higlass / higlass/higlass-python

Load local bed file

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Descripción

**Description:**

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

```python
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](https://github.com/higlass/clodius/blob/de67e9df2cd296d3681dcf438c0895638de672e4/clodius/cli/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](https://github.com/higlass/clodius/blob/de67e9df2cd296d3681dcf438c0895638de672e4/clodius/cli/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](http://hgdownload.cse.ucsc.edu/goldenpath/mm10/bigZips/mm10.chrom.sizes).

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