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

Jonathan Hilmer jkhilmer at gmail.com
Tue Dec 29 14:55:18 EST 2009

Personally, I think that the differences between Python and Perl
(although substantial) are not large enough to make the language
itself the deciding factor.

Instead, consider the larger community of software.  I haven't yet
found a situation in which Python cannot be applied: it can be used
with R (statistics); lower-level code C or fortran; visualization
software such as PyMol, Chimera, Blender, VTK; plotting with
matplotlib; and scipy/numpy or sage, which provide innumerable
benefits for computation, data-processing, etc.

Although I don't claim to have a great deal of experience with Perl, I
haven't seen the same integration with that language: I'm assuming it
can be used with R and VTK (not sure about C or fortran?).  For this
reason, unless your work is highly targeted and you have no use
programming language integration with other software, I would
recommend Python.

For perl experts, I would truly appreciate any corrections you could
offer to these observations of mine, since I wouldn't mind using perl
if it offers benefits either in general or for specific applications.


On Tue, Dec 29, 2009 at 12:15 PM, Peng Yu <pengyu.ut at gmail.com> wrote:
> 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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