Question: (Closed) Learn perl or python for bioinformatics?
0
gravatar for thjnant
3.7 years ago by
thjnant90
Germany
thjnant90 wrote:

Hello,

I know this is a repeated question but I would like to have new opinions on it as time changes preferences. I am about to finish the first year of my PhD studies in evolutionary genetics. I have a biology background. During this first year, I have tried to learn a bit of everything, from C to C++, perl and python. But now it's the time to learn one scripting language very well. From my personal experience, I found python easier to learn and understand, while I like regular expressions in perl and the fact I can easily use other unix commands with it.

In my work, I see a trend towards learning python in younger generation while the more experienced bioinformaticians all use perl. I know learning either of the languages very well will make it easy to learn the other but I am wondering which language for the moment is more used generally as I want to devote a great deal of time to really learn it well. Also, is it possible to use python for data visualization?

Thanks in advance.

python perl • 4.1k views
ADD COMMENTlink modified 3.7 years ago by mxs530 • written 3.7 years ago by thjnant90

Also, is it possible to use python for data visualization?

see matplotlib. As for your more general question, the first four answers Why You Need Perl/Python If You Know R/Shell [Ngs Data Analysis] are very good, even if the question is not exactly the same as yours. 

ADD REPLYlink written 3.7 years ago by h.mon24k

Thanks a lot!

ADD REPLYlink written 3.7 years ago by thjnant90

Hello thjnant!

We believe that this post does not fit the main topic of this site.

Subjective, has bin discussed ad nauseam. Language discussions are possibly acceptable as forum because they are highly subjective, but they do not make a real bioinformatics question.

For this reason we have closed your question. This allows us to keep the site focused on the topics that the community can help with.

If you disagree please tell us why in a reply below, we'll be happy to talk about it.

Cheers!

ADD REPLYlink modified 3.7 years ago • written 3.7 years ago by Michael Dondrup45k

Hello thjnant!

Questions similar to yours can already be found at:

We have closed your question to allow us to keep similar content in the same thread.

If you disagree with this please tell us why in a reply below. We'll be happy to talk about it.

Cheers!

ADD REPLYlink written 3.7 years ago by Michael Dondrup45k
1
gravatar for Steven Lakin
3.7 years ago by
Steven Lakin1.4k
Fort Collins, CO, USA
Steven Lakin1.4k wrote:

Perl is older than Python, and I generally support Python as a higher level language.  If you're looking to script for bioinformatics purposes, you should learn R and Python first, then if you feel the need to learn more, you can do that very easily given your knowledge of those two languages.  Python is great for some aspects of bioinformatics, and R is great for tabular data manipulation and other packages.  Both Python and R support visualization tools, though I would argue that R has better tools than Python at the moment.

ADD COMMENTlink written 3.7 years ago by Steven Lakin1.4k
1
gravatar for Antonio R. Franco
3.7 years ago by
Spain. Universidad de Córdoba
Antonio R. Franco4.0k wrote:

Python is more convenient because it is easier to write (you forget about the semicolons), the number of available library is lower because they are usually more optimized, and is becoming one of the more used programming languages nowdays (the 4th globally) (see this LINK). You can get Biophyton, Bioperl and Biojava as well

ADD COMMENTlink written 3.7 years ago by Antonio R. Franco4.0k
1
gravatar for mxs
3.7 years ago by
mxs530
mxs530 wrote:

"From my personal experience, I found python easier to learn and understand  ...  I see a trend towards learning python in younger generation while the more experienced bioinformaticians all use perl. "

I think you have your answer there. Isn't this what is happening in all fields of human activities?  "Easy to use" is the key behind every "successful" tool, whether it is  an i-phone or python or a new i8 bmw (no gears if not in sport mode). After a decade in bioinformatics I tried out a lot of programming languages but i think the key "decider" in the end was the underlying problem. If you have no affiliation towards the actual development of tools for bioinformatic research ( and I mean development of implementation-wise efficient tools) then I would suggest Python, since it provides a range of "ready to use" solutions that you can directly apply in your analysis. On the other hand if you often need to switch to some development project in which you really need to handle memory by yourself (c,c++) then, due to more syntax similarities and often the logic in thinking when working with Perl and c/c++ you will find it more pragmatic (at least I do)  to just stick to Perl. Moreover, with the availability of PDL there are less and less differences between Python and Perl regarding statistical analysis (thus possibly in the future eliminating the need for R -> highly unlikely but...).

 

mxs

 

ADD COMMENTlink written 3.7 years ago by mxs530
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