How to use .split

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  • bb64
    New Member
    • Sep 2010
    • 7
    #1

    How to use .split

    I need to write a Python script to convert two sequences to interleaved FASTA format with 10 characters per line.
    so if the input is

    >human
    ACACCGGTACCAGAT ATGATATACCGAGA
    >mouse
    ACCAGAGGGGGTTTT AAACCACAGCG

    (saved as dna.txt)
    the output should be
    >human
    ACACCGGTAC
    CAGATATGAT
    ATACCGAGA
    >mouse
    ACCAGAGGGG
    GTTTTAAACC
    ACAGCG


    i have no idea what to do.
    this is all i have so far
    Code:
    def read_data(filename):
    with open("p:/dna.txt", "r") as myfile:
        data = myfile.readlines()
        myfile.close()
    for i in range(0, len(data)):
        data[i] = data[i].rstrip("\n")

    return data

seq1 = data[1]
seq2 = data[3]
    Last edited by bvdet; Nov 8 '10, 12:32 AM. Reason: Add code tags, fix indentation
    Tags: python
    • bvdet
      Recognized Expert Specialist
      • Oct 2006
      • 2851
      #2
      Maybe this will help:
      Code:
      >>> import textwrap
>>> textwrap.wrap("ACCAGAGGGGGTTTTAAACCACAGCG", 10)
['ACCAGAGGGG', 'GTTTTAAACC', 'ACAGCG']
>>> data = [">human", "ACACCGGTACCAGATATGATATACCGAGA", ">mouse", "ACCAGAGGGGGTTTTAAACCACAGCG"]
>>> for item in data:
... 	print "\n".join([s for s in textwrap.wrap(item, 10)])
... 	
>human
ACACCGGTAC
CAGATATGAT
ATACCGAGA
>mouse
ACCAGAGGGG
GTTTTAAACC
ACAGCG
>>>

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