Forum: Some tricks from the experts
0
gravatar for dago
2.6 years ago by
dago2.5k
Germany
dago2.5k wrote:

I am not a pure bioinformatician. I self learned Unix and R and I must say I have been quite happy with the things I achieved.

However, I realized that I would need some more hands on a programming language. I choose Phyton, as it seems to be easier to learn for new comers like me.

I started looking online tutorials and wikis, and I found them really useful. However, at some point I start to think that maybe I am just wasting my time in learning basic programming aspects, which I will not really need in the real life when dealing with my data (mainly sequences). I think that this might be a common problem that biologist approaching a programming languages have. Therefore, I was wondering if you have any suggestion or advices concerning which aspects would be more useful to learn for a biologist that starts to learn a new programming language (i.e. Python, Perl).

Thanks for sharing.

programming forum python • 758 views
ADD COMMENTlink modified 2.6 years ago by Vivek2.2k • written 2.6 years ago by dago2.5k
5
gravatar for WouterDeCoster
2.6 years ago by
Belgium
WouterDeCoster39k wrote:

My suggestion would be to lock yourself up in your room and get started with solving questions on http://rosalind.info/ You get (increasingly difficult) tasks regarding bioinformatical questions which you can solve with any language you want. Not only will you get better at programming, but in addition you will get an understanding of how famous algorithms work, e.g. BLAST, by writing things like that yourself.

ADD COMMENTlink written 2.6 years ago by WouterDeCoster39k

that is a really good suggestion. I knew Rosalind, but I did not spend so much time on it. One of the "problem" I faced often is to work/edit external files. Any suggestion how to improve these skills?

ADD REPLYlink modified 2.6 years ago • written 2.6 years ago by dago2.5k

It's not clear to me what you mean, do you face problems editing an external file using your script?

ADD REPLYlink written 2.6 years ago by WouterDeCoster39k

Yes. Like, load a file and apply specific action, like keep just some lines rather than other and so on.

ADD REPLYlink written 2.6 years ago by dago2.5k

So in R you would read the file in memory using the read.table() function, make some changes and save an object back to the disk using write.table(). In python you would open a file, either in memory or iterating over it, and writing modified lines back to disk. What exactly is the problem?

ADD REPLYlink written 2.6 years ago by WouterDeCoster39k
2
gravatar for Vivek
2.6 years ago by
Vivek2.2k
Denmark
Vivek2.2k wrote:

A couple of minor tips if you haven't already adopted them:

  1. Learning and practicing version control is important albeit often ignored but pays good dividends in the end. Set up Git on your Desktop if you haven't already done it and keep your repositories synchronized. Good organization and proper documentation is a lifesaver if you are writing scripts that you might use for different projects at a later date or collaborate with others in your lab. Even if you are just solving Rosalind problems, putting up code on Git and linking your repository on your resume helps in job interviews where people want to see your code samples before even deciding to call you for an interview.

  2. If you write R scripts that you might reuse or distribute to others, get familiar with dplyr and write code in the dplyr way. I found that it instantly makes my Rscripts far more readable for others and even myself when I revisit them a few months down the line.

ADD COMMENTlink modified 2.6 years ago • written 2.6 years ago by Vivek2.2k
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