, comments, imports, etc.

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• Some major performace improvements, fix imports, refactor functions. Including major improvent on the sum correlations function, compute the correlation matrix once (with numpy) -that depricates fo…

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Commits on Jan 25, 2024

• Remove canvas call at the end of the plotly graphs module.

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• Code rearrangement to better handle tasks between the major app and the visualisation package.

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• Some prelim fixes on GREAT PDB under development, package. Not any real implementation.

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• Remove some extraneous seek() commands and remove a hardcoded varianble. More to optimise in a later pass.

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• Fix some typos on the integration file.

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• Add vscode configuration file into gitignore.

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• Add an unimplemented function for parsing PDB files.

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• Re-include the reseting of genome and positions files (seek) as they needed elswhere in the app.

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• Fix some docstrings on the base_calc module.

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• First working implementation of the modular approach for plotting and graph interactions. Genome contour load and visualisation.

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• Proper implementation of gene posiytions file based on geometric reconstruction of start sites.

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• Implementation of the visualise genes function with the right gene start sites.

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• Add the genes visualisation on the main program and include a new command line argument the resolution to reflect teh new functionality and comput the gene 3D coordinates based on its start site.

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• Merge pull request #21 from parisepigenetics/dev-gene-positions

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