Replace a FASTA sequence according to its id with gaps

Question

[yoshikal]

I have 2000 fasta sequence in a file, like this:

 >T1        
AQSFDRATVFEARRAGYQRESRVALGKSTGVLEWHVFHVWAPRETTILVETLSQIECSGKGIADRRQENPLTI------ATAI--TSQLLELVDIVIMDFKAITQFFL     
>T484      
AQSFDRATVFEARRAGYQREARVALGKSTGKLEWQVFHVWAPRETTILVETLSQLECSGKGIADRRQENPLKI------ATAI--TSQLLELVDIVIMDFKAITQFFL     
>T582      
AQSFDRATVFEKRRAGYQREARVALGKSTGKLEWQVFHVWAPRETTILVETLSQLECSGKGIADRRQENPLKI------ATAI--TSQLLELVDIVIMDFKAITQFFL     
>T1424     
AQSFDRATVFEKRRAGYQLEARVALGKSTGKLEWQVFHVWAPRETTILVETLSQLECSGKGIANRRQENPLKI------ATAI--TSQLLELVDILIMDFKAITQFFL     
>T1552     
AQSFDRATIFEKRRAGYQIEARVALGKSTGKLEWQVYHAWAPRETTILVETLSQLENAGKGVANRRHENPLKI------ATAI--TSQLLELVDILMMDFKAITQFFL     
.
.
.

I randomly draw f (f = 2) sequence from N (N = 2000).

For example if I have drawn 120 and 1500, I get the Fasta sequence:

> T1424
AQSFDRATVFEKRRAGYQLEARVALGKSTGKLEWQVFHVWAPRETTILVETLSQLECSGKGIANRRQENPLKI ------ ATAI - TSQLLELVDILIMDFKAITQFFL
> T1552
AQSFDRATIFEKRRAGYQIEARVALGKSTGKLEWQVYHAWAPRETTILVETLSQLENAGKGVANRRHENPLKI ------ ATAI - TSQLLELVDILMMDFKAITQFFL

What I want to do is replace these sequences with gaps of length 55:

> T1424
-----------------------------------------------------------------------------------------------------------------------------
> T1552
-----------------------------------------------------------------------------------------------------------------------------

I tried with this code:

from Bio import SeqIO 
from random import *

records = list(SeqIO.parse("fichier1.txt", "fasta")) 
#print(records[0].id)  # first record
#print(records[0].seq)

N=len(records) #2000 

f=2 

l=[] 

for i in range(f):
    x=randint(1, N)
    l.append(x)

d={} 
for i2 in l:
    print(records[i2].id,records[i2].seq)
    d[str(records[i2].id)]=str(records[i2].seq)
    with open("fichier1.txt") as fichier, open("newfile.txt", "w") as newfile:
        texte = fichier.read()

        new_text += texte.replace(str(records[i2].seq), "---------------------------------------")
        nouveaufichier.write(new_text)

print(d)

What does not work because sometimes there can be the same sequence in the file but with a different identifier.

From the ID and the corresponding sequence, I would like to change the sequence to introduce gaps.

[Ram]

Switch to BioPython and replace the sequence based on the identifier. This seems to be a very specific "solve my code problem" question. What is the purpose of this task?

EDIT: Just saw that you're already using BioPython.

Answer 1

[Joe]

As easy as:

Code

from Bio import SeqIO

seqs = list(SeqIO.parse("seqs.fa", "fasta"))

for rec in seqs:
    if rec.id == "chimpanze":
        rec.seq = "-"*len(rec.seq)
    print(">{}\n{}".formatrec.id,rec.seq))

Input data

>mutant
GTTGGGAGGCTATGTGTTGACTGGAAGGACGTCCTGTCGGGTGGCGAGAAGCAGAGAATC
>gorrila
GTTGGGAGGCTATGTGTGACTGGAAGGACATCCTGTCGGGTGGCGAGAAGCAGAGAATC
>chimpanze
GTTGGGAGGCTGTGTGTGACTGGAAGGACGTCCTGTCGGGTGGCGAGAAGCAGAGAATC
>human
GTTGGGAGGCTATGTGTGACTGGAAGGACGTCCTGTCGGGTGGCGAGAAGCAGAGAATC
>olive
GTTGGGAGGCTATGTGTGACTGGAAGGACGTCCTGTCGGGTGGCGAGAAGCAAAGAATC

Run code

>mutant
GTTGGGAGGCTATGTGTTGACTGGAAGGACGTCCTGTCGGGTGGCGAGAAGCAGAGAATC
>gorrila
GTTGGGAGGCTATGTGTGACTGGAAGGACATCCTGTCGGGTGGCGAGAAGCAGAGAATC
>chimpanze
-----------------------------------------------------------
>human
GTTGGGAGGCTATGTGTGACTGGAAGGACGTCCTGTCGGGTGGCGAGAAGCAGAGAATC
>olive
GTTGGGAGGCTATGTGTGACTGGAAGGACGTCCTGTCGGGTGGCGAGAAGCAAAGAATC

You can probably add the logic for your random n choose k bit.