add efoldmine module #251
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add efoldmine module #251
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mtiberti
requested changes
May 23, 2024
mavisp/modules.py
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extra newlines to be removed
mavisp/modules.py
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extra newlines to be removed
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mavisp/modules.py
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| for mut in mutations: | ||
| mut_resn = int(mut[1:-1]) | ||
| row = efoldmine_parsed[efoldmine_parsed['residue_index'] == mut_resn] | ||
| if not row.empty and row['earlyFolding'].iloc[0] > 0.169: | ||
| prev_row = efoldmine_parsed[efoldmine_parsed['residue_index'] == mut_resn - 1] | ||
| next_row = efoldmine_parsed[efoldmine_parsed['residue_index'] == mut_resn + 1] | ||
| if not prev_row.empty and not next_row.empty and prev_row['earlyFolding'].iloc[0] > 0.169 and next_row['earlyFolding'].iloc[0] > 0.169: | ||
| result.append((True, row['earlyFolding'].iloc[0])) | ||
| else: | ||
| result.append((False, row['earlyFolding'].iloc[0])) | ||
| else: | ||
| result.append((False, row['earlyFolding'].iloc[0])) |
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we should change the approach to:
- we precompute on the sequence which residues are part of early folding regions and which aren't by using a sliding window approach
- we then compare it with our mutations to determine which ones are in early folding regions
mtiberti
requested changes
Jun 3, 2024
| result.append((True, row['earlyFolding'].iloc[0])) | ||
| else: | ||
| result.append((False, row['earlyFolding'].iloc[0])) | ||
| row = efoldmine_parsed[efoldmine_parsed['residue_index'] == mut_resn] |
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can we have a sanity check that we get only one row here?
mavisp/modules.py
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| else: | ||
| result.append((False, row['earlyFolding'].iloc[0])) | ||
| row = efoldmine_parsed[efoldmine_parsed['residue_index'] == mut_resn] | ||
| if not row.empty: |
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what does it mean if the row is empty? Should we issue a warning? The value should be well-defined for all residues
…for presence of 'residue_index'and 'earlyFolding' columns and check for not valid or missing early folding scores
mtiberti
previously approved these changes
Jun 6, 2024
mtiberti
approved these changes
Jun 6, 2024
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fixes #250