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Python workflows#82

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panushri25 merged 89 commits intomasterkundajelab/chrombpnet:masterfrom python-workflowskundajelab/chrombpnet:python-workflowsCopy head branch name to clipboardJan 25, 2023

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Commits

Commits on Dec 10, 2022

• modisco-lite-integration

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• removing logs from main, only keeping in branch

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Commits on Dec 11, 2022

• integrating automatic shift detection scripts

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• updating docker with the bioconda pybigwig fix

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• removed warning and changed data type to ATAC and DNASE

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• added data directory files

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• fixed indirect import for meme and some file naming

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• removed warning and added tomtom installation

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• added pdf output for modisco reports

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• changed ATAC_PE to ATAC

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• shift only end when + and start when - on strand, prevents negative value errors in bedgraph

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• remove print statements

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Commits on Dec 12, 2022

• adding chrombpnet_makebigwig output to logs

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• changing tutorial directory

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• changing chrombpnet_wo_bias.h5 to chrombpnet_nobias.h5

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• changing chrombpnet_wo_bias.h5 to chrombpnet_nobias.h5

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• fixing typos

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• added flags for input and fixed type in step 6

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• moved tutorial to a different folder

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• updated shorted readme

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• testing model pdf display

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• new pdf chrombpnet image

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• README update, fix syntax in train_chrombpnet workflow script, add command line to generate contribution score bigwigs

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• Added outline for two main workflow commands in README

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• Added hyperlinks to input file formats

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• hyperlink fragment, tagaligns and full documentation

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• workflow to input fragment and tagaligns too

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• Documentation for bias model training added

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Commits on Dec 13, 2022

• png files with better names

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• added bias threshold factor

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Commits on Dec 14, 2022

• module for reference data and associated references, version bump to 1.3

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• meme_motif_file typo fix

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• updated README to reference pip installation

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• can't publish to pypi with git url in requirements.txt, commenting out shap dep

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• fix typo

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• updated README to point to latest docker tag

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• making sure data text/tsv files get included in pypi release

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Commits on Dec 15, 2022

• fixing data reference in step5

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• pwm args

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• reverting to original

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• reverting to original and arguments compatibility and main args input

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• chrombpnet main and parser

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• changin how args is input to main to enable function calls

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• removing old calls and adding only main chrombpnet

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• removed threshold from readme

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• workflow updates to enable input arguments

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Commits on Dec 16, 2022

• fixed meme file path and moving a path

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• epochs default changed back

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• changed directory creation step

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• added notes on how to use bias threshold

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• fixed jsd metric to compare with worst case

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• Updated with python command line arguments

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• Update README.md

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• ifrag input format corrected and added comments

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Commits on Dec 19, 2022

• generate summary reports

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• updated pipeline to generate reports

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• added file prefix as an additional argument

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• non peaks metrics for bias model pipeline

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Commits on Dec 20, 2022

• restructuring to move pipelines to a different folder, added chrombpnet prep commans, prefix for output added

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• seperated reports for training, qc and pipeline

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• added output prefix

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• added gc matching to python command line

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• added init file for scripting

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• adding metrics evaluation

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• adding script to generate splits

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• removing tutorial and gc matched negatives from setup

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• 1.3 version fix

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Commits on Dec 21, 2022

• removed counts interpret and modisoc in the chrombpnet pipeline to reduce time, added shap to requirements

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• reproducible gc matching nonpeaks with seed

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Commits on Dec 22, 2022

• downgrading weasyprint to not require recent versions of pango

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• added tn5 and dnase pwms to meme database

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• fixing imports for modisco reports

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• fixed stride to have -st

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• moved modisco html directory to evaluation

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Commits on Jan 2, 2023

• updated readme with latest command

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• added input arguments link

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• added input arguments link

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Commits on Jan 13, 2023

• shorted meme tn5 motifs

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• fixing tabs

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• removing redundant json file saving

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• added more detailed comments in the report, added warning for bias counts pearsonr in -0.3 to -0.5 range

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• added html_prefix argument

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• increase bias model performance in peaks check, print statement to show pearsonr

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Commits on Jan 14, 2023

• removed findfont warnings, typos in printing, import fix

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• updated modisco lite requirement that reduces findfont error

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Commits on Jan 24, 2023

• Fixed different syntax for uncorrected

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• added html prefixing for bias model

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• updating setup file

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Commits on Jan 25, 2023

• updated version to base

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