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Sourcery refactored master branch #2

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46 changes: 22 additions & 24 deletions scripts/S02_3.2.4_uniqueIDs.py
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Original file line number Diff line number Diff line change
Expand Up @@ -9,27 +9,25 @@
os.makedirs(pathTo2)
except OSError:
pass
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]
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@sourcery-ai sourcery-ai Bot Dec 5, 2023

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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)

idname=re.sub('\.fasta$', '', vname)
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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$', '', vname)
Outside the loop: pattern = re.compile('\\.fasta$')

with open(item, "r") as f4:
f5 = open(f"{pathTo2}/{str(idname)}_renamed.fasta", "w")
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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:

line4=f4.readline()
count=1
while line4:
line4=str.rstrip(line4)
if '>' in line4:
line44 = f">{str(idname)}_{str(count)}"
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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}"

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()
Comment on lines -12 to +33
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Lines 12-35 refactored with the following changes:

This removes the following comments ( why? ):

# change appropriately how do you want to call log table
# change appropriately pattern in your file naming

27 changes: 18 additions & 9 deletions scripts/S03_3.3.9_MSA.py
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Original file line number Diff line number Diff line change
Expand Up @@ -11,15 +11,24 @@
import numbers

# ref: https://www.geeksforgeeks.org/print-colors-python-terminal/
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")
Comment on lines -14 to +15
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Function prRed refactored with the following changes:

def prGreen(skk):
print(f"\033[92m {skk}\033[00m")
Comment on lines -15 to +17
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Function prGreen refactored with the following changes:

def prYellow(skk):
print(f"\033[93m {skk}\033[00m")
Comment on lines -16 to +19
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Function prYellow refactored with the following changes:

def prLightPurple(skk):
print(f"\033[94m {skk}\033[00m")
Comment on lines -17 to +21
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Function prLightPurple refactored with the following changes:

def prPurple(skk):
print(f"\033[95m {skk}\033[00m")
Comment on lines -18 to +23
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Function prPurple refactored with the following changes:

def prCyan(skk):
print(f"\033[96m {skk}\033[00m")
Comment on lines -19 to +25
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Function prCyan refactored with the following changes:

def prLightGray(skk):
print(f"\033[97m {skk}\033[00m")
Comment on lines -20 to +27
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Function prLightGray refactored with the following changes:

def prBlack(skk):
print(f"\033[98m {skk}\033[00m")
Comment on lines -21 to +29
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Function prBlack refactored with the following changes:

def prBlue(skk):
print(f"\033[94m {skk}\033[00m")
Comment on lines -22 to +31
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Function prBlue refactored with the following changes:


# from BioPython
def read_fasta(fp):
Expand Down