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

William Heath wgheath at gmail.com
Tue Dec 29 15:16:39 EST 2009

The biggest reason to go with python is the ease of use.  Biologists are not
programmers and the learning curve for python is much smaller than that of
perl.  I like perl but choose python because of this issue.  Perl 6 does
address some of these issues however but this has not been fully implemented
as of yet.



I love, love, love cpan though which is only for perl right now :(

On Tue, Dec 29, 2009 at 11:55 AM, Jonathan Hilmer <jkhilmer at gmail.com>wrote:

> 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.
> Jonathan
> 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
> >>
> >
> > _______________________________________________
> > Biopython mailing list  -  Biopython at lists.open-bio.org
> > http://lists.open-bio.org/mailman/listinfo/biopython
> >
> _______________________________________________
> Biopython mailing list  -  Biopython at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/biopython

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