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closes 25 add proper error message when input does not overlap with d…
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…atabase.
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@SeppeDeWinter
SeppeDeWinter committed Oct 2, 2023
1 parent 16d14b9 commit d50c6f4
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8 changes: 8 additions & 0 deletions src/pycistarget/utils.py
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Original file line number Diff line number Diff line change
Expand Up @@ -282,6 +282,14 @@ def target_to_query(target: Union[pr.PyRanges, List[str]],
query_pr=query

join_pr = target_pr.join(query_pr, report_overlap = True)
if len(join_pr) == 0:

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@ghuls

ghuls Oct 4, 2023

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It is probably better to use: if join_pr.empty:

In [18]: a1 = pr.PyRanges(chromosomes="chr1", starts=(1, 5), ends=[3, 149], strands=("+", "-"), int64=True)

In [19]: a2 = pr.PyRanges(chromosomes="chr1", starts=(1001, 1005), ends=[1003, 1149], strands=("+", "-"), int64=True)

In [20]: j = a1.join(a2)

In [21]: j
Out[21]: Empty PyRanges

In [22]: j.empty
Out[22]: True

In [23]: a1.empty
Out[23]: False
raise ValueError(
"""
None of the regions in the bed file overlap with the cistarget database.
Check wether the chromosome names of the input regions are correctly

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@casblaauw

casblaauw Oct 6, 2023

Very small typo, but this should be 'whether' ;)
formatted and that you are using the correct database.
"""
)
join_pr.Overlap_query = join_pr.Overlap/(join_pr.End_b - join_pr.Start_b)
join_pr.Overlap_target = join_pr.Overlap/(join_pr.End - join_pr.Start)
join_pr = join_pr[(join_pr.Overlap_query > fraction_overlap) | (join_pr.Overlap_target > fraction_overlap)]
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