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Old 12-08-2011, 07:27 AM   #1
anna_
Member
 
Location: germany

Join Date: Dec 2010
Posts: 15
Question 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.
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Old 12-08-2011, 11:45 PM   #2
simonandrews
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Location: Babraham Inst, Cambridge, UK

Join Date: May 2009
Posts: 869
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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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