Sourcery refactored master branch #10
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| test = True | ||
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| raw_sequence = reference_sequence.replace("-", "") | ||
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| length = len(raw_sequence) | ||
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| for position in sequence_feature_positions: | ||
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| if position > length: | ||
| test = False | ||
| test = all(position <= length for position in sequence_feature_positions) |
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Function confirm_seq_feature_in_ref refactored with the following changes:
- Use any() instead of for loop (
use-any) - Invert any/all to simplify comparisons (
invert-any-all)
| test = True | ||
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| # check that all positions are in sequence | ||
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| if all(i <= seq_length for i in positions): | ||
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| for position in positions: | ||
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| if reference_sequence[position - 1] == "-": | ||
| test = False | ||
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| return test | ||
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| else: | ||
| if any(i > seq_length for i in positions): | ||
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| return False | ||
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| return all(reference_sequence[position - 1] != "-" for position in positions) |
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Function check_reference_positions refactored with the following changes:
- Swap if/else branches (
swap-if-else-branches) - Invert any/all to simplify comparisons (
invert-any-all) - Remove unnecessary else after guard condition (
remove-unnecessary-else) - Use any() instead of for loop (
use-any) - Inline variable that is immediately returned (
inline-immediately-returned-variable)
| vt_id = "VT-%03d" % (i,) | ||
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| return vt_id | ||
| return "VT-%03d" % (i,) |
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Function vt_count refactored with the following changes:
- Inline variable that is immediately returned (
inline-immediately-returned-variable)
| df_selected = df[df['VT'].isin(vts_to_select)] | ||
| return df_selected | ||
| return df[df['VT'].isin(vts_to_select)] |
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Function select_var_types_to_plot refactored with the following changes:
- Inline variable that is immediately returned (
inline-immediately-returned-variable)
| sequence_feature_temp = ''.join([sequence[index] for index in vt_positions]) | ||
| sequence_feature_temp = ''.join(sequence[index] for index in vt_positions) |
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Function compute_variant_types refactored with the following changes:
- Replace unneeded comprehension with generator (
comprehension-to-generator)
Sourcery Code Quality Report✅ Merging this PR will increase code quality in the affected files by 0.03%.
Here are some functions in these files that still need a tune-up:
Legend and ExplanationThe emojis denote the absolute quality of the code:
The 👍 and 👎 indicate whether the quality has improved or gotten worse with this pull request. Please see our documentation here for details on how these metrics are calculated. We are actively working on this report - lots more documentation and extra metrics to come! Help us improve this quality report! |
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