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Regular expression problem while trying to interpolate variable as pattern in Python

I'm trying to learn Python to perform some tasks in the lab.

I was trying to find a pattern in a FASTA file, interpolating pattern and fasta as string variables. This way the program doesn't find anything. On the other hand, when I try to do the same, but writing the pattern string instead of using the variable interpolation, it works and finds the pattern. Could you please help me to figure out what the problem is?

Here is my code:

   firstname = "header1"
   for record in SeqIO.parse("prueba_fasta.fasta", "fasta"):
        print ">" + record.id + "\n" + record.seq
        fa = strrecord.id)
        print fa
        fir = str(firstname)
        print fir
        matches = re.search (fir, fa)
        if matches:
            print ">" + record.id + "\n" + record.seq

Thanks in advance

Uxue

python biopython regex
• 2,808 views • link
updated by Damian Kao Damian Kao • written by uxue33 • uxue33

Unrelated advice, you should/could use print(seq_record.format("fasta").strip()) to properly write (to stdout) instead of using the awkward print ">" + record.id + "\n" + record.seq

In addition, you miss something here: fa = strrecord.id), I guess you mean: fa = str( record.id)

• 1 views • link
written by WouterDeCoster WouterDeCoster

I'm sorry for the mistake, this is the right version of the code:

 firstname = "header1"
       for record in SeqIO.parse("prueba_fasta.fasta", "fasta"):
            print ">" + record.id + "\n" + record.seq
            fa = strrecord.id)
            print fa
            fir = str(firstname)
            print fir
            matches = re.search (fir, fa)
            if matches:
                print(record.format("fasta").strip())

Thank you!

• 1 views • link
written by uxue33 • uxue33

Oh right, there is some weird auto formatting going on with str( record.id).

Which pattern exactly are you trying to match? So if something occurs in the fasta identifier you want to keep it?

• 1 views • link
written by WouterDeCoster WouterDeCoster

2 answers

try to use matches.group()

re.search return object so if you use the method group() it will return string if it found matches, other wise it returns None

• 1 views • link
written by Medhat Medhat

Thank you very much for your inside! I will try to follow your recomendations in order to fix this problem.

• 1 views • link
written by uxue33 • uxue33

You just want to print any fasta entry where the header contains the text "header1"?

you can just:

for record in SeqIO.parse("prueba_fasta.fasta", "fasta"):
    if strrecord.id).find('header1') != -1:
        print ">" + record.id + "\n" + record.seq
• 1 views • link
written by Damian Kao Damian Kao

Thank you for you answer. I have already fix the problem.

• 1 views • link
written by uxue33 • uxue33

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