Comments (8)
fairliereese
commented on September 27, 2024
1
I've been having issues like this as well. Rolling back to 0.0.127 seems to work for me to solve some issues.
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endrebak
commented on September 27, 2024
I'll look into it soon. Thanks!
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fairliereese
commented on September 27, 2024
To give some more detail, I'm having issues when trying to use join on two stranded PyRanges objects. I suspect something under the hood is causing this issue.
Pdb) bed1.head()
+--------------+-----------+-----------+--------------+----------------------+----------------------------+------------+-------+
| Chromosome | Start | End | Strand | Name | source | novelty | +3 |
| (category) | (int64) | (int64) | (category) | (object) | (object) | (object) | ... |
|--------------+-----------+-----------+--------------+----------------------+----------------------------+------------+-------|
| chr1 | 75945539 | 75945646 | + | ENCODEMG000099158_1 | lapa | Novel | ... |
| chr1 | 85973317 | 85973418 | + | ENCODEMG000101206_1 | lapa,polya_atlas | Novel | ... |
| chr1 | 166166458 | 166166560 | + | ENSMUSG00000000544_1 | vM25,vM21,lapa,polya_atlas | Known | ... |
| chr1 | 166154085 | 166154186 | + | ENSMUSG00000000544_2 | vM25,vM21,lapa,polya_atlas | Known | ... |
| chr1 | 166157478 | 166157579 | + | ENSMUSG00000000544_3 | vM25,vM21 | Known | ... |
| chr1 | 36528186 | 36528287 | + | ENSMUSG00000001138_1 | vM25,vM21,lapa,polya_atlas | Known | ... |
| chr1 | 36519523 | 36519624 | + | ENSMUSG00000001138_2 | vM25,vM21,lapa | Known | ... |
| chr1 | 36520384 | 36520485 | + | ENSMUSG00000001138_3 | vM25,vM21,lapa | Known | ... |
+--------------+-----------+-----------+--------------+----------------------+----------------------------+------------+-------+
Stranded PyRanges object has 8 rows and 10 columns from 1 chromosomes.
For printing, the PyRanges was sorted on Chromosome and Strand.
3 hidden columns: gene_id, tes, id
Pdb) bed2.head()
+--------------+-----------+-----------+--------------+----------------------+------------+--------------------+-----------+-------+
| Chromosome | Start | End | Strand | Name | source | gene_id | tes | +2 |
| (category) | (int64) | (int64) | (category) | (object) | (object) | (object) | (int64) | ... |
|--------------+-----------+-----------+--------------+----------------------+------------+--------------------+-----------+-------|
| chr1 | 36527164 | 36527265 | + | ENSMUSG00000001138_1 | s2 | ENSMUSG00000001138 | 1 | ... |
| chr1 | 36528186 | 36528287 | + | ENSMUSG00000001138_2 | s2 | ENSMUSG00000001138 | 2 | ... |
| chr1 | 39545328 | 39545429 | + | ENSMUSG00000003135_1 | s2 | ENSMUSG00000003135 | 1 | ... |
| chr1 | 39546822 | 39546933 | + | ENSMUSG00000003135_2 | s2 | ENSMUSG00000003135 | 2 | ... |
| chr1 | 172130960 | 172131061 | + | ENSMUSG00000003464_1 | s2 | ENSMUSG00000003464 | 1 | ... |
| chr1 | 172135229 | 172135333 | + | ENSMUSG00000003464_2 | s2 | ENSMUSG00000003464 | 2 | ... |
| chr1 | 172135725 | 172135826 | + | ENSMUSG00000003464_3 | s2 | ENSMUSG00000003464 | 3 | ... |
| chr1 | 172136439 | 172136540 | + | ENSMUSG00000003464_4 | s2 | ENSMUSG00000003464 | 4 | ... |
+--------------+-----------+-----------+--------------+----------------------+------------+--------------------+-----------+-------+
Stranded PyRanges object has 8 rows and 10 columns from 1 chromosomes.
For printing, the PyRanges was sorted on Chromosome and Strand.
2 hidden columns: novelty, id
PyRanges join command:
temp_joined = bed1.join(bed2,
strandedness='same',
suffix='_new',
slack=slack,
how='left')Error:
AssertionError: Can only do stranded operations when both PyRanges contain strand info
Hopefully this extra detail helps!
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fairliereese
commented on September 27, 2024
Okay I've actually taken a look at what is actually going on here. Looks like when PyRanges objects are initialized, possibly from older PyRanges objects that were already read in, or from PyRanges objects that have been converted to pandas DataFrames and back, this condition is satisfied because the Strand PyRanges column is by default given a Categorical dtype with categories '.', '+', and '-':
(From check_strandedness() in methods/init.py
if str(df.Strand.dtype) == "category" and (set(df.Strand.cat.categories) - set("+-")):
contains_more_than_plus_minus_in_strand_col = TrueI'm not going to try to submit a PR to change this because I want to make sure the bug can be addressed in a way that's consistent with how the rest of the package behaves, but I will probably just comment out the above code in my fork so that I can get on with my life. Hopefully this also helps!
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endrebak
commented on September 27, 2024
Thanks. I have Friday in two weeks off and will look at it then.
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endrebak
commented on September 27, 2024
Looking at it now :) Perhaps related to the fix for
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endrebak
commented on September 27, 2024
I am unable to reproduce. Can you show me a reproducible example? Perhaps by sharing the data you use? :D
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endrebak
commented on September 27, 2024
The reported issue might also be different from yours @fairliereese Would you mind creating a new issue and I'll have a look?
Btw: I started a hypothesis run that generated 10,000 example triplets of PyRanges and tried joining them in a chain with how="left" and I did not get your reported error once.
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Related Issues (20)
- Additional how-to-pages HOT 1
- Stable non-conflicting interface: v.1.0.0 HOT 2
- Return overlap between PyRanges objects, keeping columns from both? HOT 6
- subtract does not respect strandedness default
- when using .coverage: AttributeError: module 'numpy' has no attribute 'long' HOT 1
- count_overlaps causes overflow errors when number of reads are large HOT 1
- ModuleNotFoundError: No module named 'pyfaidx' HOT 2
- count_overlaps documentation says it supports nb_cpu but it is not implemented HOT 4
- overlap default strandedness argument incorrectly documented
- pr.get_sequence may not be working? HOT 4
- PyRanges.intersect - "invert=True" kwarg behavior HOT 1
- pyranges.cluster() Exception: Starts/Ends not int64 or int32: int64 HOT 9
- PyRanges read_bed produces wrong number of chromosomes when cast to categorical HOT 1
- ResourceWarning: files opened in readers.read_bed are never closed HOT 3
- SyntaxError: invalid syntax for L131 in names.py HOT 12
- `join` method exits unexpectedly HOT 4
- `np.bool` error in gr.head()
- Add importable constants for Chromosome, Start, End, etc. HOT 2
- Can only do stranded operations when both PyRanges contain strand info HOT 2
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