Tehila test #3
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Tehila test #3
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Added requirements.txt (to be filled) Added ability to run mock data cleanly (run_mock.sh) Added README.md
…equences.py (the right one is unique_rpm) Fixed input argument to extract_clusters_sequences Fixed UnitPSSMs and pssm_score_peptide_script paths Added parallel mode in local run Updated weblogo imports Commented out weblogo generation to save time
Updated python requirements
…t to workers). Added run_using_celery to global_params.py. Updated docker to support worker mode. WIP updated README.
Added acks late to submit task
…nizing shared drives (e.g. EFS) Added support for multiple files in filter_reads. Added Agg backend for matplotlib to support running in servers without display Updated aws script to new account Updated README
Added seed for creating random PSSMs per motif Added random seed for generating random peptides Fixed reading single fastq file Added seed to random forest Changed split_meme_and_cutoff_files batch size to 1 for better parallelism Support for pValues merge with more than 100 files
Added ability to run meme cutoffs calculation in parallel Added ability to add comments in seq2sam, sam2bc using '#' line start Added ability to split meme without cutoffs by setting 'skip' as input Added run_rabbit.sh and docker-compose as example
Added shuffles generator example and patterns (WIP)
Added number of memes to process in hits for testing Added hits verbose output
…s_filtration/module_wraper.py
…eline IgOmeProfiling_pipeline.py
mapping (f,y together and w alone) Mapitop representation changed to be one of the 20 original letters (for example instead of r,k = b the mapping now is r,k = r) Updated the option for minimum sequence length with a flag in the reads_filtraion/module_wrapper.py
change the calculate of p-value
fix the variable names
change the variable of df to train_data
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