[Bioperl-l] How to Obtain Nucleotide Sequence from SeqIO::fastq

Roy Chaudhuri roy.chaudhuri at gmail.com
Tue Jul 27 13:14:48 EDT 2010


Hi Alan,

It looks like there wasn't any problem with the earlier e-mail, and that 
your file is not Fastq, but rather some unusual Fastq-like format - 
where did you get the file from?

Here's a one-liner to convert your file into standard Fastq:

perl -ne 'print; $_=<>; s/^\+//; print; $_=<>; s/^\+//; print "+\n$_";' 
< exampleData.fastq > standard.fastq

I've assumed that your sequences and qualities are all single-line with 
a + prefix.

Once you have a standard Fastq file you should be able to parse it with 
BioPerl.

Roy.

On 27/07/2010 17:36, Alan Twaddle wrote:
> Here's some of the data I would like to parse; the entire file was too
> big to send via email. Also, if there is some problem with the data, I
> would appreciate any scripting advice since I am unfortunately a noob
> :-/
>
> Let me know what you think!
>
> Thank you all very much!
>
> On Tue, Jul 27, 2010 at 12:18 PM, Dave Messina<David.Messina at sbc.su.se>  wrote:
>>> Maybe sending this single record as an attachment would work better (is that
>>> encouraged on this mailing list?).
>>
>> Absolutely, please try resending as an attachment, Alan.
>>
>>
>> Dave
>>
>>
>
>
>
>
>
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