Foldseek #15
Foldseek #15
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using symlinks.
and convert fs to summary.
to summary
| unique_af_ids.add(file_stub) | ||
| foldseek_reader = get_foldseek_reader(fs_input_file) | ||
| for foldseek_result_as_dict in foldseek_reader: | ||
| result = FoldseekSummary(**foldseek_result_as_dict) |
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You could move this link into foldseek_reader (so that it yields a FoldseekSummary object rather than dict)
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Tried changing that, but it breaks the code. I am still haven't understood how to pass from DictReader to a mapping.
| and int(result.bits) >= DEFAULT_FS_BITS_CUTOFF | ||
| and result.query in unique_af_ids | ||
| ): | ||
| best_hits.add(result.query) |
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So, I am wondering if we should output something for every query (1) or just report what's in the foldseek output (2).
For (1) Best_HIT is there to store queryids that have a foldseek hit. Then I was planning to intersect the two sets and for query_ids where we don't have a Foldseek hit we output 'NO_HIT' or something like that.
I could finish implementing (1) or remove it to keep it like (2).
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Sorry, only just seen this response. My original question was because this set was only keeping track of the unique query names, rather than keeping track of the best match for each query (presumably the foldseek results can have multiple targets for multiple queries).
Use native os.symlink Check if symlink exists before creating it.
with check=True
Conflicts: .gitignore cath_alphaflow/cli.py cath_alphaflow/io_utils.py
Add possibility to do symlinking for a querydb
to cath_alphaflow.models.domains
Remove temp files using shutil, removed unecessary loop Cleaned leftover labels from chopping in click Introduced default for AF_version Introduce safeguard to delete af_tmp_dir only if present, defaults to none.
Add comments Introduce filters
Require target databases and raw files Expand click options on coverage and aligner Remove temporary files
Merge branch 'main' into foldseek
protein_letters_3to1 to avoid warning about deprecation warning
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