[Biopython-dev] 5/9 BioStar - Biopython Questions

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1. I wonder why it is so important to use Seq objects in stead of plain ol' strings in Biopyton?
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May 8, 2010 at 5:10 PM

This may seem like a superfluous question, and perhaps it is, but it's important to get the basic raison d'etres of the programming habits that are encouraged in the tutorial straight. (Wow that's a strange and awkward sentence but it's good to write in English and show off literal non-skills.)

In short: Why use:

    >>> from Bio.Seq import Seq
    >>> from Bio.Alphabet import IUPAC

    >>> messenger_rna = Seq("AUGGCCAUUGUAAUGGGCCGCUGAAAGGGUGCCCGAUAG",
        IUPAC.unambiguous_rna)
    >>> messenger_rna
        Seq('AUGGCCAUUGUAAUGGGCCGCUGAAAGGGUGCCCGAUAG', 
        IUPACUnambiguousRNA())
    >>> messenger_rna.translate()
        Seq('MAIVMGR*KGAR*', HasStopCodon(IUPACProtein(), '*'))


When you can simply use:

    >>> from Bio.Seq import translate

    >>> my_string_messenger_rna = "AUGGCCAUUGUAAUGGGCCGCUGAAAGGGUGCCCGAUAG"
    >>> translate(my_string_messenger_rna)
        'MAIVMGR*KGAR*'

http://biostar.stackexchange.com/questions/1001/i-wonder-why-it-is-so-important-to-use-seq-objects-in-stead-of-plain-ol-strings

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Source: http://biostar.stackexchange.com/questions/tagged/biopython
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