Metadata-Version: 1.1
Name: snp-mutator
Version: 1.0.0
Summary: Generate mutated sequence files from a reference genome.
Home-page: https://github.com/CFSAN-Biostatistics/snp-mutator
Author: Hugh Rand
Author-email: Hugh.Rand@fda.hhs.gov
License: BSD
Description: ===============================
        SNP Mutator
        ===============================
        
        
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        Generate mutated sequence files from a reference genome.
        
        SNP Mutator was developed by the United States Food
        and Drug Administration, Center for Food Safety and Applied Nutrition.
        
        * Free software
        * Documentation: https://snp-mutator.readthedocs.io/en/latest/readme.html
        * Source Code: https://github.com/CFSAN-Biostatistics/snp-mutator
        * PyPI Distribution: https://pypi.python.org/pypi/snp-mutator
        
        
        Features
        --------
        
        * Reads a fasta file and generates any number of mutated fasta replicate files.
        * Mutations can be any number of single-base substitutions, insertions, and deletions at randomly
          chosen positions, uniformly distributed across the genome.
        * Mutations can be chosen from a subset (pool) of all possible positions.
        * Replicates can be partitioned into multiple groups with each group sharing a pool of eligible positions.
        * Generates a summary file listing the original base and the mutation for all mutated positions.
        * Mutations can be either monomorphic or polymorphic.
        * VCF file generation.
        * Various metrics can be saved to an output file.
        
        Citing SNP Mutator
        --------------------------------------
        
        To cite SNP Mutator, please cite the publication below:
        
            `Davis S, Pettengill JB, Luo Y, Payne J, Shpuntoff A, Rand H, Strain E. (2015)
            CFSAN SNP Pipeline: an automated method for constructing SNP matrices from next-generation sequence data.
            PeerJ Computer Science 1:e20   https://doi.org/10.7717/peerj-cs.20 <https://doi.org/10.7717/peerj-cs.20>`_
        
        License
        -------
        
        See the LICENSE file included in the SNP Mutator distribution.
        
        
        
        
        History
        -------
        
        1.0.0 (2018-10-12)
        ---------------------
        * Mutations can be chosen from a subset (pool) of all possible positions.
        * Replicates can be partitioned into multiple groups with each group sharing a pool of eligible positions.
        * Mutations can be either monomorphic or polymorphic.
        * Add the capability to generate VCF output files.
        * Add the capability to generate a metrics output file.
        * The installer creates an executable script called ``snpmutator``.
        * Insertions are now placed after the original reference position, not before, as in prior versions of
          snpmutator.  This means it will not be possible to exactly reproduce the results of prior versions
          of this software.
        
        0.2.0 (2016-01-15)
        ---------------------
        
        * Allow lowercase bases in the input fasta file.
        * Do not mutate gaps or ambiguous positions.
        * Add a command line switch to show the program version.
        
        0.1.1 (2015-06-17)
        ---------------------
        
        * Remove spaces from the summary file column headings.  This will simplify downstream
          analysis in some scripting languages.
        
        
        0.1.0 (2015-05-21)
        ---------------------
        
        * First release on GitHub, Read the Docs, and PyPI.
        
Keywords: bioinformatics,NGS,snp-mutator
Platform: UNKNOWN
Classifier: Development Status :: 2 - Pre-Alpha
Classifier: Intended Audience :: Developers
Classifier: License :: OSI Approved :: BSD License
Classifier: Natural Language :: English
Classifier: Programming Language :: Python :: 2
Classifier: Programming Language :: Python :: 2.6
Classifier: Programming Language :: Python :: 2.7
Classifier: Programming Language :: Python :: 3
Classifier: Programming Language :: Python :: 3.3
Classifier: Programming Language :: Python :: 3.4
