Metadata-Version: 2.1
Name: vcfy
Version: 0.0.9
Summary: Generate VCF file with random variants from reference genome
Home-page: https://github.com/cartoonist/vcfy
Author: Ali Ghaffaari
Author-email: ali.ghaffaari@mpi-inf.mpg.de
License: MIT
Download-URL: https://github.com/cartoonist/vcfy/tarball/0.0.9
Description: VCFY
        ====
        It generates a VCF file with simulated random variants based on the given probability model.
        
        Tools
        -----
        ### vcfy
        
            Usage: vcfy [OPTIONS] REFERENCE
            
              Generate VCF file with simulated variants in specified range [low, high)
              for the given region of the reference genome (in FASTA format). In case
              that the region is not specified the first region is used. If no range is
              provided, it is assumed that the variants are scattered throughout the
              region.
            
              For more information, consult with the README file.
            
            Options:
              -o, --output FILENAME      Write to this file instead of standard output.
              -m, --mutation-rate FLOAT  Base mutation rate.  [required]
              -r, --region TEXT          Region ID (default=first region in the reference)
              -l, --low INTEGER          Range lower bound (default=first locus in the
                                         region)
              -h, --high INTEGER         Range upper bound (default=last locus in the
                                         region)
              --help                     Show this message and exit.
        
        ### ksnper
        
            Usage: ksnper [OPTIONS] [VCF]
            
              Report the number of SNPs in all k-mers. Specify the k and the VCF file,
              it reports number of SNPS occurred in each k-mer.
            
            Options:
              -o, --output FILENAME           Write to this file instead of standard
                                              output.
              -r, --reference FILENAME        Reference genome FASTA file. It will be
                                              inferred from VCF header, if not specified.
              -k INTEGER                      The value of k.  [required]
              -c                              Set if the input VCF is compressed
              -d, --dialect [unix|excel-tab|excel]
                                              Use this CSV dialect.  [default: unix]
              --help                          Show this message and exit.
        
Keywords: vcf genome genomics variation DNA sequence ngs
Platform: UNKNOWN
Classifier: Development Status :: 2 - Pre-Alpha
Classifier: Environment :: Console
Classifier: License :: OSI Approved :: MIT License
Classifier: Programming Language :: Python :: 3
Classifier: Programming Language :: Python :: 3.6
Classifier: Programming Language :: Python :: 3.7
Classifier: Programming Language :: Python :: 3.8
Classifier: Programming Language :: Python :: 3.9
Classifier: Intended Audience :: Science/Research
Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
Description-Content-Type: text/markdown
Provides-Extra: test
