Metadata-Version: 1.2
Name: sorting_hat
Version: 0.0.4
Summary: Sorts indels into mutational classes
Home-page: https://github.com/allisonseiden/sorting_hat
Author: Allison Seiden
Author-email: ahseiden@gmail.com
License: UNKNOWN
Description: ===========
        Sorting Hat
        ===========
        
        Sorts indels into classes defined as follows:
          - **homopolymer run (HR):** mutation is in a region where there are 6 or more
            copies of the nucleotide being inserted or deleted
          - **change in copy count (CCC):** the allele being inserted or deleted has 1 or
            more repeats in the mutation region
          - **no change in copy count (non-CCC):** the allele being inserted or deleted is
            not repeated in the mutation region
        
        In order to use sorting_hat, you must ensure the following are installed:
          - `Python >=3.5.0`_
          - `bedtools >=2.27.0`_
        
        
        To install, use *pip*:
        
        .. code-block::
        
            pip install sorting_hat
        
        
        Example run
        
        .. code-block:: bash
        
            sorting_hat --bed test.bed \
                        --fasta test.fasta \
                        --repeat repeat_masker.txt
        
        Usage
        
        .. code-block::
        
            sorting_hat [-h] -b BED -f FASTA -r REPEAT [-o OUTPUT]
        
        Sorts indels into mutational classes
        
          -b BED, --bed BED     Location of BED file with all variants. Must be
                                formatted as Chrom/Start/End/Ref/Alt/PatientID.
          -f FASTA, --fasta FASTA
                                Location of reference fasta file.
          -r REPEAT, --repeat REPEAT
                                Location of RepeatMasker file downloaded from UCSC
                                Genome Browser. Refer to docs to see how to download
                                RepeatMasker.
          -o OUTPUT, --output OUTPUT
                                Name of output file, if not chosen then will print to
                                stdout.
        
        To download RepeatMasker from UCSC Genome Browser, see photos in 'data'
        folder on github: https://github.com/allisonseiden/sorting_hat
        
        Allison Seiden <ahseiden@gmail.com>
        
        
        .. _Python >=3.5.0: https://www.python.org/downloads/release/python-350/
        .. _bedtools >=2.27.0: http://bedtools.readthedocs.io/en/latest/
        
Platform: UNKNOWN
Classifier: Programming Language :: Python :: 3
Classifier: License :: OSI Approved :: MIT License
Classifier: Operating System :: OS Independent
Requires-Python: >=3
