need new feature: subset cool file by chrom start and end to a new cool file

[seqyuan]

I want to take the interaction matrix of a chromosome or a segment of a chromosome from cool and save it to another cool.

[Phlya]

Please try using cooltools rearrange-cooler from this PR in cooltools open2c/cooltools#448

The help for the command should be enough to understand how it works, but feel free to ask if it's unclear.

[nvictus]

UPDATE: as @Phlya posted earlier, the cooltools rearrange command is now released and can be used to do this as well.

For a single intrachromosomal subset {chrom} or {chrom}:{start}-{end}, you can also accomplish this using:

$ cooler dump --join -r {chrom}:{start}-{end} {input_cool} | cooler load --format bg2 {chrom.sizes}:{binsize} - {output_cool}

Include -r2 to select an interchromosomal zone.

[kalavattam]

Is there a way to do this while retaining any pre-calculated weights associated with the bins that make up the subset?

[LucasMcNU]

what is the usage for cooltools rearrange? I'm trying to get rid of extraneous chromosomes and just keep 1:22,X,Y. I have a bed file with but I am getting an error when I use the following command with this bedfile cooltools rearrange --view hg38.chrom.bed MB_80kb_merged.cool test.cool

[Phlya]

Is it tab delimited?

[LucasMcNU]

it is!

[LucasMcNU]

I tried exporting it as a bed using plyranges and got the following error instead

Traceback (most recent call last):
File "/home/lmc0633/.local/lib/python3.9/site-packages/cooltools/lib/checks.py", line 428, in is_compatible_viewframe
_ = bioframe.is_viewframe(view_df, raise_errors=True)
File "/home/lmc0633/.local/lib/python3.9/site-packages/bioframe/core/checks.py", line 240, in is_viewframe
raise ValueError(
ValueError: Invalid view: entries in region_df[view_name_col] must be unique

[Phlya]

Ah try adding another column with region names. E.g. copy the chrom column again in the end.

[LucasMcNU]

ohp! that worked - thank you!