how to load bed file using higlass-python

[smitkadvani]

Description:

When I try to load a bedfile using the following code:

import higlass as hg
ts3 = hg.bed2ddb('Regular/H3K27ac_EA92-97_peaks.xls.bed.beddb')

hg.view(
    hg.track("top-axis"),
    ts3.track("chromosome-labels"),
    ts3.track("horizontal-bar"),
)

File "/Users/smit/anaconda3/envs/3dfolding/lib/python3.11/site-packages/higlass/tilesets.py", line 46, in tiles return self._tiles(tile_ids) ^^^^^^^^^^^^^^^^^^^^^ File "/Users/smit/anaconda3/envs/3dfolding/lib/python3.11/site-packages/clodius/tiles/bed2ddb.py", line 41, in tiles return tiles_1d(filepath, tile_ids) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/Users/smit/anaconda3/envs/3dfolding/lib/python3.11/site-packages/clodius/tiles/bed2ddb.py", line 64, in tiles_1d to_return += [(tile_id, get_1d_tiles(filepath, int(z), int(x))[int(x)])] ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/Users/smit/anaconda3/envs/3dfolding/lib/python3.11/site-packages/clodius/tiles/bed2ddb.py", line 117, in get_1d_tiles rows = c.execute(query).fetchall() ^^^^^^^^^^^^^^^^ sqlite3.OperationalError: no such column: fromX

While debugging, I reviewed the clodius repository in the aggregate.py file and found out that the _bedpe format uses the fromX column. As a result, my beddb file doesn't have this column information.

Direct reference: aggregate.py#L346

However, hg.bed2ddb is expecting the 'fromX' column name.

Supporting Information:

Bed file format

chr1	3062508	3062700	H3K27ac_EA92-97_peak_1	1.50105
chr1	3671399	3672083	H3K27ac_EA92-97_peak_2	2.19707
chr1	4491709	4492214	H3K27ac_EA92-97_peak_3	2.94584
chr1	4493155	4493533	H3K27ac_EA92-97_peak_4	3.21493
chr1	4571589	4571963	H3K27ac_EA92-97_peak_5	1.64992
chr1	4653954	4654123	H3K27ac_EA92-97_peak_6	1.64383

Command to convert bed file to bed2d format:

clodius aggregate bedfile --chromsizes-filename ../CUT-Tag_NIPBL/CUT-Tag_NIPBL-FKBP-EA18.1/mm10.size.txt Regular/H3K27ac_EA92-97_peaks.xls.bed mm10.size.txt was retrieved from this link.