Update annotate.py to fix a TypeError with annotations.py #29
Conversation
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
Fixed error regarding unhashable SeqFeatures.
Error was as follows:
```bash
warnings.warn(
Traceback (most recent call last):
File "/projects/kr58/software/conda_envs/bactabolize_v1.0.1/bin/bactabolize", line 10, in <module>
sys.exit(entry())
File "/projects/kr58/software/conda_envs/bactabolize_v1.0.1/lib/python3.9/site-packages/bactabolize/main.py", line 23, in entry
run_draft_model(config)
File "/projects/kr58/software/conda_envs/bactabolize_v1.0.1/lib/python3.9/site-packages/bactabolize/main.py", line 49, in run_draft_model
annotate.run(config.assembly_fp, config.assembly_genbank_fp)
File "/projects/kr58/software/conda_envs/bactabolize_v1.0.1/lib/python3.9/site-packages/bactabolize/annotate.py", line 50, in run
match_existing_orfs_updated_annotations(output_fp, assembly_genbank_fp)
File "/projects/kr58/software/conda_envs/bactabolize_v1.0.1/lib/python3.9/site-packages/bactabolize/annotate.py", line 128, in match_existing_orfs_updated_annotations
features_matched = discover_overlaps(positions, overlap_min)
File "/projects/kr58/software/conda_envs/bactabolize_v1.0.1/lib/python3.9/site-packages/bactabolize/annotate.py", line 202, in discover_overlaps
if (feature_new, feature_existing) in features_matched:
TypeError: unhashable type: 'SeqFeature'
```
Sign up for free
to join this conversation on GitHub.
Already have an account?
Sign in to comment
Add this suggestion to a batch that can be applied as a single commit.
This suggestion is invalid because no changes were made to the code.
Suggestions cannot be applied while the pull request is closed.
Suggestions cannot be applied while viewing a subset of changes.
Only one suggestion per line can be applied in a batch.
Add this suggestion to a batch that can be applied as a single commit.
Applying suggestions on deleted lines is not supported.
You must change the existing code in this line in order to create a valid suggestion.
Outdated suggestions cannot be applied.
This suggestion has been applied or marked resolved.
Suggestions cannot be applied from pending reviews.
Suggestions cannot be applied on multi-line comments.
Suggestions cannot be applied while the pull request is queued to merge.
Suggestion cannot be applied right now. Please check back later.
Fixed error regarding unhashable SeqFeatures.
Error was as follows:
Would you be able to test this @helena-bethany ?