[Biopython] Comparison between bioperl and biopython?

[William Heath]

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.

-Tim

P.S.

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
> >>
> >
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> >
>
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