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  • extracting scores from *.qual files HELP

    Hi,

    I want to extract the quality scores of certain contigs from a 454.qual-file. The file looks like this:

    >contigs003410
    27 27 30 64 64 64 64 64 64 64
    64 64 64 64 64 19 64 64 64 64
    64 64 64 64 64 64 64 64 64 64
    64 64 64 64 64 20 64 64 64 64
    64 64 7 7
    >contigs003411
    19 18 30 64 64 64 64 64 64 64
    64 64 64 64 64 19 64 64 64 64
    64 64 64 64 12 64 64 64 64 64
    64 64 64 64 64 20 64 64 64 64
    64 64 64 64

    and so on

    For the fasta type. I used the the NCBI Blast Command Line Tools. But for this kind of files they don't work.

    Does anybody have a unix command for this?

    Thanks, anna.

  • #2
    You might need to be a bit more specific about exactly what you want, what you've tried and how it went wrong.

    At first glance it seems pretty simple to extract the scores for a specified contig. Read the file until you find the header for that contig, read data until you hit the next contig, split the data on spaces and you have an array of scores.

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