Metadata-Version: 1.1
Name: BackTranslate
Version: 0.0.5
Summary: BackTranslate: Functions for reverse translation.
Home-page: https://github.com/mutalyzer/backtranslate
Author: LUMC, Jeroen F.J. Laros
Author-email: J.F.J.Laros@lumc.nl
License: MIT License
Description: # Back translation
        This library provides functions for back translation from amino acids to
        nucleotides.
        
            from __future__ import unicode_literals
        
            from backtranslate.backtranslate import BackTranslate
        
            # Create a class instance, optionally giving the translation table id.
            bt = BackTranslate()
            # Find all substitutions that transform the codon 'TTG' into a stop codon.
            substitutions = bt.with_dna('TGG', '*')
        
        
        Sometimes we do not have access to the DNA sequence so we have to find
        possible substitutions from the amino acids directly.
        
            # Find all substitutions that transform a Tryptophan into a stop codon.
            substitutions = bt.without_dna('W', '*')
        
        To find out which substitution predictions can be improved by adding codon
        information, use the following function.
        
            bt.improvable()
        
        To get substitutions in a readable format, we can use the following:
        
            from backtranslate.util import subst_to_cds
        
            # Transform the substitutions to CDS coordinates.
            variants = subst_to_cds(substitutions, 12)
        
        ## Command line interface
        Use the command `backtranslate` to find substitutions that explain an amino
        acid change:
        
            $ backtranslate with_dna -o 210 data/mhv.fa - 1 Leu
            1       A       C
            1       A       T
        
        
        If no reference is available, use the `without_dna` subcommand:
        
            $ backtranslate without_dna - Asp 92 Tyr
            274     G       T
        
        
        The command `find_stops` finds a list of positions and substitutions that lead
        to stop codons. This list of destructive substitutions are useful when
        analysing a pool of viral transcripts. Counting the appropriate nucleotides at
        the given positions gives insight into how many transcripts are active.
        
            $ backtranslate find_stops -o 210 data/mhv.fa -
            216     A       T
            225     A       T
            230     C       A
            230     C       G
            243     A       T
            ...
        
Keywords: bioinformatics
Platform: any
Classifier: Development Status :: 3 - Alpha
Classifier: Intended Audience :: Science/Research
Classifier: Intended Audience :: Developers
Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
Classifier: License :: OSI Approved :: MIT License
Classifier: Operating System :: OS Independent
Classifier: Programming Language :: Python
Classifier: Programming Language :: Python :: 2
Classifier: Programming Language :: Python :: 3
Classifier: Programming Language :: Python :: 2.7
Classifier: Programming Language :: Python :: 3.3
Classifier: Programming Language :: Python :: 3.4
