[Bioperl-l] [Biopython] Comparison between bioperl and biopython?

Peng Yu pengyu.ut at gmail.com
Tue Dec 29 14:15:14 EST 2009

On Tue, Dec 29, 2009 at 11:03 AM, Sean Davis <sdavis2 at mail.nih.gov> wrote:
> On Tue, Dec 29, 2009 at 11:08 AM, Peng Yu <pengyu.ut at gmail.com> wrote:
>> May I ask somebody who are versitile in both bioperl and biopython
>> comment on the pros and cons of bioperl and biopython? I'm sending
>> this email to both bioperl and biopython mailing lists. But I hope
>> that it will not result in any contention.
>> I assume that the functionality between bioperl or biopython is the
>> same, i.e., tasks can be done in bioperl can be done biopython and
>> vice versa, as both libraries have been out there over 10 years.
>> Please correct me if my understanding is not true.
> The two projects have similar goals, but saying that the functionality
> is the same would be an extreme oversimplification.  You will need to
> define what you want to do and then check to see what the two projects
> have to offer.  This will, in general, require perusing the websites
> for both projects as well as the relevant documentation.

According to your experience, are there some tasks that are easier
with one than with another?

>> Given that a task that can be done with either bioperl or biopython,
>> I, in particularly, want to know how long it will take to write the
>> code for the task in bioperl and biopython, with the same readability
>> requirement (see below) and the assumption that users have the same
>> fluency in perl and python.
> Again, you will want to define the task(s) to be accomplished and then
> weigh the pros and cons of each project combined with local expertise.
>  If you don't know what you want to do, then you can certainly read
> some examples on the websites and see which project strikes you as a
> "winner" for you.
>> python is claimed to be good for maintainability. But perl is
>> criticized for there-are-many-ways-for-a-given-task. Since there are
>> multiple ways in perl, let us assume that we always use perl in a
>> readable way.
> These two statements are generalizations that provide little insight
> into the strengths or weaknesses of the languages.  In other words,
> one can write good or bad code in both languages.
> Hope that helps.
> Sean

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