Repetitive writing in output using list of characters - python

Question

In a file, I have some characters to be substituted.

letters = ["B", "Z", "J", "U", "O"]

for record in SeqIO.parse(inFile, "fasta"):
    for letter in letters:
        if letters in str(record.seq):
            print record.id 
            record.seq = str(record.seq).replace(letter, "X")
            outFile.write(">%s\n%s\n" % (record.description, record.seq))
        else:
            outFile.write(">%s\n%s\n" % (record.description, record.seq))
            #pass

The problem is that the output looks like this, writing the outputs as many characters I have in letters:

> >ID:WP_004160595.1|Erwinia_amylovora_01SFR-BO|01SFR-BO|50S_ribosomal_protei..|630|NZ_CAPA01000010(58437):26053-26682:-1
> MIGLVGKKVGMTRIFTEDGVSIPVTVIEIEANRVTQVKGLENDGYTAIQVTTGAKKANRVTKPAAGHFAKAGVEAGRGLWEFRTAEGAEFTVGQSINVDIFADVKKVDVTGTSKGKGFAGTVKRWNFRTQDATHGNSLSHRVPGSIGQNQTPGKVFKGKKMAGQLGNERVTVQSLDVVRVDAERNLLLVKGAVPGATGSDLIVKPAVKA
> >ID:WP_004160595.1|Erwinia_amylovora_01SFR-BO|01SFR-BO|50S_ribosomal_protei..|630|NZ_CAPA01000010(58437):26053-26682:-1
> MIGLVGKKVGMTRIFTEDGVSIPVTVIEIEANRVTQVKGLENDGYTAIQVTTGAKKANRVTKPAAGHFAKAGVEAGRGLWEFRTAEGAEFTVGQSINVDIFADVKKVDVTGTSKGKGFAGTVKRWNFRTQDATHGNSLSHRVPGSIGQNQTPGKVFKGKKMAGQLGNERVTVQSLDVVRVDAERNLLLVKGAVPGATGSDLIVKPAVKA
> >ID:WP_004160595.1|Erwinia_amylovora_01SFR-BO|01SFR-BO|50S_ribosomal_protei..|630|NZ_CAPA01000010(58437):26053-26682:-1
> MIGLVGKKVGMTRIFTEDGVSIPVTVIEIEANRVTQVKGLENDGYTAIQVTTGAKKANRVTKPAAGHFAKAGVEAGRGLWEFRTAEGAEFTVGQSINVDIFADVKKVDVTGTSKGKGFAGTVKRWNFRTQDATHGNSLSHRVPGSIGQNQTPGKVFKGKKMAGQLGNERVTVQSLDVVRVDAERNLLLVKGAVPGATGSDLIVKPAVKA
> >ID:WP_004160595.1|Erwinia_amylovora_01SFR-BO|01SFR-BO|50S_ribosomal_protei..|630|NZ_CAPA01000010(58437):26053-26682:-1
> MIGLVGKKVGMTRIFTEDGVSIPVTVIEIEANRVTQVKGLENDGYTAIQVTTGAKKANRVTKPAAGHFAKAGVEAGRGLWEFRTAEGAEFTVGQSINVDIFADVKKVDVTGTSKGKGFAGTVKRWNFRTQDATHGNSLSHRVPGSIGQNQTPGKVFKGKKMAGQLGNERVTVQSLDVVRVDAERNLLLVKGAVPGATGSDLIVKPAVKA
> >ID:WP_004160595.1|Erwinia_amylovora_01SFR-BO|01SFR-BO|50S_ribosomal_protei..|630|NZ_CAPA01000010(58437):26053-26682:-1
> MIGLVGKKVGMTRIFTEDGVSIPVTVIEIEANRVTQVKGLENDGYTAIQVTTGAKKANRVTKPAAGHFAKAGVEAGRGLWEFRTAEGAEFTVGQSINVDIFADVKKVDVTGTSKGKGFAGTVKRWNFRTQDATHGNSLSHRVPGSIGQNQTPGKVFKGKKMAGQLGNERVTVQSLDVVRVDAERNLLLVKGAVPGATGSDLIVKPAVKA

Answer 1

I think what you are trying to do is replace the ambiguous IUPAC amino acid codes (plus some additional letters that you have somehow gained?) with 'X' .

Better to use str.translate() (in Python 3) to do all your replacements at once. Also, since you're using Biopython to read the file, you can also write the output file easily with Biopython.

from Bio import SeqIO
from Bio.Seq import Seq

letters = ["B", "Z", "J", "U", "O"]
trans_tab = str.maketrans(''.join(letters), 'X'*len(letters))

def yield_seqs(in_file):
    for record in SeqIO.parse(in_file, 'fasta'):
        record.seq = Seq(str(record.seq).translate(trans_tab))
        yield record

SeqIO.write(yield_seqs('input.fasta'), 'output.fasta', 'fasta')

Example:

$ cat input.fasta 
>1
MBZJ
$ python3 myscript.py
$ cat output.fasta 
>1
MXXX

Answer 2

You have a typo.

if letters in str(record.seq):

instead of

if letter in str(record.seq)

so, your check always fails, and prints the else part for every single letter.