How to concatenate lines in text file?

Question

So i have been tasked with joining text in a text file but its like whatever i try is not working. I tried split but it needs strings and not arrays and join doesn't help me at all, since i have code that already does that job.

The text file with the words is as follows (filename = demo_fasta_file_2019.fsa):

>sequence_1
GATCGATCGAGATCGATCGAGATCGATCGAGATCGATCGAGATCGATCGAGATCGATCGAGATCGATCGAGATCGATCGA
>sequence_2
GATCGATCGAGATCGATCGAGATCGATCGAGATCGATCGAGATCGATCGAGATCGATCGAGATCGATCGAGATCGATCGA
GATCGATCGAGATCGATCGAGATCGATCGAGATCGATCGAGATCGATCGAGATCGATCGAGATCGATCGAGATCGATCGA
GATCGATCGAGATCGATCGAGATCGATCGAGATCGATCGAGATCGATCGAGATCGATCGAGATCGATCGAGATCGATCGA
GATCGATCGAGATCGATCGAGATCGATCGAGATCGATCGAGATCGATCGAGATCGATCGAGATCGATCGAGATCGATCGA
GATCGATCGAGATCGATCGAGATCGATCGAGATCGATCGAGATCGATCGAGATCGATCGAGATCGATCGAGATCGATCGA
>sequence_3
TTTTGGAAAATTTTGGAAAATTTTGGAAAATTTTGGAAAATTTTGGAAAATTTTGGAAAATTTTGGAAAATTTTGGAAAA
TTTTGGAAAATTTTGGAAAATTTTGGAAAATTTTGGAAAATTTTGGAAAATTTTGGAAAATTTTGGAAAATTTTGGAAAA
>sequence_4
GGTTAACCATGGATC

And the code that i have is as follows:

#def Read_FastA_Names_And_Sequences(filepath):

#############
filepath=str("demo_fasta_file_2019.fsa")
##sequence_names,sequences = Read_FastA_Names_And_Sequences(filepath)
sequence_names=[]
sequences=[]
number_of_sequences=4
#############
textfile = open(filepath, 'r')

sequence = textfile.readlines()

for i in sequence:
    if i.__contains__('>'):
        a=i[1:]
        sequence_names.append(a[:a.__len__()-1])
    i=+1
print(sequence)
#list1 = sequence
#s = "\n"
#s = s.join(list1)
#print(s)
list2 = sequence
words2 = list2.split(">")
print(words2)

So my question is, how can i join only the text without >sequence_1, >sequence_2, >sequence_3, >sequence_4 ?

Answer 1

This can be easily achieved using Biopython , which might also be useful for further tasks on fasta files:

from Bio import SeqIO

concatenated_sequence = ""

fasta_sequences = SeqIO.parse(open(input_file),'fasta')
for fasta in fasta_sequences:
    # id is stored in fasta.id
    # the sequence is stored in fasta.seq, and need to be transformed to str()
    concatenated_sequence +=  str(fasta.seq)

Answer 2

您可以使用生成器表达式过滤不以>开头的行，并使用str.join将它们连接起来：

print(''.join(line for line in open("demo_fasta_file_2019.fsa") if not line.startswith('>')))