Dealing with the outputs of MCL

[AlexAG1996]

Hi all,
I am a beginner to using MCL, so I have generated the output file in the ABC format. I am wondering if there is a way to extract the clusters individually and place them in separate files. I am also wondering if there a way to limit the number of clusters that are generated.

Kind regards,
Alex

[micans]

Hi Alex,

I assume you are working on a linux or unix-type system. The mcl output orders clusters from large to small; I assume you are interested in the N largest clusters. E.g. if N=10 you can do

head -n 10 MCL-OUTPUT-FILE | split -l 1 - foo.

This will create files foo.aa, foo.ab, foo.ac and so on. If you want numeric suffixes:

head -n 10 MCL-OUTPUT-FILE | split -l 1 - foo. --numeric-suffixes=1 --verbose

Change foo to some other string to pick the prefix you want. -l 1 indicates split will split line-by-line, and the single dash - after that indicates that it reads from STDIN (which is what it gets sent by the head program). Hope this is what you need, let me know if you have further questions.

[AlexAG1996]

Thanks Micans,
just on the off chance do you know how to extract the names contained within each cluster and place them into a format that can be used as a dictionary please.

Kind regards,
Alex

[micans]

Hi,

That can be done in all programming languages, I imagine a sequence of file read, splitting a line, and setting dictionary keys is required. Each of these should be fairly easy to find examples of in your favourite language.

Good luck!
Stijn

[AlexAG1996]

thanks Stijn 🤠