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Fasta file substitution

I have a batch protein FASTA file. I wan to create output file with position for each amino acid with possible mutation (remaining 19 aa) in tab-delimited file.

e.g. sequence

>sp|Q6NUK1|SCMC1_HUMAN Calcium-binding mitochondrial carrier protein
MLRWLRDFVLPTAACQDAEQPTRYETLFQALDRNGDGVVDIGELQEGLRNLGIPLGQDAE
>sp|Q6KCM7|SCMC2_HUMAN Calcium-binding mitochondrial carrier protein
MLCLCLYVPVIGEAQTEFQYFESKGLPAELKSIFKLSVFIPSQEFSTYRQWKQKIVQAGD

Output file; (Protein ID, position, amino acid, substitution(19). It will be given for all protein(around 4000)

Q6NUK1    1    M    A
Q6NUK1    1    M    R
Q6NUK1    1    M    N
Q6NUK1    1    M    D
Q6NUK1    1    M    C
Q6NUK1    1    M    Q
Q6NUK1    1    M    E
Q6NUK1    1    M    G
Q6NUK1    1    M    H
Q6NUK1    1    M    I
Q6NUK1    1    M    L
Q6NUK1    1    M    K
Q6NUK1    1    M    F
Q6NUK1    1    M    P
Q6NUK1    1    M    S
Q6NUK1    1    M    T
Q6NUK1    1    M    W
Q6NUK1    1    M    Y
Q6NUK1    1    M    V
snp sequence
• 2,404 views • link
updated by Ram Ram • written by max1415r • max1415r

1 answer

It's very easy using BioPython:

from Bio import SeqIO
from Bio.Alphabet import IUPAC

for seq_record in SeqIO.parse("example.fasta", "fasta"):
    record_name=seq_record.id.split("|")[1]
    for I in range(0,len(seq_record.seq)):
        letter=seq_record.seq[i]
        position=i+1
        IUPAC_list=list(IUPAC.protein.letters)
        IUPAC_list.remove(letter)
        for item in IUPAC_list:
            new_list=[record_name,str(position),letter,item]
            print(("\t").join(new_list))
• 0 views • link
updated by Ram Ram • written by mkulecka mkulecka

Thank you. It was very helpful.

• 0 views • link
written by max1415r • max1415r

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