Metadata-Version: 2.1
Name: pymugen
Version: 1.2.1
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
        
          ::
        
            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
        
          ::
        
            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
