Having Issues Concatenating Strings into list without \n - Python3 - python-3.x

Question

I am currently having some issues trying to append strings into a new list. However, when I get to the end, my list looks like this:
['MDAALLLNVEGVKKTILHGGTGELPNFITGSRVIFHFRTMKCDEERTVIDDSRQVGQPMH\nIIIGNMFKLEVWEILLTSMRVHEVAEFWCDTIHTGVYPILSRSLRQMAQGKDPTEWHVHT\nCGLANMFAYHTLGYEDLDELQKEPQPLVFVIELLQVDAPSDYQRETWNLSNHEKMKAVPV\nLHGEGNRLFKLGRYEEASSKYQEAIICLRNLQTKEKPWEVQWLKLEKMINTLILNYCQCL\nLKKEEYYEVLEHTSDILRHHPGIVKAYYVRARAHAEVWNEAEAKADLQKVLELEPSMQKA\nVRRELRLLENRMAEKQEEERLRCRNMLSQGATQPPAEPPTEPPAQSSTEPPAEPPTAPSA\nELSAGPPAEPATEPPPSPGHSLQH\n']
I'd like to remove the newlines somehow. I looked at other questions on here and most suggest to use .rstrip however in adding that to my code, I get the same output. What am I missing here? Apologies if this question has been asked.
My input also looks like this(took the first 3 lines):
sp|Q9NZN9|AIPL1_HUMAN Aryl-hydrocarbon-interacting protein-like 1 OS=Homo sapiens OX=9606 GN=AIPL1 PE=1 SV=2
MDAALLLNVEGVKKTILHGGTGELPNFITGSRVIFHFRTMKCDEERTVIDDSRQVGQPMH
IIIGNMFKLEVWEILLTSMRVHEVAEFWCDTIHTGVYPILSRSLRQMAQGKDPTEWHVHT
from sys import argv
protein = argv[1] #fasta file
sequence = '' #string linker
get_line = False #False = not the sequence
Uniprot_ID = []
sequence_list =[]
with open(protein) as pn:
for line in pn:
line.rstrip("\n")
if line.startswith(">") and get_line == False:
sp, u_id, name = line.strip().split('|')
Uniprot_ID.append(u_id)
get_line = True
continue
if line.startswith(">") and get_line == True:
sequence.rstrip('\n')
sequence_list.append(sequence) #add the amino acids onto the list
sequence = '' #resets the str
if line != ">" and get_line == True: #if the first line is not a fasta ID and is it a sequence?
sequence += line
print(sequence_list)

Answer 1

Per documentation, rstrip removes trailing characters – the ones at the end. You probably misunderstood others' use of it to remove \ns because typically those would only appear at the end.
To replace a character with something else in an entire string, use replace instead.
These commands do not modify your string! They return a new string, so if you want to change something 'in' a current string variable, assign the result back to the original variable:
>>> line = 'ab\ncd\n'
>>> line.rstrip('\n')
'ab\ncd' # note: this is the immediate result, which is not assigned back to line
>>> line = line.replace('\n', '')
>>> line
'abcd'

Answer 2

When I asked this question I didn't take my time in looking at documentation & understanding my code. After looking, I realized two things:
my code isn't actually getting what I am interested in.
For the specific question I asked, I could have simply used line.split() to remove the '\n'.
sequence = '' #string linker
get_line = False #False = not the sequence
uni_seq = {}
"""this block of code takes a uniprot FASTA file and creates a
dictionary with the key as the uniprot id and the value as a sequence"""
with open (protein) as pn:
for line in pn:
if line.startswith(">"):
if get_line == False:
sp, u_id, name = line.strip().split('|')
Uniprot_ID.append(u_id)
get_line = True
else:
uni_seq[u_id] = sequence
sequence_list.append(sequence)
sp, u_id, name = line.strip().split('|')
Uniprot_ID.append(u_id)
sequence = ''
else:
if get_line == True:
sequence += line.strip() # removes the newline space
uni_seq[u_id] = sequence
sequence_list.append(sequence)