liu-bioinfo-lab/schictools

a computational tool for analyzing single cell Hi-C data

schictools's Issues

Minor issue when genome_reference is a dict

Hi,

I think on line 91 of load_hic_file.py there's a small bug. The value of that dictionary should be divided by the resolution. Otherwise it would lead to an extremely large "maps" variable.

How should get the data format？

The Readme file uses the data test/data/cell_01', 'test/data/cell_02', 'test/data/cell_03 in test folder, but how can I transfer my data (fastq/ncc/hic) to the test data format?

About creating loaded_data

Can the scHiCs( ) run the type of files which is " .matrix " ? If yes, which file format should I choose?

ValueError: negative dimensions are not allowed

files = ['MII-13.allValidPairs.hic', 'MII-20.allValidPairs.hic']

Sus_scrofa = {'1': 274330532, '2': 151935994, '3': 132848913, '4':130910915, '5':104526007, '6':170843587, '7':121844099,'8':138966237,'9':139512083,'10':69359453,
'11':79169978,'12':61602749,'13':208334590,'14':141755446,'15':140412725,'16':79944280,'17':63494081,'18':55982971,'X':125939595,'Y':43547828,'MT':16613}

loaded_data = scHiCs(files, reference_genome=Sus_scrofa, resolution=40000,
max_distance=4000000, format='.hic', adjust_resolution=True,
chromosomes='all', operations=['convolution'], kernel_shape=3,
keep_n_strata=10, store_full_map=True)
assert x.num_of_cells==len(files)

Hello, I encountered this problem when running the above code, may I ask if I have misunderstood somewhere, and how should I solve it?

Questions in scHiCTools

Hi,
Thank you for this great software! However, I encountered two problems right now.

The first is that I don't really understand the format of the input data. Right now I have txt files looking like the input of "scHiCluster", which is like below:
1 1 9
1 2 1
.....
The first two columns are positions, and the third is count number. Which format does this belong to? matrix_txt?

The second question is that in my code, I wrote explicitly that chromosomes='chr1' (and I only have data in chr1 in that folder.), however, it asks for chr2. Did I do something wrong?

loaded_data = scHiCs(
files, sparse=True, reference_genome='mm9',
resolution=1000000, keep_n_strata=10,
format='matrix_txt', adjust_resolution=False, header=0, chromosomes='chr1',
operations=['convolution']
)

Processing 1 out of 1 files: C:/Users/solei/Downloads/Ren/FreeHiC_sc/2i
Traceback (most recent call last):
File "", line 5, in
File "C:\Users\solei\miniconda3\envs\scHiCTools\lib\site-packages\schictools-0.0.3-py3.7.egg\scHiCTools\load\ContactMaps.py", line 142, in init
**kwargs)
File "C:\Users\solei\miniconda3\envs\scHiCTools\lib\site-packages\schictools-0.0.3-py3.7.egg\scHiCTools\load\load_hic_file.py", line 166, in load_HiC
mat = np.loadtxt('{0}/{1}.txt'.format(file, chromosome))
File "C:\Users\solei\miniconda3\envs\scHiCTools\lib\site-packages\numpy-1.19.1-py3.7-win-amd64.egg\numpy\lib\npyio.py", line 961, in loadtxt
fh = np.lib._datasource.open(fname, 'rt', encoding=encoding)
File "C:\Users\solei\miniconda3\envs\scHiCTools\lib\site-packages\numpy-1.19.1-py3.7-win-amd64.egg\numpy\lib_datasource.py", line 195, in open
return ds.open(path, mode, encoding=encoding, newline=newline)
File "C:\Users\solei\miniconda3\envs\scHiCTools\lib\site-packages\numpy-1.19.1-py3.7-win-amd64.egg\numpy\lib_datasource.py", line 535, in open
raise IOError("%s not found." % path)
OSError: C:/Users/solei/Downloads/Ren/FreeHiC_sc/2i/chr2.txt not found.

Yours Sincerely,
Siqi Shen