Sourcery refactored master branch #2
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| f1 = open(param1, "r") | ||
| a1 = f1.readlines() | ||
| f2 = open(param2, "r") | ||
| a2 = f2.readlines() | ||
| f1.close() | ||
| with open(param1, "r") as f1: | ||
| a1 = f1.readlines() | ||
| f2 = open(param2, "r") | ||
| a2 = f2.readlines() | ||
| f2.close() | ||
| record_ids1 = list() | ||
| record_ids2 = list() | ||
| record_ids1 = [] | ||
| record_ids2 = [] | ||
| record_ids1 = list(map(str.strip, a1)) | ||
| record_ids2 = list(map(str.strip, a2)) | ||
|
|
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| with open(param4, 'w') as outFile: | ||
| for record in SeqIO.parse(param3, 'fasta'): | ||
| # print(record.id) | ||
| if record.id not in record_ids1: | ||
| SeqIO.write(record, outFile, 'fasta') | ||
| else: | ||
| if record.id in record_ids1: |
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Lines 13-41 refactored with the following changes:
- Use
withwhen opening file to ensure closure (ensure-file-closed) - Replace
list()with[][×2] (list-literal) - Swap if/else to remove empty if body (
remove-pass-body) - Hoist repeated code outside conditional statement (
hoist-statement-from-if)
This removes the following comments ( why? ):
# print(record.description)
# print(record)
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PR Type: Refactoring
Summary of PR: This PR introduces refactoring changes to a script that processes FASTA files, aiming to improve code readability and maintainability by using context managers for file operations and simplifying list initializations.
General PR suggestions
- Ensure that all file operations are consistently using context managers to guarantee that files are properly closed even if errors occur.
- Verify the logic changes related to the handling of record IDs are intentional and preserve the desired functionality of the script.
- Remove any redundant code, such as unnecessary variable reassignments or setting a variable to None before immediately reassigning it.
- Confirm that the changes in the behavior of writing records to the output file are correct and align with the expected outcomes of the script.
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| f1.close() | ||
| with open(param1, "r") as f1: | ||
| a1 = f1.readlines() | ||
| f2 = open(param2, "r") |
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issue (llm): The file 'param2' is opened without a context manager, which may lead to the file not being closed if an error occurs before the close call. It's recommended to use a 'with' statement for opening files to ensure they are properly closed.
| f2 = open(param2, "r") | |
| + with open(param2, "r") as f2: |
| f2.close() | ||
| record_ids1 = list() | ||
| record_ids2 = list() | ||
| record_ids1 = [] |
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nitpick (llm): The reassignment of 'record_ids1' to an empty list is redundant since it's immediately re-populated with the stripped lines from 'a1'. The same applies to 'record_ids2'.
| record_ids1 = [] | |
| -record_ids1 = [] |
| if record.id not in record_ids1: | ||
| SeqIO.write(record, outFile, 'fasta') | ||
| else: | ||
| if record.id in record_ids1: |
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suggestion (llm): The logic has been inverted here, which changes the behavior of the script. Previously, records not in 'record_ids1' were written to the output file. Now, only records in 'record_ids1' are being modified and written. Ensure this is the intended behavior.
| if record.id in record_ids1: | |
| - if record.id not in record_ids1: |
| # print(record.description) | ||
| # print(record) | ||
| SeqIO.write(record, outFile, 'fasta') | ||
| SeqIO.write(record, outFile, 'fasta') |
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thought (llm): The 'SeqIO.write' function is now called outside of the conditional block, which means it will execute for every record. This is a change in behavior from the original code, where it was only called if the record ID was not in 'record_ids1'. Confirm that this change is intentional and that it won't cause any undesired side effects.
Branch
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