Metadata-Version: 1.1
Name: sufam
Version: 0.4
Summary: So U Found A Mutation?
Home-page: https://github.com/inodb/sufam
Author: Ino de Bruijn
Author-email: ino@ino.pm
License: MIT
Description: So U Found A Mutation? (SUFAM)
        ==============================
        .. image:: https://badge.fury.io/py/sufam.svg
            :target: http://badge.fury.io/py/sufam
        .. image:: http://anaconda.org/inodb/sufam/badges/version.svg
            :target: http://anaconda.org/inodb/sufam
        .. image:: https://travis-ci.org/inodb/sufam.svg?branch=master
            :target: https://travis-ci.org/inodb/sufam
        
        Found a mutation in one or more samples? Now you want to check if they are in
        another sample. Unfortunately mutect, varscan or whatever other variant caller
        is not calling them. Use SUFAM. The super sensitive validation caller that
        calls everything on a given position. All you need is a vcf with the mutations
        that you are interested in and the sam/bam file of the sample where you want to
        find the same inconsipicuous mutation.
        
        Installation
        ------------
        ::
        
            pip install sufam
        
        Run
        ---
        ::
        
            usage: sufam [-h] [--sample_name SAMPLE_NAME] [--format {matrix,sufam}]
                        reffa vcf bam
        
            positional arguments:
            reffa                 Reference genome (fasta)
            vcf                   VCF with mutations to be validated
            bam                   BAM to find mutations in
        
            optional arguments:
            -h, --help            show this help message and exit
            --sample_name SAMPLE_NAME
                                    Set name of sample, used in output.
            --format {matrix,sufam}
                                    Set output format
        
        Example
        ~~~~~~~
        VCF file like::
        
            #CHROM	POS	ID	REF	ALT
            17	7574012	COSM11286,COSM214290	C	G
            17	7574012	COSM11286,COSM214290	C	A
        
        Check if given mutations are in a bam file::
        
            sufam human_g1k_v37_chr17.fa mutations.vcf subset1.bam 2> example/sufam.log > example/sufam.tsv
        
        Output:
        
        - `example/sufam.log <example/sufam.log>`_
        - `example/sufam.tsv <example/sufam.tsv>`_
         
        Developers
        ----------
        Tests
        ~~~~~
        In root dir run::
        
            nosetests
        
        For individual tests::
        
            nosetests -s tests/test_validation.py:TestValidation.test_validate_mutations_indel
        
Keywords: Python validation mutation mpileup samtools pileup vcf bam
Platform: UNKNOWN
Classifier: Development Status :: 2 - Pre-Alpha
Classifier: Intended Audience :: Science/Research
Classifier: Natural Language :: English
Classifier: License :: OSI Approved :: MIT License
Classifier: Operating System :: OS Independent
Classifier: Programming Language :: Python
Classifier: Programming Language :: Python :: 2
Classifier: Programming Language :: Python :: 2.6
Classifier: Programming Language :: Python :: 2.7
Classifier: Topic :: Software Development :: Libraries :: Python Modules
