[Biopython] Comparison between bioperl and biopython?

[Sean Davis]

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.

> 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