[Bioperl-l] Comparison between bioperl and biopython?

Andreas Kähäri ak at ebi.ac.uk
Tue Dec 29 11:57:18 EST 2009

On Tue, Dec 29, 2009 at 10:08:09AM -0600, Peng Yu 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.
> 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.
> 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.

Assuming, as you do, that the functionality of BioPerl and BioPython is
the same:  Which of the two programming languages are you (or your team)
most proficient in?  Use that language.


Andreas Kähäri, Ensembl Software Developer
European Bioinformatics Institute (EMBL-EBI)
Wellcome Trust Genome Campus, Hinxton
Cambridge CB10 1SD, United Kingdom

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