Metadata-Version: 1.1
Name: mmsplice
Version: 0.2.1
Summary: Predict splicing variant effect from VCF
Home-page: https://github.com/s6juncheng/mmsplice
Author: Jun Cheng
Author-email: chengju@in.tum.de
License: MIT license
Description: # mmsplice
        
        [![pypi](https://img.shields.io/pypi/v/mmsplice.svg)](https://pypi.python.org/pypi/mmsplice)
        [![travis](https://img.shields.io/travis/s6juncheng/mmsplice.svg)](https://travis-ci.org/s6juncheng/mmsplice)
        
        Predict splicing variant effect from VCF
        
        * Free software: MIT license
        
        
        ## Usage example
        ------
        
        NOTE: make sure you split and left-normalize the input VCF file.
        
        Check notebooks/example.ipynb
        
        ```python
        # Import
        from mmsplice.vcf_dataloader import SplicingVCFDataloader
        from mmsplice import MMSplice, predict_all_table
        from mmsplice.utils import max_varEff
        
        # example files
        gtf = 'tests/data/test.gtf'
        vcf = 'tests/data/test.vcf.gz'
        fasta = 'tests/data/hg19.nochr.chr17.fa'
        gtfIntervalTree = '../tests/data/test.pkl' # pickle exon interval Tree
        
        # dataloader to load variants from vcf
        dl = SplicingVCFDataloader(gtf, 
                                  fasta,
                                  vcf,
                                  out_file=gtfIntervalTree,
                                  split_seq=False)
        
        # Specify model
        model = MMSplice(
            exon_cut_l=0,
            exon_cut_r=0,
            acceptor_intron_cut=6,
            donor_intron_cut=6,
            acceptor_intron_len=50,
            acceptor_exon_len=3,
            donor_exon_len=5,
            donor_intron_len=13)
        
         # Do prediction
         predictions = predict_all_table(model, dl, batch_size=1024, split_seq=False, assembly=False)
        
         # Summerize with maximum effect size
         predictionsMax = max_varEff(predictions)
        ```
        
        =======
        History
        =======
        
        0.1.0 (2018-07-17)
        ------------------
        
        * First release on PyPI.
        
Keywords: mmsplice
Platform: UNKNOWN
Classifier: Development Status :: 2 - Pre-Alpha
Classifier: Intended Audience :: Developers
Classifier: License :: OSI Approved :: MIT License
Classifier: Natural Language :: English
Classifier: Programming Language :: Python :: 3
Classifier: Programming Language :: Python :: 3.4
Classifier: Programming Language :: Python :: 3.5
Classifier: Programming Language :: Python :: 3.6
