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fix DNA valid check and output path #1

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merged 1 commit into from
Feb 14, 2024
Merged

fix DNA valid check and output path #1

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15 changes: 8 additions & 7 deletions correct_primer_positions.py
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Original file line number Diff line number Diff line change
Expand Up @@ -12,15 +12,16 @@
import os.path

def verify(sequence):
'''This code verifies if a sequence is a DNA'''
'''This code verifies if a sequence is a DNA or contains ambiguous bases according to the IUPAC code.'''

# set the input sequence
seq = set(sequence)

# confirm if its elements is equal to the set of valid DNA bases
# Use a union method to ensure the sequence is verified if does not
# contain all the bases
if seq == {"A", "T", "C", "G"}.union(seq):
# Set of valid DNA bases including IUPAC ambiguity codes
valid_bases = {"A", "T", "C", "G", "Y", "R", "S", "W", "K", "M", "B", "D", "H", "V", "N"}

# confirm if its elements are only from the set of valid DNA bases
if seq.issubset(valid_bases):
return "DNA"
else:
return "Invalid DNA sequence"
Expand Down Expand Up @@ -130,8 +131,8 @@ def main(argv):
primer_bed_df.iloc[:,1] = s_pos
primer_bed_df.iloc[:,2] = e_pos

primer_bed_df.to_csv(os.path.dirname(argv[3])+'/'+os.path.basename(argv[3])+'.position.corrected.bed', index=False, sep='\t', header=False)
print("Primer.bed file has been updated. See: \n"+os.path.dirname(argv[3])+'/'+os.path.basename(argv[3])+'.position.corrected.bed')
primer_bed_df.to_csv('./'+os.path.dirname(argv[3])+'/'+os.path.basename(argv[3])+'.position.corrected.bed', index=False, sep='\t', header=False)
print("Primer.bed file has been updated. See: \n./"+os.path.dirname(argv[3])+'/'+os.path.basename(argv[3])+'.position.corrected.bed')
except Exception as e: # pragma: nocover
return "An error has occured: " + str(e)
if __name__ == "__main__": # pragma: nocover
Expand Down