paulsengroup / hictk Goto Github PK

It looks like there are only versions of hictk available for the linux-64 platform, so the installation instructions you give for Mac are not working. To check, I ran mamba search hictk --info and conda search hictk --info which only list bioconda/linux-64 in the URL.

Would you be able to publish builds for Mac? This is useful software, it would be very nice to have an easy install for my non-Linux-running collaborators! Thank you!.

Firstly, thanks for hiktk - it is a very handy conversion, hard to find and works fast.
Does it know how to handle format_version:3 from a recent cooler release?
I'm new to hic so just guessing it might not. Odd that the recent one has 'nchroms': 37688, - currently rebuilding with a reference dm3.fasta to see if that helps.

Attached are two samples in coolsamples.zip:

• hicex_dm4.cooler is a cooler-0.9.3 file generated using the hicexplorer infrastructure on Galaxy, and
• matrix.cool is an older one that's part of the Galaxy library test data from cooler-0.7.6

With hictk 0.0.8 on the command line:

• Both validate as ok.
• The old one works with convert into hic
• The new one freezes with 100% cpu spinning - no output with dump or convert.

It's possible to open both with the python api which is how I found out the cooler versions so that was really handy - thanks!

import hictkpy as htk
f = htk.File("matrix.mcool")
>>> f = htk.File("matrix.cool", resolution=1)
>>> f.attributes()
{'bin_size': 5000, 'bin_type': 'fixed', 'format': 'HDF5::Cooler', 'format_version': 2, 'storage-mode': None, 'creation-date': 
'2017-11-15T19:04:25.627510', 'generated-by': 'cooler-0.7.6', 'assembly': 'unknown', 'metadata': '{}', 'format-url': 
'https://github.com/mirnylab/cooler', 'nbins': 33754, 'nchroms': 15, 'nnz': 35857, 'sum': 37321, 'cis': None}
>>> f = htk.File("hicex_dm4.cool", resolution=1)
>>> f.attributes()
{'bin_size': 10000, 'bin_type': 'fixed', 'format': 'HDF5::Cooler', 'format_version': 3, 'storage-mode': 'symmetric-upper', 'creation-
date': '2024-02-03T03:46:02.531452', 'generated-by': 'HiCMatrix-16', 'assembly': "b'dm3'", 'metadata': '{"format": 
"HDF5::Cooler", "format-url": "https://github.com/mirnylab/cooler", "generated-by": "HiCMatrix-16", "generated-by-cooler-lib": 
"cooler-0.9.3", "tool-url": "https://github.com/deeptools/HiCMatrix", "matrix-generated-by": "b\'HiCExplorer-3.7.2\'", "matrix-
generated-by-url": "b\'https://github.com/deeptools/HiCExplorer\'", "genome-assembly": "b\'dm3\'"}', 'format-url': 
'https://github.com/mirnylab/cooler', 'nbins': 50717, 'nchroms': 37688, 'nnz': 19482, 'sum': 4314105, 'cis': None}
>>>