Metadata-Version: 2.1
Name: pygor3
Version: 0.0.2
Summary: Python package to manipulate and run IGoR data files
Home-page: https://github.com/alfaceor/pygor3
Author: Carlos Olivares
Author-email: carlos.olivares@phys.ens.fr
License: GNU GPLv3
Description: # pygor3
        pygor3 is a python3 library to manipulate IGoR inputs/outputs and easyly make plots and scripts tasks.
        pygor3 repository
        synopsis
        
        # Installation
        0. (Optional) Install conda https://docs.conda.io/en/latest/ (or anaconda https://www.anaconda.com/) and create (or use ) a virtual environment
          $ conda create --name pygor3 python=3.7
          $ conda activate pygor3
        
        1. Install requirements:
        
        $ pip3 install -r requirements.txt
        
        2. Install pygor3 package from this directory
        
        $ pip3 install -e .
        
        # simple usage.
        
        1. Download new gene templates from IGMT website:
        $ pygor3-cli imgt get-ref-genome -t VDJ --imgt-species Homo+sapiens --imgt-chain TRB
        
        2. Make a new model from a ref_genome directory
        
        $ pygor3-cli -M models/Homo+sapiens/TRB/ model create -t VDJ
        
        3. Explore default model
        
        $ pygor3-cli -M models/Homo+sapiens/TRB/ model plot
        
        4. Infer model
        $ pygor3-cli -M HumanTRB/ igor-infer -i test_seqs.csv -o myfile.db
        
        5. Evaluate model
        $ pygor3-cli -D myfile.db igor-evaluate -i test_seqs.csv -o mewdatabase.db
        
        # if -o option is None then use the same myfile.db, so the sequences to use should be 
        
        Show the tables in database:
        $ pygor3-cli db-ls -D myfile.db
        
        Delete elements in database:
        $ pygor3-cli db-rm -D myfile.db --sequences --model --alignments
        
        Extract elements in database:
        $ pygor3-cli db-extract -D myfile.db --sequences --model --alignments -o newfile.db
        
        Attach elements in database:
        $ pygor3-cli db-attacht -D myfile.db --sequences --model --alignments -i another.db
        
        
        
        
        
        
        ## pygor3-load_database 
        
        Script to load genomes references and alignments in a single file
        
        usage: pygor3-load_database [-h] [-s SPECIES] [-c CHAIN] [-M MODEL_PATH]
                                    [-g PATH_REF_GENOME] [-w WORKING_DIRECTORY]
                                    [-b BATCH]
        
        optional arguments:
          -h, --help            show this help message and exit
          -M MODEL_PATH, --model_path MODEL_PATH
                                IGoR model directory path, this path include
                                ref_genomes and model_parms
          -g PATH_REF_GENOME, --path_ref_genome PATH_REF_GENOME
                                Directory where genome references are stored:
                                genomicDs.fasta, genomicJs.fasta, genomicVs.fasta,
                                J_gene_CDR3_anchors.csv, V_gene_CDR3_anchors.csv
          -w WORKING_DIRECTORY, --WD WORKING_DIRECTORY
                                Path where files gonna be created.
          -b BATCH, --batch BATCH
                                Batchname to identify run. If not set random name is
                                generated
        
        IGoR default models:
          -s SPECIES, --species SPECIES
                                Igor species
          -c CHAIN, --chain CHAIN
                                Igor chain
        
        
        ## pygor3-load_database 
        
        usage: pygor3-naive_align [-h] [-o OUTPUT] [-D DATABASE]
        
        optional arguments:
          -h, --help            show this help message and exit
          -o OUTPUT, --output OUTPUT
                                filename of csv file to export data
          -D DATABASE, --database DATABASE
                                Igor database created with database script.
        
        
        # Scripts
        pygor3-model_export : Human readable tab-separated models in different files (http://physics.princeton.edu/~ccallan/TCRPaper/results/event_distributions.xls,) 
        Usage: pygor3-model_export [options]
        
        Options:
          -h, --help            show this help message and exit
          -s SPECIES, --species=SPECIES
                                Igor species
          -c CHAIN, --chain=CHAIN
                                Igor chain
          -b BATCH, --batch=BATCH
                                Batchname to identify run. If not set random name is
                                generated
          -o OUTPUT, --output=OUTPUT
                                filename of csv file to export data
          -p MODEL_PARAMS, --model_params=MODEL_PARAMS
                                IGoR model_params.txt
          -m MODEL_MARGINALS, --model_marginals=MODEL_MARGINALS
                                IGoR model_marginals.txt
        
        
        pygor3-plot_marginals : Export csv file with real probability marginals from IGoR models.
        Usage: pygor3-plot_marginals [options]
        
        Options:
          -h, --help            show this help message and exit
          -s SPECIES, --species=SPECIES
                                Igor species
          -c CHAIN, --chain=CHAIN
                                Igor chain
          -o OUTPUT, --output=OUTPUT
                                filename of csv file to export data
          -p MODEL_PARAMS, --model_params=MODEL_PARAMS
                                IGoR model_params.txt
          -m MODEL_MARGINALS, --model_marginals=MODEL_MARGINALS
                                IGoR model_marginals.txt
        
        
        
        [dev]
        pygor3-pgen_sequences: Simple script to get the pgen of input sequences given an output filename, no batch required but optional.
        pygor3-infer: A script to run any model given gene templates Is incomplete only works for VDJ for the moment. I found a bug for VJ I'm solving it :|
        pygor3-bs_export: Given an IGoR batchname, species and chain it captures the model and convert the values of best scenarios to explicit values and not indexes.
        
        
        
        
        
        
        
        # pygor command line
        
        ## Common options
        Usage: pygor [OPTIONS] COMMAND [ARGS]...
        
        Options:
          -s, --set_igor_species TEXT     Species in IGoR's format: human, mouse
          -c, --set_igor_chain TEXT       Chain in IGoR's format, e.g. alpha, beta,
                                          TRB, TRA
        
          -m, --set_igor_model <model_parms.txt> <model_marginals.txt>
                                          IGoR model_params.txt and
                                          model_marginals.txt filenames.
        
          -M, --set_model_path <model_directory_path>
                                          IGoR model directory path, this path include
                                          ref_genomes and model_parms
        
          -g, --set_path_ref_genome TEXT  Directory where genome references are
                                          stored: genomicDs.fasta,  genomicJs.fasta,
                                          genomicVs.fasta,  J_gene_CDR3_anchors.csv,
                                          V_gene_CDR3_anchors.csv
        
          -w, --set_wd TEXT               Sets the working directory to path
                                          [default: ./]
        
          -b, --set_batch TEXT            Sets batchname to identify run. If not set
                                          random name is generated
        
          -D, --set_database TEXT         Igor database created with database script.
          --help                          Show this message and exit.
        
        Commands:
          db-attach         Attach tables to database.
          db-export         Export database model in igor formatted files
          db-ls             List tables in database by groups and show number of...
          db-rm             Delete tables in database by groups.
          db-test           Manipulations of models
          igor-align        IGoR's call to aligns
          igor-evaluate     IGoR's call to evaluate input sequences
          igor-generate     IGoR's call to generate sequences
          igor-infer        IGoR's call to infer model from input sequences and...
          igor-pgen         IGoR's call to calculate pgen of input sequences
          igor-read-seqs    IGoR's call to read_seqs
          igor-scenarios    IGoR's call to get best scenarios.
          imgt-get-genomes  Get genomes from imgt website of specifing species and...
          model-create      Make a new default model VJ or VDJ with uniform...
          model-export      Export IGoR's models from txt (model_parms.txt,...
          model-plot        Plot real marginals of the bayesian network events
        
        
        ## pygor subcommands
        
        ### pygor imgt
        
        Usage: pygor imgt-get-genomes [OPTIONS]
        
          Get genomes from imgt website of specifing species and chain in imgt
          format.
        
        Options:
          --info                          List species and chain avialable in imgt
                                          website.
        
          -t, --recombination_type [VJ|VDJ]
                                          Igor recombination type.
          --imgt-species TEXT             IMGT species name for name specifications
                                          run imgt --info.
        
          --imgt-chain TEXT               IMGT chain name e.g. TRA, TRB.
          --help                          Show this message and exit.
        
        
        ### pygor model-create
        Usage: pygor model-create [OPTIONS]
        
          Make a new default model VJ or VDJ with uniform probability distribution
        
        Options:
          -t, --recombination_type [VJ|VDJ]
                                          Igor recombination type.
          --help                          Show this message and exit.
        
        
        ### pygor model-plot
        Usage: pygor model-plot [OPTIONS]
        
          Plot real marginals of the bayesian network events
        
        Options:
          -o, --output-prefix TEXT  Prefix to pdf files with model plots.
          --help                    Show this message and exit.
        
        
        ### pygor model-export
        Usage: pygor model-export [OPTIONS]
        
          Export IGoR's models from txt (model_parms.txt, model_marginals.txt) files
          to db viceversa
        
        Options:
          --from-txt TEXT...  Export Igor's model from txt files model_parms.txt and
                              model_marginals.txt.
        
          --from-db TEXT      Export Igor's model from database file.
          --to-txt TEXT...    Output filename of Igor recombination model to
                              <model_parms.txt> <model_marginals.txt>.
        
          --to-db TEXT        Output filename of Igor recombination model to
                              <model.db>.
        
          --help              Show this message and exit.
        
        
        
        ### pygor igor-evaluate
        Usage: pygor igor-evaluate [OPTIONS]
        
          IGoR's call to evaluate input sequences
        
        Options:
          -i, --input-sequences TEXT  Input sequences in FASTA, TXT or CSV formats.
          -o, --output-db TEXT        Output database file.
          --help                      Show this message and exit.
        
        
        
        
        ### pygor db-attach
        Usage: pygor db-attach [OPTIONS]
        
          Attach tables to database.
        
        Options:
          --from-db TEXT                  Database copy source filename.
          --from-batch TEXT               Database copy source filename.
          --from-genome-dir TEXT          Database copy source filename.
          --from-model-path TEXT          Database copy source filename.
          --igor-model-dir <model.db>     IGoR model database file.
          --igor-model-parms <model_parms.txt>
                                          IGoR model parms (or params) file.
          --igor-model-marginals <model_marginals.txt>
                                          IGoR model marginals file.
          --scenarios TEXT                If --from-db no need to add filename
          --pgen TEXT                     If --from-db no need to add filename
          --genomes TEXT                  Copy V, (D) and J genetic data to database
          --genomesV TEXT                 Copy just V genomes tables to database.
          --genomesD TEXT                 Copy just D genomes tables to database.
          --genomesJ TEXT                 Copy just J genomes tables to database.
          --genomesCDR3 TEXT              Copy just CDR3 anchors tables to database.
          --alignments TEXT               Copy all available alignments tables to
                                          database.
        
          --alignmentsV TEXT              Copy V alignments tables to database.
          --alignmentsD TEXT              Copy D alignments tables to database.
          --alignmentsJ TEXT              Copy J alignments tables to database.
          --alignmentsCDR3 TEXT           Copy indexed cdr3 table to database.
          --help                          Show this message and exit.
        
        
        
        
Platform: UNKNOWN
Requires-Python: >=3.5
Description-Content-Type: text/markdown
