Reading a file in python and sending contents to two different variables

Question

I am trying to read the file and put the two sequences (ie Spar and Sbay) into two variables seq1 and seq2. So far I only know how to pass everything to one sequence by using this code.

filename = 'AQY2.fasta'
readfile = open(filename, 'r')
seq1 = ''
seq2 = ''
for line in readfile.readlines():
     if ( line[0] == '>' ):
         header = line[1:]
     else:
         seq1 = seq1 + line

readfile.close() 
print(seq1)

Can anyone help me to read the two sequences into seq1 and seq2?

The image contains two sequences

I'm not sure this is what you mean, but you can add `seq2 = seq2 + line` just below `seq1 = seq1 + line` (with the same indentation, that's important!). You might also want to print `seq2` as well, to check it's ok, so add `print(seq2)` below `print(seq1)`. Finally, you should probably handle the file with `with`, but that's maybe for another time. — Orius, Feb 13 '22 at 04:02
Please paste text not images of text or links to images of text — Mark Tolonen, Feb 13 '22 at 04:05
FYI, there are libraries for parsing FASTA files in Python, you don't have to code it yourself. — Barmar, Feb 13 '22 at 04:08
To follow up on what Barmar said, check out Biopython or [pyfaidx](https://github.com/mdshw5/pyfaidx). There's a lot of examples with Biopython in their documentation and at Biostars.org. Both of those separate each sequence record/entry without you needing to code it. — Wayne, Feb 13 '22 at 04:36

Udesh · Answer 1 · 2022-02-13T04:29:53.323

I am using two vaiable matchSpar and matchSbay to read the file and seq a dictionary to store the corresponding result.

if matchSpar is set to True then lines added append to '>Spar' key in seq dictionary if matchSbay is set to True then lines added append to '>Sbay' key in seq dictionary.

filename = 'AQY2.fasta'
readfile = open(filename, 'r')
seq= {
        '>Spar' : "",
        '>Sbay' : ""
        }
matchSpar = False
matchSbay = False
lines = []
for line in readfile.readlines():
    line = line.replace('\n', '')
    if line == '>Spar':
        matchSpar = True
        matchSbay = False

    if line == '>Sbay':
        matchSpar = False
        matchSbay = True

    if matchSpar :
        seq[">Spar"] += line+"\n"
    if matchSbay :
        seq[">Sbay"] += line+"\n"

readfile.close() 

print(seq['>Spar'])
print(seq['>Sbay'])

Its recommended to use with keyword to file handling in python :

filename = 'AQY2.fasta'
seq= {
        '>Spar' : "",
        '>Sbay' : ""
        }
matchSpar = False
matchSbay = False

with open(filename, 'r') as readfile:
 for line in readfile.readlines():
    if line == '>Spar\n':
        matchSpar = True
        matchSbay = False

    if line == '>Sbay\n':
        matchSpar = False
        matchSbay = True

    if matchSpar :
        seq[">Spar"] += line
    if matchSbay :
        seq[">Sbay"] += line

print(seq['>Spar'])
print(seq['>Sbay'])

Reading a file in python and sending contents to two different variables

1 Answers1