Feature/gcf tree #75
Feature/gcf tree #75
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looks good so far, just some minor things.
Potential refactor idea in the future is to split figuring out the comparable region from calculating the scores, so that there is not a large amount of data being returned in the yield. the workflow is a bit complicated to do this but still.
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Nice, but to optimize performance can you change this to send the numbers directly instead of the entire pair object? See inline comments.
And to keep the order consistent everywhere, let's do:
(
pair_a_id,
pair_b_id,
dist,
jaccard,
adjacency,
dss,
[lcs stuff],
[start and stops after extend],
[reverse],
[alignment mode]
)| distance, jaccard, adjacency, dss = results[idx] | ||
| # for idx, pair in enumerate(task_batch): | ||
| # distance, jaccard, adjacency, dss = results[idx] | ||
| for pair, distance, jaccard, adjacency, dss in results: |
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In another branch I discovered this can be simplified:
for a, b, c, d in some_tuple:
yield (a, b, c, d)is equivalent to
yield from some_tuple| @@ -251,13 +269,13 @@ def calculate_scores_pair( | |||
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| for pair in pairs: | |||
| if pair.region_a.parent_gbk == pair.region_b.parent_gbk: | |||
| results.append((0.0, 1.0, 1.0, 1.0)) | |||
| results.append((pair, 0.0, 1.0, 1.0, 1.0)) | |||
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results.append(0,0, 1.0, 1.0, 1.0, [lcs stuff], [comparable distance starts and stops], [reverse], [alignment mode])
big_scape/network/network.py
Outdated
| @@ -96,7 +96,7 @@ def get_edge( | |||
| if edge is None: | |||
| return None | |||
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| return cast(tuple[int, int, float, float, float, float, str], edge) | |||
| return cast(tuple[int, int, float, float, float, float, str], edge[0:7]) | |||
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While you're here, can you refactor this a bit to select columns in the select_statement on 86 instead of getting everything and returning a slice of the result. e.g.
distance_table = DB.metadata.tables["distance"]
select_columns = (
distance_table.c.region_a_id,
distance_table.c.region_b_id, # note the last comma; this is a tuple
)
select_statement = (
distance_table
.select(columns)something like that. not essential if you want to skip it.
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| Returns: | ||
| Written file containing protein domain alignment | ||
| """ |
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can you add a sneaky TODO: refactor to this docstring? just to indicate that this is not our code 😎
Contains GCF alignment and tree building, as well as highlights of compared region (i.e. protocluster/core).