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Commit 319c242f authored by Samuel Mondal's avatar Samuel Mondal
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Removal of old function from script

parent 501332df
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1 merge request!38Removal of old function from script
def exon_concatenation_old(
filename: str
) -> list:
"""Concatenates all sequences in fasta file with the same transcript ID header and then outputs a list containing sequence headers (Transcript ID) and sequences that have been concatenated.
Args:
filename: The name of the fasta file having multiple entries for the same transcript ID.
Returns:
A list with headers in the even indices and their corresponding sequences in the odd indices
"""
fa = open(filename,'r')
lines = fa.readlines()
to_write_to_file = []
for x in range(int(len(lines)/2)):
if x == 0:
annotation = lines[0][0:16]
read = lines[1][:-1]
if x >= 1:
if lines[2*x][1:16] == lines[2*(x-1)][1:16]:
read+= lines[(2*x)+1][:-1]
else:
to_write_to_file.append(annotation)
to_write_to_file.append(read)
annotation = lines[2*x][0:16]
read = lines[(2*x)+1][:-1]
to_write_to_file.append(annotation)
to_write_to_file.append(read)
return to_write_to_file
def exon_concatenation(
post_bedtools_fasta: str
) -> list:
......
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