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Tehila test#3

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tehilayehudai wants to merge 66 commits intoorenavram:masterorenavram/IgomeProfiling:masterfrom Webiks:Tehila_testWebiks/IgomeProfiling:Tehila_testCopy head branch name to clipboard

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Commits on Feb 6, 2020

• Merge pull request #1 from orenavram/master

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• Added support for local run (Linux)

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Commits on Feb 13, 2020

• Fixed bug where the wrong faa file is passed as input to upper_case_sequences.py (the right one is unique_rpm)

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Commits on Feb 14, 2020

• Added docker support including AWS upload

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• Changed random forest running to support local run (previous code assumed TA cluster)

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Commits on Feb 16, 2020

• Fixed docker file

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Commits on Feb 17, 2020

• Added support for distributed (multi servers) run using celery (submit to workers).

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• Added prefetch multiplier of 1 to worker entrypoint

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Commits on Feb 21, 2020

• Added sleep with retries in verify_file_is_not_empty for late synchronizing shared drives (e.g. EFS)

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Commits on Feb 29, 2020

• Changed batch sizes for better concurrency

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Commits on Mar 2, 2020

• Added support for setting meme_split_size

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Commits on Mar 23, 2020

• Added support for setting run script in docker.

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Commits on Mar 25, 2020

• Calculating hits faster (base for td-idf)

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Commits on Mar 27, 2020

• Completed hits

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• Implemented TF-IDF (not yet connected to wrapper)

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• Completed TF-IDF incluing pipeline parameters

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Commits on Mar 28, 2020

• Fixed wrong faa input to scan peptides (sometimes unique instead of regular)

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Commits on Apr 3, 2020

• Skipping completed run to allow resuming the pipeline

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• fix argument passing

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• Added tfidf output retaining original memes order

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• fixed correct pvalues merge for > 100 memes

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Commits on Apr 4, 2020

• Added calculate tf-idf score for BC sequences only (default)

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• fixed sorted output of pvalues

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Commits on Apr 7, 2020

• Added controlled shuffles generator

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Commits on Apr 24, 2020

• Fixed support for windows \r\n in C++ code

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• Added hpp output to shuffles generator (python)

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Commits on Apr 25, 2020

• Added whether to output sequeneces in hits

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• Added shuffle hits (no rating yet)

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• Added meme rating vs shuffles in hits

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• Fixed log

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• Added shuffle to pipeline

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Commits on May 7, 2020

• Updated README

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Commits on Jun 14, 2020

• Fixed running executable directly in cluster pipeline

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Commits on Jul 21, 2020

• added mapitope encoding

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• removed break

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Commits on Jul 22, 2020

• code review fixes

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• distributed mapitope encoding

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• added mapitope encoding to phase 3

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Commits on Aug 20, 2020

• added an option to set the minimum length of sequence to read in reads_filtration/module_wraper.py

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• Added - option to set minimum sequence length to read in the main pipeline IgOmeProfiling_pipeline.py

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Commits on Aug 30, 2020

• updated mapitope_conversion.py:

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Commits on Sep 27, 2020

• correction of small errors after local tests.

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Commits on Oct 5, 2020

• fix PR+ extract n_splits to an argument

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• change n_splits to positinal argument

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• missing seed value in sample_configuration

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Commits on Oct 6, 2020

• use only cv_num_splits parameter, no need for n_splits

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Commits on Jan 26, 2021

• change the calculate of p-value

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• Change following the sorting direction of the array

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Commits on Feb 11, 2021

• change the pvalue, change normalization color RF and change mistake of varible name

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• changes PR

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• changes the variable name from use_mapitop to use_mapitope

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• Merge pull request #16 from Webiks/pvalue_polynomial_fit

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Commits on Feb 15, 2021

• fix the variable names

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• Merge pull request #17 from Webiks/fix_run_model_fitting

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Commits on Mar 10, 2021

• change the variable of df to train_data

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Commits on Mar 14, 2021

• Merge pull request #19 from Webiks/hits_color_heatmap

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Commits on Apr 12, 2021

• change cd hit to 0.5 similarity

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Commits on Apr 18, 2021

• paired end

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Commits on Apr 25, 2021

• reads_filt_paired_end

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Commits on Nov 22, 2021

• add commit to file

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Commits on Nov 23, 2021

• add commit to file

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Commits on Dec 10, 2023

• check for frameshifts

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