{ "info": { "author": "Jerome Lane", "author_email": "jerome.lane@hotmail.com", "bugtrack_url": null, "classifiers": [ "Development Status :: 3 - Alpha", "Environment :: Console", "Intended Audience :: Science/Research", "Operating System :: OS Independent", "Programming Language :: Python", "Topic :: Scientific/Engineering :: Bio-Informatics" ], "description": "pepbox\n======\n\n.. raw:: html\n\n

\n\nT cell activation that leads to a productive T-cell reaction against a\npathogen agent is linked to its T cell receptor (TCR) specificity. The\nability of the TCR to distinguish between structurally unrelated to\nsimilar peptides defines the T cell specificity. The affinity drives the\nspecifcity. A T cell that binds to peptide-MHC complex with enough\naffinity will increase the magnitude of the immune response (i.e.\u00a0T cell\nexpansion). Therefore, expansion is a powerful feature to measure TCRs\nspecifity. This application has the goal to quantify if T cell\nclonotypes (i.e.\u00a0group of T cells sharing the same TCR) are\nsignificantly expanded by comparing their respective frequency before\nand after contact with a peptide. To improve performance of peptide\nspecific clonotypes selection, irrelevant peptide stimulated cultured T\ncells or/and medium cultured T cells can be provided as negative\ncontrols. A list of reference TCRs known to be specific to the relevant\npeptide (e.g.\u00a0obtained from tetramer staining, IFNg capture) are used to\ndefine optimal expansion thresholds for selecting positively and\nnegatively expanded T cells\n\n.. raw:: html\n\n

\n\n.\n\nParameters\n==========\n\nusage:\n------\n\npepbox.py [-h] [-merge] [-expansion] [-analyze] [-reproducibility]\n[-aacdr3] [-genes_cdr3_aacln] [-optimize] [-timepoints] [-geneusage]\n[-detailed] [-input_folder INPUT_FOLDER] [-output_folder OUTPUT_FOLDER]\n[-workdir WORKDIR] [-nolog] [-compress] [-v] [\u2013version] [-debug]\n\noptional arguments:\n-------------------\n\n- -h, \u2013help show this help message and exit\n- -merge Merge Adaptive Biotechnologies TCR sequencing txt file\n (default: False)\n- -expansion Calculate expansion p-values using a Fisher exact test\n (default: False)\n- -analyze Produce basic statistics summary tables and figures\n (default: False)\n- -reproducibility Creating heatmap of reproducibility (default: False)\n- -aacdr3 Define the clonotype at the amino acid cdr3 level (default:\n False)\n- -genes_cdr3_aacln Define the clonotype at the amino acid cdr3 and V,\n J gene level (default: False)\n- -optimize Creating negative control vs relevant peptide stimulated\n clonotype p-value plot (default: False)\n- -timepoints Analyzes samples from different time points (default:\n False)\n- -geneusage Provide gene usage statistics (default: False)\n- -detailed Provide more details\n- -input_folder INPUT_FOLDER Input folder (default: current directory)\n- -output_folder OUTPUT_FOLDER Output folder (default: current\n directory)\n- -workdir WORKDIR Folder where input and output files should be\n (default: current directory)\n- -compress Compress output folder (default: False)\n\n- -nolog Disable default log file (default: False)\n- -v Turns on verbosity (more details)\n- \u2013version show program\u2019s version number and exit\n- -debug Debug using small input size to test specific cases.\n\n# Usage\n\n.. code:: python\n\n # Merge Adaptive Biotechnologies TCR sequencing txt formatted files\n python pepbox.py -merge -workdir myworkdir\n # Common pipeline\n python pepbox.py -merge -expansion -analyze -optimize -workdir myworkdir", 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