Tool: CBioInfCpp.h as a C++ lib containing some functions for bioinformatics
gravatar for chernouhov
12 days ago by
chernouhov0 wrote:

Dear Sirs.

Though I am not a professional programmer, bionformatics is very interesting interdisciplinary field for me.

I see it, the Python is a "standart language" in this field.

But when I solved problems at rosalind info, I used C++. So as a result a "lib of some function" has been borned.

The lib contains 3 groups of functions. The first one - input-output ones (in order to read-write vectors, matrixes, graphs from-to a file via only one commsnd as it is in Python).

The second group is "Working with strings". Contains some functions from computing GC-content, Edit Distance etc to finding all mutated strings in a given one.

The third is "Working with graphs". A data structure "Adjacency vector" is suggested. By the way, in general case, vertices may have negative integers assigned and graphs may have multiple loops and edges. Some function such as Eulerian Cycle, Path finding, topological sorting etc are implemented.

May it be useful for some tasks?

By the way, that algorithmic functions and problems should be included or maybe solved here?

I understand that this lib haven't a great majority of features. For example it is not able now to work with bioinformatic databases, but here I can not to implement it by myself only.

Free distributed source code and info is here:

(This is a link to directory (not to a file) that contains source code file and readme files)

My profile at Rosalind info

Best regards, Chernouhov Sergey

tool c++ • 156 views
ADD COMMENTlink modified 7 days ago • written 12 days ago by chernouhov0

Hi, maybe you're interested in contributing to the c++ SeqAn library?

ADD REPLYlink written 9 days ago by colindaven1.2k


Thanks. It's a great idea. Why not?

By the way, maybe you use SeqAn library or maybe you participate in its development?

ADD REPLYlink modified 7 days ago • written 8 days ago by chernouhov0

I would consider putting the code on Github, rather than distributing it as a google link. People are often wary of downloading code from behind random links without first being able to inspect the source.

ADD REPLYlink written 9 days ago by jrj.healey12k

Hi. Thanks. It is a good idea and I plan to do it a little later (as I haven't used Github yet).

But I must confess as nowadays the lib CBioInfCpp consists only one header file (as free source code) it is not so bad to use google drive too? Also there are 2 files - pdf and rtf - that contain the same description of the functions of CBioInfCpp in different formats (pdf and rtf). One may use any of them depending on preferable format.

ADD REPLYlink written 8 days ago by chernouhov0

Well, look at it this way: I haven't clicked on your link yet, even though I trust you, because I don't know if it will take me to a page, or will start a download immediately. If it starts a download immediately, I don't know if I'm getting a zip file, naked source code, or something masquerading as either.

If you want to contribute to projects, or have people contribute to improving your code, github (and its friends) is absolutely the way to go. To get started with github you need only three commands really: git pull, git commit, git push. Everything else is a bonus ;)

There are plenty of good youtube tutorials etc to get you going.

ADD REPLYlink written 8 days ago by jrj.healey12k

I'll see it.

But there are no zip or immediat downloads, it is a link to a directory

ADD REPLYlink modified 8 days ago • written 8 days ago by chernouhov0

Sure, but its hard to tell that from the link alone, so people are unlikely to click it.

ADD REPLYlink written 7 days ago by jrj.healey12k

The beauty of Git is its simplicity and version control. Every change you make is documented and at all times comprehensibly. Most major bioinformatics software packages are hosted there, you should definitely give it a try.

ADD REPLYlink written 7 days ago by ATpoint15k

I also don't think google drive is appropriate. Software in the days of google code, sourceforge etc was (and still in some cases is) far more poorly documented, intransparent, and unversioned. As a developer I think you'll enjoy github very much.

ADD REPLYlink written 8 days ago by colindaven1.2k

What jrj.healey said was the first thought to cross my mind. I'm not clicking on a google drive link. I really want to look at the code, the code structure and a README before I decide if something is worth a download.

ADD REPLYlink written 7 days ago by RamRS21k
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