Metadata-Version: 2.1
Name: coreugate
Version: 2.0.1
Summary: calculate pair-wise allelic distances from cgMLST implements chewBBACAs
Home-page: https://github.com/kristyhoran/coreugate
Author: Kristy Horan
Author-email: kristyhoran15@gmail.com
License: UNKNOWN
Description: 
        # COREugate - A pipeline for cgMLST
        ## From contigs to cgMLST profile and SLC.
        
        COREugate has had a small facelift!! Under the hood we are now using [NextFlow](https://www.nextflow.io) as our pipeline engine and have introduced some additional functionality for clustering the profiles.
        
        1. PrepSchema (if necessary) and Call alleles using [chewBBACA](https://github.com/B-UMMI/chewBBACA/wiki).
        2. Combine profiles and statisitics for the whole dataset.
        3. Calculate pairwise allelic distances (missing data is ignored)
        4. Perform SLC to group related profiles, based on user supplied thresholds.
        
        ### Dependencies
        ```
        Python >=3.7
        Biopython >=1.70
        Nextflow >=20.10
        chewBBACA >=2.6
        ```
        
        ### NextFlow
        Ensure that you have NextFlow installed. Detailed instructions can be found [here](https://www.nextflow.io/docs/latest/getstarted.html#installation)
        
        ### chewBBACA
        [chewBBACA](https://github.com/B-UMMI/chewBBACA/) is used here to prepare the schema, by selecting exemplar alleles for comparison and to call allele profiles. More information about chewBBACA and how it is works can be found [here](https://github.com/B-UMMI/chewBBACA/wiki). COREugate can use a singularity version of chewBBACA, however if you want to install the latest version (>=2.0.16)
        
        ### Run COREugate
        
        #### Get COREugate
        ```
        pip3 install git+https://github.com/kristyhoran/Coreugate
        ```
        
        If you are installing COREugate on a server using `--user` please ensure that your `~/.local/bin` is part of your PATH
        ```
        export PATH=$PATH:/path/to/.local/bin
        ```
        
        #### Running COREugate
        
        ```
        coreugate [-h] [-v] [--input_file INPUT_FILE]
                         [--schema_path SCHEMA_PATH]
                         [--prodigal_training PRODIGAL_TRAINING] [--workdir WORKDIR]
                         [--threads THREADS]
                         [--filter_samples_threshold FILTER_SAMPLES_THRESHOLD]
                         [--cluster] [--cluster_thresholds CLUSTER_THRESHOLDS]
                         [--force] [--report]
        
        Coreugate - a cgMLST pipeline implementing chewBACCA
        
        optional arguments:
          -h, --help            show this help message and exit
          -v, --version         show program's version number and exit
          --input_file INPUT_FILE, -i INPUT_FILE
                                Input file tab-delimited file3 columns isolate_id
                                path_to_input_file (contigs) (default: )
          --schema_path SCHEMA_PATH, -s SCHEMA_PATH
                                Path to species schema/allele db (or url if using
                                chewie Nomenclature server) (default: )
          --prodigal_training PRODIGAL_TRAINING, -p PRODIGAL_TRAINING
                                Prodigal file to be used in allele calling. See https:
                                //github.com/B-UMMI/chewBBACA/tree/master/CHEWBBACA/pr
                                odigal_training_files for options (default: )
          --workdir WORKDIR, -w WORKDIR
                                Working directory, default is current directory
                                (default: /home/khhor/validation/salmonella_typing/rev
                                erification_20210322)
          --threads THREADS, -t THREADS
                                Number of threads to run chewBACCA (default: 16)
          --filter_samples_threshold FILTER_SAMPLES_THRESHOLD, -ft FILTER_SAMPLES_THRESHOLD
                                The proportion of loci present in a sample for an
                                sample to be included in further analysis (0-1)
                                (default: 0.95)
          --cluster, -c         If you would like to cluster the pairwise distance
                                matrix. If selected you must provide a list of
                                thresholds. (default: False)
          --cluster_thresholds CLUSTER_THRESHOLDS, -ct CLUSTER_THRESHOLDS
                                Provide a comma separate list (NO SPACES) eg 20,40,200
                                (default: )
          --force, -f           If you want to force chewBBACA to re-run. (default:
                                False)
          --report              Save nextflow reports. (default: False)
                                         Display this help message
        ```
        
        
        ###### Sample data
        
        *Assemblies*
        ```
        isolate_name	path/to/assembly.fa	
        ```
        ###### Species cgMLST schema
        COREugate requires an exisiting cgMLST schema, this can be a schema generated by the user or downloaded from one of the publically available databases. These schema should be in the format of a `fasta` file for each loci, each file should contain the different alleles for each loci. It should be noted that during allele calling, chewBBACA (implemented by COREugate) will add inferred alleles ([more information](https://github.com/B-UMMI/chewBBACA/wiki)) to your schema, so it is recommended that the schema path be fixed, that is that the schema is kept in a central location and a single version is used for each species/study.
        
        ###### Other optional arguments
        * `prodigal_training` a prodigal training file for allele calling. Recommended by chewBBACA developers, a list of default training files and further information can be found [here](https://github.com/B-UMMI/chewBBACA/wiki).
        
        
        ### Limitations of the pipeline
        * Coreugate is only able to work with pre-exisiting schemas that have been prep as described above, to derive profiles for isolates.
        * Possibly more, I just haven't found them yet!!
        
        
Platform: UNKNOWN
Classifier: Programming Language :: Python :: 3.7
Classifier: Operating System :: OS Independent
Classifier: Development Status :: 4 - Beta
Classifier: Intended Audience :: Science/Research
Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
Classifier: License :: OSI Approved :: GNU General Public License v3 (GPLv3)
Requires-Python: >=3.7
Description-Content-Type: text/markdown
Provides-Extra: tests
