Metadata-Version: 2.1
Name: pymugen
Version: 1.2
Summary: Management about FASTA and VCF files.
Home-page: https://github.com/agranadosb/pymugen
Author: Alejandro Granados
Author-email: agranadosb55199@outlook.com
License: MIT
Download-URL: https://github.com/agranadosb/pymugen/archive/refs/heads/main.zip
Description: pymugen
        -------
        
        This module allows to manage data about genomic sequences, specificaly getting sequences from a FASTA file.
        
        The module's other functionality is the ability to get sequences with a mutation from a VCF file and transform it to another representation.
        
        
        Installation
        ------------
        
        Install pymugen with python
        
        ``pip3 install pymugen``
        
        Usage/Examples
        --------------
        
        Fasta example
        
        .. code-block:: python
        
          from pymugen.fasta import FastaReader
        
          fasta = FastaReader("fasta.fa")
        
          chromosome = fasta['chr1']
          sequence = chromosome.sequence(10, 5, 5)
        
          sequence[1]
          >>> A
        
          sequence[:]
          >>> CATGCATGCAT
        
          str(sequence)
          >>> C-A-T-G-C,A,T-G-C-A-T
        
          chromosome[5: 16]
          >>> CATGCATGCAT
        
        
        VCF example
        
        .. code-block:: python
        
          from pymugen.transformers import ExtendedTransformer
          from pymugen.fasta import FastaReader
        
          vcf = ExtendedTransformer("vcf.vcf", "fasta.fa")
        
          fasta = FastaReader("fasta.fa")
        
          chromosome = fasta['chr1']
          sequence = chromosome.sequence(10, 5, 5)
        
          mutated = vcf.method(sequence, "CGT")
        
          str(mutated)
          >>> 'A|w-q-r-e-w,s-d-f,v-c-x-z-v'
        
          mutated[:]
          >>> 'wqrewsdfvcxzv'
        
Keywords: VCF,FASTA,Genomics
Platform: UNKNOWN
Classifier: Development Status :: 3 - Alpha
Classifier: Intended Audience :: Developers
Classifier: Topic :: Software Development :: Build Tools
Classifier: License :: OSI Approved :: MIT License
Classifier: Programming Language :: Python :: 3.8
Description-Content-Type: text/markdown
