pygor3 0.0.2

Python package to manipulate and run IGoR data files

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.