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  • write fastq with Python

    Hello. My problem seems so super basic, I haven't found an answer in this forum... I'm really brand new in this field..

    I want to convert a .sff into a .fastq according the Biopython manual:

    >>> from Bio import SeqIO
    >>> from StringIO import StringIO
    >>> out_handle = StringIO()
    >>> count = SeqIO.convert("c:HPISTN001.sff", "sff",
    ... out_handle, "fastq")

    But how do i GET the .fastq file, stored on c:?

  • #2
    You've asked Biopython to write the FASTQ file to a string in memory, actually a special object called StringIO which mimics a file in memory.

    All you need to do is this:

    Code:
    from Bio import SeqIO
    count = SeqIO.convert(r"c:\HPISTN001.sff", "sff", r"C:\HPSITN001.fastq", "fastq")
    print "Converted %i records" % count
    Also note the use of r"xxxxx" to mean a raw string where \ is just a slash. Otherwise by default Python treats \n as a new line, and \t as a tab etc - which can be unhelpful with Windows style paths.

    Which bit of the tutorial did you find unclear? I'd like to clarify it if possible.
    Last edited by maubp; 06-29-2012, 06:38 AM. Reason: Formating

    Comment


    • #3
      Sff_extract.py script

      Comment

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