Sourcery refactored master branch #2
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| f0 = open(pathTo2+"/Genotype_fasta-headers-rename.log", "a+") # change appropriately how do you want to call log table | ||
| fname=glob.glob(pathTo1+"/assemblerNameGenotype*.fasta") # change appropriately pattern in your file naming | ||
| for i in range (len(fname)): | ||
| vname=fname[i].split("/") | ||
| vname=vname[len(vname)-1] | ||
| idname=re.sub('\.fasta$', '', vname) | ||
| f4 = open(fname[i], "r") | ||
| f5 = open(pathTo2+"/"+str(idname) + "_renamed.fasta", "w") | ||
| line4=f4.readline() | ||
| count=1 | ||
| while line4: | ||
| line4=str.rstrip(line4) | ||
| if '>' in line4: | ||
| line44=">"+str(idname)+"_"+str(count) | ||
| f5.write("%s\n" % (line44)) | ||
| f0.write("%s\t" % (line4)) | ||
| f0.write("%s\n" % (line44)) | ||
| count=count+1 | ||
| else: | ||
| f5.write("%s\n" % (line4)) | ||
| line4 = f4.readline() | ||
| f4.close() | ||
| f5.close() | ||
| f0.close() | ||
| with open(f"{pathTo2}/Genotype_fasta-headers-rename.log", "a+") as f0: | ||
| fname = glob.glob(f"{pathTo1}/assemblerNameGenotype*.fasta") | ||
| for item in fname: | ||
| vname = item.split("/") | ||
| vname=vname[len(vname)-1] | ||
| idname=re.sub('\.fasta$', '', vname) | ||
| with open(item, "r") as f4: | ||
| f5 = open(f"{pathTo2}/{str(idname)}_renamed.fasta", "w") | ||
| line4=f4.readline() | ||
| count=1 | ||
| while line4: | ||
| line4=str.rstrip(line4) | ||
| if '>' in line4: | ||
| line44 = f">{str(idname)}_{str(count)}" | ||
| f5.write("%s\n" % (line44)) | ||
| f0.write("%s\t" % (line4)) | ||
| f0.write("%s\n" % (line44)) | ||
| count=count+1 | ||
| else: | ||
| f5.write("%s\n" % (line4)) | ||
| line4 = f4.readline() | ||
| f5.close() |
Author
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Lines 12-35 refactored with the following changes:
- Use f-string instead of string concatenation [×8] (
use-fstring-for-concatenation) - Use
withwhen opening file to ensure closure [×2] (ensure-file-closed) - Replace index in for loop with direct reference (
for-index-replacement)
This removes the following comments ( why? ):
# change appropriately how do you want to call log table
# change appropriately pattern in your file naming
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| def prRed(skk): print("\033[91m {}\033[00m" .format(skk)) | ||
| def prGreen(skk): print("\033[92m {}\033[00m" .format(skk)) | ||
| def prYellow(skk): print("\033[93m {}\033[00m" .format(skk)) | ||
| def prLightPurple(skk): print("\033[94m {}\033[00m" .format(skk)) | ||
| def prPurple(skk): print("\033[95m {}\033[00m" .format(skk)) | ||
| def prCyan(skk): print("\033[96m {}\033[00m" .format(skk)) | ||
| def prLightGray(skk): print("\033[97m {}\033[00m" .format(skk)) | ||
| def prBlack(skk): print("\033[98m {}\033[00m" .format(skk)) | ||
| def prBlue(skk): print("\033[94m {}\033[00m" .format(skk)) | ||
| def prRed(skk): | ||
| print(f"\033[91m {skk}\033[00m") |
Author
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Function prRed refactored with the following changes:
- Replace call to format with f-string (
use-fstring-for-formatting)
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| def prGreen(skk): print("\033[92m {}\033[00m" .format(skk)) | ||
| def prYellow(skk): print("\033[93m {}\033[00m" .format(skk)) | ||
| def prLightPurple(skk): print("\033[94m {}\033[00m" .format(skk)) | ||
| def prPurple(skk): print("\033[95m {}\033[00m" .format(skk)) | ||
| def prCyan(skk): print("\033[96m {}\033[00m" .format(skk)) | ||
| def prLightGray(skk): print("\033[97m {}\033[00m" .format(skk)) | ||
| def prBlack(skk): print("\033[98m {}\033[00m" .format(skk)) | ||
| def prBlue(skk): print("\033[94m {}\033[00m" .format(skk)) | ||
| def prRed(skk): | ||
| print(f"\033[91m {skk}\033[00m") | ||
| def prGreen(skk): | ||
| print(f"\033[92m {skk}\033[00m") |
Author
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Function prGreen refactored with the following changes:
- Replace call to format with f-string (
use-fstring-for-formatting)
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| def prYellow(skk): print("\033[93m {}\033[00m" .format(skk)) | ||
| def prLightPurple(skk): print("\033[94m {}\033[00m" .format(skk)) | ||
| def prPurple(skk): print("\033[95m {}\033[00m" .format(skk)) | ||
| def prCyan(skk): print("\033[96m {}\033[00m" .format(skk)) | ||
| def prLightGray(skk): print("\033[97m {}\033[00m" .format(skk)) | ||
| def prBlack(skk): print("\033[98m {}\033[00m" .format(skk)) | ||
| def prBlue(skk): print("\033[94m {}\033[00m" .format(skk)) | ||
| def prRed(skk): | ||
| print(f"\033[91m {skk}\033[00m") | ||
| def prGreen(skk): | ||
| print(f"\033[92m {skk}\033[00m") | ||
| def prYellow(skk): | ||
| print(f"\033[93m {skk}\033[00m") |
Author
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Function prYellow refactored with the following changes:
- Replace call to format with f-string (
use-fstring-for-formatting)
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| def prLightPurple(skk): print("\033[94m {}\033[00m" .format(skk)) | ||
| def prPurple(skk): print("\033[95m {}\033[00m" .format(skk)) | ||
| def prCyan(skk): print("\033[96m {}\033[00m" .format(skk)) | ||
| def prLightGray(skk): print("\033[97m {}\033[00m" .format(skk)) | ||
| def prBlack(skk): print("\033[98m {}\033[00m" .format(skk)) | ||
| def prBlue(skk): print("\033[94m {}\033[00m" .format(skk)) | ||
| def prRed(skk): | ||
| print(f"\033[91m {skk}\033[00m") | ||
| def prGreen(skk): | ||
| print(f"\033[92m {skk}\033[00m") | ||
| def prYellow(skk): | ||
| print(f"\033[93m {skk}\033[00m") | ||
| def prLightPurple(skk): | ||
| print(f"\033[94m {skk}\033[00m") |
Author
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Function prLightPurple refactored with the following changes:
- Replace call to format with f-string (
use-fstring-for-formatting)
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| def prPurple(skk): print("\033[95m {}\033[00m" .format(skk)) | ||
| def prCyan(skk): print("\033[96m {}\033[00m" .format(skk)) | ||
| def prLightGray(skk): print("\033[97m {}\033[00m" .format(skk)) | ||
| def prBlack(skk): print("\033[98m {}\033[00m" .format(skk)) | ||
| def prBlue(skk): print("\033[94m {}\033[00m" .format(skk)) | ||
| def prRed(skk): | ||
| print(f"\033[91m {skk}\033[00m") | ||
| def prGreen(skk): | ||
| print(f"\033[92m {skk}\033[00m") | ||
| def prYellow(skk): | ||
| print(f"\033[93m {skk}\033[00m") | ||
| def prLightPurple(skk): | ||
| print(f"\033[94m {skk}\033[00m") | ||
| def prPurple(skk): | ||
| print(f"\033[95m {skk}\033[00m") |
Author
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Function prPurple refactored with the following changes:
- Replace call to format with f-string (
use-fstring-for-formatting)
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| def prCyan(skk): print("\033[96m {}\033[00m" .format(skk)) | ||
| def prLightGray(skk): print("\033[97m {}\033[00m" .format(skk)) | ||
| def prBlack(skk): print("\033[98m {}\033[00m" .format(skk)) | ||
| def prBlue(skk): print("\033[94m {}\033[00m" .format(skk)) | ||
| def prRed(skk): | ||
| print(f"\033[91m {skk}\033[00m") | ||
| def prGreen(skk): | ||
| print(f"\033[92m {skk}\033[00m") | ||
| def prYellow(skk): | ||
| print(f"\033[93m {skk}\033[00m") | ||
| def prLightPurple(skk): | ||
| print(f"\033[94m {skk}\033[00m") | ||
| def prPurple(skk): | ||
| print(f"\033[95m {skk}\033[00m") | ||
| def prCyan(skk): | ||
| print(f"\033[96m {skk}\033[00m") |
Author
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Function prCyan refactored with the following changes:
- Replace call to format with f-string (
use-fstring-for-formatting)
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| def prLightGray(skk): print("\033[97m {}\033[00m" .format(skk)) | ||
| def prBlack(skk): print("\033[98m {}\033[00m" .format(skk)) | ||
| def prBlue(skk): print("\033[94m {}\033[00m" .format(skk)) | ||
| def prRed(skk): | ||
| print(f"\033[91m {skk}\033[00m") | ||
| def prGreen(skk): | ||
| print(f"\033[92m {skk}\033[00m") | ||
| def prYellow(skk): | ||
| print(f"\033[93m {skk}\033[00m") | ||
| def prLightPurple(skk): | ||
| print(f"\033[94m {skk}\033[00m") | ||
| def prPurple(skk): | ||
| print(f"\033[95m {skk}\033[00m") | ||
| def prCyan(skk): | ||
| print(f"\033[96m {skk}\033[00m") | ||
| def prLightGray(skk): | ||
| print(f"\033[97m {skk}\033[00m") |
Author
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Function prLightGray refactored with the following changes:
- Replace call to format with f-string (
use-fstring-for-formatting)
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| def prBlack(skk): print("\033[98m {}\033[00m" .format(skk)) | ||
| def prBlue(skk): print("\033[94m {}\033[00m" .format(skk)) | ||
| def prRed(skk): | ||
| print(f"\033[91m {skk}\033[00m") | ||
| def prGreen(skk): | ||
| print(f"\033[92m {skk}\033[00m") | ||
| def prYellow(skk): | ||
| print(f"\033[93m {skk}\033[00m") | ||
| def prLightPurple(skk): | ||
| print(f"\033[94m {skk}\033[00m") | ||
| def prPurple(skk): | ||
| print(f"\033[95m {skk}\033[00m") | ||
| def prCyan(skk): | ||
| print(f"\033[96m {skk}\033[00m") | ||
| def prLightGray(skk): | ||
| print(f"\033[97m {skk}\033[00m") | ||
| def prBlack(skk): | ||
| print(f"\033[98m {skk}\033[00m") |
Author
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Function prBlack refactored with the following changes:
- Replace call to format with f-string (
use-fstring-for-formatting)
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| def prBlue(skk): print("\033[94m {}\033[00m" .format(skk)) | ||
| def prRed(skk): | ||
| print(f"\033[91m {skk}\033[00m") | ||
| def prGreen(skk): | ||
| print(f"\033[92m {skk}\033[00m") | ||
| def prYellow(skk): | ||
| print(f"\033[93m {skk}\033[00m") | ||
| def prLightPurple(skk): | ||
| print(f"\033[94m {skk}\033[00m") | ||
| def prPurple(skk): | ||
| print(f"\033[95m {skk}\033[00m") | ||
| def prCyan(skk): | ||
| print(f"\033[96m {skk}\033[00m") | ||
| def prLightGray(skk): | ||
| print(f"\033[97m {skk}\033[00m") | ||
| def prBlack(skk): | ||
| print(f"\033[98m {skk}\033[00m") | ||
| def prBlue(skk): | ||
| print(f"\033[94m {skk}\033[00m") |
Author
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Function prBlue refactored with the following changes:
- Replace call to format with f-string (
use-fstring-for-formatting)
Author
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PR Type: Refactoring
Summary of PR: This PR introduces refactoring changes to two Python scripts, aiming to improve code readability and maintainability. It applies context management for file operations and updates string formatting to use f-strings.
General PR suggestions
- Ensure that all file operations are performed using context managers (
withstatements) to guarantee that files are properly closed after their operations are complete, especially in the case of exceptions. - Precompile regular expressions that are used within loops to enhance performance, as the pattern does not change during iterations.
- When using f-strings, avoid unnecessary calls to
str()for variables, as f-strings automatically handle the conversion to strings. - Consider using built-in path manipulation functions like
os.path.basenamefor extracting file names from paths to make the code more robust and platform-independent. - Review the consistency of error handling and resource management across the codebase to ensure that the refactoring maintains or improves the current standards.
Your trial expires on December 19, 2023. Please email [email protected] to continue using Sourcery ✨
| vname=vname[len(vname)-1] | ||
| idname=re.sub('\.fasta$', '', vname) | ||
| with open(item, "r") as f4: | ||
| f5 = open(f"{pathTo2}/{str(idname)}_renamed.fasta", "w") |
Author
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issue (llm): The file opened as 'f5' should be managed using a 'with' statement to ensure it is properly closed even if an error occurs.
Suggested change
| f5 = open(f"{pathTo2}/{str(idname)}_renamed.fasta", "w") | |
| + with open(f"{pathTo2}/{str(idname)}_renamed.fasta", "w") as f5: |
| for item in fname: | ||
| vname = item.split("/") | ||
| vname=vname[len(vname)-1] | ||
| idname=re.sub('\.fasta$', '', vname) |
Author
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suggestion (llm): Consider precompiling the regular expression outside of the loop for better performance, as it does not change per iteration.
Suggested change
| idname=re.sub('\.fasta$', '', vname) | |
| Outside the loop: pattern = re.compile('\\.fasta$') |
| while line4: | ||
| line4=str.rstrip(line4) | ||
| if '>' in line4: | ||
| line44 = f">{str(idname)}_{str(count)}" |
Author
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nitpick (llm): The 'str' function is redundant when using formatted string literals (f-strings).
Suggested change
| line44 = f">{str(idname)}_{str(count)}" | |
| + line44 = f">{idname}_{count}" |
| fname = glob.glob(f"{pathTo1}/assemblerNameGenotype*.fasta") | ||
| for item in fname: | ||
| vname = item.split("/") | ||
| vname=vname[len(vname)-1] |
Author
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suggestion (llm): Using 'os.path.basename' would be a more robust method for extracting the file name from a path.
Suggested change
| vname=vname[len(vname)-1] | |
| + vname = os.path.basename(item) |
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Branch
masterrefactored by Sourcery.If you're happy with these changes, merge this Pull Request using the Squash and merge strategy.
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