Metadata-Version: 2.1
Name: bio-ting
Version: 1.0
Summary: ting - T cell receptor interaction grouping
Home-page: https://github.com/FelixMoelder/ting
Author: Felix Mölder
Author-email: felix.moelder@uni-due.de
License: MIT License
Description: # ting
        
        ting - T cell receptor interaction grouping
        
        Synopsis
        --------
        
        ting [options]
        
        Options
        -------
        
        Required Input
        ~~~~~~~~~~~~~~
        
        The user must provide a list of CDR3b sequences.
        For compatibility reasons the tab seperated table of TCR sequences required for gliph is supported, too.
        
            --tcr_sequences tcr_sequences   The format of the table is tab delimited, expecting only the first
                                            column. The header is optional, but if included only use column
                                            names as shown in the example.
        
            --kmer_file K-MER_FILE          The k-mer file holds all 2-, 3- and 4-mers considered for local
                                            clustering. If file does not exist it will automatically be
                                            generated.
        
            --reference                     Reference file used for simulation of sample sets.
        
        Example:
        
        CDR3b		TRBV	TRBJ	CDR3a		TRAV		TRAJ	Sample-ID
        CAADTSSGANVLTF	TRBV30	TRBJ2-6	CALSDEDTGRRALTF	TRAV19		TRAJ5	09/02171
        CAATGGDRAYEQYF	TRBV2	TRBJ2-7	CAASSGANSKLTF	TRAV13-1	TRAJ56	03/04922
        CAATQQGETQYF	TRBV2	TRBJ2-5	CAASYGGSARQLTF	TRAV13-1	TRAJ22	02/02591
        CACVSNTEAFF	TRBV28	TRBJ1-1	CAGDLNGAGSYQLTF	TRAV25		TRAJ28	PBMC8631
        CAGGKGNSPLHF	TRBV2	TRBJ1-6	CVVLRGGSQGNLIF	TRAV12-1	TRAJ42	02/02071
        CAGQILAGSDTQYF	TRBV6-4	TRBJ2-3	CATASGNTPLVF	TRAV17		TRAJ29	09/00181
        CAGRTGVSTDTQYF	TRBV5-1	TRBJ2-3	CAVTPGGGADGLTF	TRAV41		TRAJ45	02/02591
        CAGYTGRANYGYTF	TRBV2	TRBJ1-2	CVVNGGFGNVLHC	TRAV12-1	TRAJ35	01/08733
        
        Optional Input
        
        
        
            --use_structural_boundaries     If set, the first and last three amino acids will be included
                                            in kmer counting and global clustering.
        
            --no_global                     No global clustering will be performed.
        
            --no_local                      No local clustering will be performed.
        
            --simulations                   Number of simulations that will be done for motif preprocessing. 
                                            Default is 1000.
        
            --min_kmer_occurence            Only kmers which occure at least min_kmer_occurences times in the
                                            sequence sample set will be taken in account. Default is 3.
            
            --max_p_value                   Only kmers with p_value < max_p_value will be used for clustering
            
            --cores                         Number of cores used for multiprocessing. Multiprocessing is done 
                                            during sample set simulation. Default: 1
        
            --stringent_filtering           Only TCRs starting with a cystein and ending with phenylalanine will be
                                            used (IGMT definition of CDR3 region). Default: False
        
        
Platform: UNKNOWN
Classifier: Development Status :: 5 - Production/Stable
Classifier: Environment :: Console
Classifier: Intended Audience :: Science/Research
Classifier: License :: OSI Approved :: MIT License
Classifier: Programming Language :: Python :: 3
Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
Description-Content-Type: text/markdown
