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

Alan Twaddle twaddlac at gmail.com
Tue Jul 27 14:57:16 EDT 2010


Ahh thank you very much, everyone!!!!

The data was from a GS-FLX Titanium sequencer but it was parsed out of
a database into the format that was the "incorrect" fastq style.
However, the script worked (though I'm not confident I understand what
it just did) and I have successfully parsed the data out of it via
BioPerl!

Thanks again!!

On Tue, Jul 27, 2010 at 1:14 PM, Roy Chaudhuri <roy.chaudhuri at gmail.com> wrote:
> 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
>>>
>>>
>>
>>
>>
>>
>>
>> _______________________________________________
>> Bioperl-l mailing list
>> Bioperl-l at lists.open-bio.org
>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>
>



-- 

Alan Twaddle, B.S.
MUC class of 2010



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