Merging inputs of hicpro2fithic.py

[Mzwanele Ngubo]

Hi.

Is it possible to merge separately the inputs of hicpro2fithic.py : raw matrix files, abs bed files and iced matrix files? Can I do this with cat and sort?

Thanks,

Mzwanele

[Ferhat Ay]

Not sure what you mean by "merge" as files like abs.bed will likely be identical anyway and there is no clear way to combine two different matrix files. Do you want to just sum them up which would make sense for raw but not for iced matrix files?

[Mzwanele Ngubo]

Yes. I want to sum up the raw files. I'm struggling with a proper R or python syntax to use. Any rough example of a syntax would be helpful. Thanks.

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[Ferhat Ay]

You can create a "key" from the i j pair in the matrix file and then read the first file then the second into the same dictionary in python while summing counts if they come from both files. In awk it is also easy. you can create a key with $1"-"$2 then sort and join the two files using -a option of join. Then depending on the number of resulting columns you can either sum the counts if they come from both files or just use the count from the single file it comes from.