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  • Biopython Translate function

    Hi all!

    I'm having problems using Biopython to translate sequences into all 3 forward reading frames.

    I wrote this script (and it works):

    ######################
    #!/bin/python

    #translate dna to protein

    from Bio import SeqIO
    input = open("input.fasta", "rU")

    for record in SeqIO.parse(input, "fasta") :
    protein_id = record.id
    print(">" + protein_id)
    print(record.seq.translate(to_stop=True))

    input.close()
    #########################

    But this only gives me the default reading frame. After extensive searching, I still can't find how I edit the script so I can translate the +2 and +3 frames also.

    Any help? Thanks!

  • #2
    I thought this was covered in the Biopython Tutorial http://biopython.org/DIST/docs/tutorial/Tutorial.html or the docstrings (API documentation), but can't find a specific example.

    The basic idea is cut off the first base, or first two bases to get the next frames, e.g.

    Code:
    print("In frame")
    print(record.seq.translate(to_stop=True))
    print("Offset by one")
    print(record.seq[1:].translate(to_stop=True))
    print("Offset by two")
    print(record.seq[2:].translate(to_stop=True))

    Comment


    • #3
      Thank you so much! I was about to rip my hair out! I really appreciate it!

      Comment


      • #4
        Thank you for asking - this is useful feedback to improve the Biopython documentation:

        Comment


        • #5
          This is very udeful! I like this info!

          Comment

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