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

Alan Twaddle twaddlac at gmail.com
Tue Jul 27 10:55:58 EDT 2010


I'm not certain that I'm using the latest BioPerl, but I can check. In
the mean time, I'll send you the example data!

@FQ4HLCS02EO12Q region=2 tag=H
+GCGAAGAACCTTACCTACTCTTGACATCCAGAGAATTCGCTAGAGATAGCTTAGTGCCTTCGGGAACTCTGAGACAGGTGCTGCATGGCTGTCGTCAGCTCGTGTTGTGAAATGTTGGGTTAAGTCCCGCAACGAGCGCAACCCTTATCCTTTGTTGCCAGCGAGTAATGTCGGGAACTCAAAGGAGACTGCCGGTGACAAACCGGAGGAAGGTGGGGATGACGTCAACTCATCATGCCCCTTGCTGATAC
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIHHHIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIID666IIIIHHHIIIIIIHHHIIIIIIIIIIDCCHHHIIIIIIGGGIIIIIIIIIIIHHHIIIHH???HHIII???IIIIIIIIIIIIIIIIHHHIIIIIIIIIIIICC@@HIIIIIIIIIIGEGGGGG?4444CCIIIGGGII
@FQ4HLCS02EO12T region=2 tag=B
+GATGAATTGACGTCATCCCCACCTTCCTCCGGTTTATTACCGGCAGTCTCGCTAGAGTGCCCAACTAAATGATGGCAACTAACAATAGGGGTTGCGCTCGTTGCGGGACTTAACCCAACATTTCACAACACGAGCTGACGACAGCCATGCACCACCTGTCACTTTGTCCCCGAAGGGAACTTCTATCTCTAGAAGGGTCAAAGGATGTCAAGATTTGGTAAGGTTCTTCGCGTTGCAATTCGATGTCGAGC
+DDDGDGGGIIIIIIII@@@@IIIIIIIIIIIIHHB985DFI<<;==DDDGDBDADBG=644466AGB==GDEEFHHEEEHHHHHHHH====GE=D<<<;DBGED;;;;:9955000247<;;;;DGGGGHHHHHBBBHGGGHGGBBB@@@@>;;666EGGEEBBDD<97550//4--,,.62426468=ADD>>6666BBDDEEAEGEG;;;B>@@B;266;;GGDBA?:::995/////9>>9989=9:5


On Tue, Jul 27, 2010 at 10:50 AM, Roy Chaudhuri <roy.chaudhuri at gmail.com> wrote:
> Hi Alan,
>
> It sounds like there's a problem with reading in your Fastq file. Are you
> using the latest BioPerl version? There have been many bug fixes to
> Bio::SeqIO::fastq over the last couple of years. If you are using an
> up-to-date BioPerl, please could you send an example Fastq entry which gives
> the error messages?
>
> Roy.
>
> On 27/07/2010 15:37, Alan Twaddle wrote:
>>
>> Whenever I try to access the sequence I get the following error message:
>>
>>
>> --------------------- WARNING ---------------------
>> MSG: Seq/Qual descriptions don't match; using sequence description
>>
>> ---------------------------------------------------
>>
>> --------------------- WARNING ---------------------
>> MSG: Fastq sequence/quality data length mismatch error
>>
>> ---------------------------------------------------
>>
>> --------------------- WARNING ---------------------
>> MSG: seq doesn't validate with [0-9A-Za-z\*\-\.=~\\/\?], mismatch is +
>> ---------------------------------------------------
>>
>> ------------- EXCEPTION: Bio::Root::Exception -------------
>> MSG: Attempting to set the sequence to
>>
>> [+GCGAAGAACCTTACCTACTCTTGACATCCAGAGAATTCGCTAGAGATAGCTTAGTGCCTTCGGGAACTCTGAGACAGGTGCTGCATGGCTGTCGTCAGCTCGTGTTGTGAAATGTTGGGTTAAGTCCCGCAACGAGCGCAACCCTTATCCTTTGTTGCCAGCGAGTAATGTCGGGAACTCAAAGGAGACTGCCGGTGACAAACCGGAGGAAGGTGGGGATGACGTCAACTCATCATGCCCCTTGCTGATAC]
>> which does not look healthy
>> STACK: Error::throw
>> STACK: Bio::Root::Root::throw
>> /usr/lib/perl5/site_perl/5.8.8/Bio/Root/Root.pm:357
>> STACK: Bio::PrimarySeq::seq
>> /usr/lib/perl5/site_perl/5.8.8/Bio/PrimarySeq.pm:270
>> STACK: Bio::PrimarySeq::new
>> /usr/lib/perl5/site_perl/5.8.8/Bio/PrimarySeq.pm:221
>> STACK: Bio::LocatableSeq::new
>> /usr/lib/perl5/site_perl/5.8.8/Bio/LocatableSeq.pm:109
>> STACK: Bio::Seq::Meta::Array::new
>> /usr/lib/perl5/site_perl/5.8.8/Bio/Seq/Meta/Array.pm:167
>> STACK: Bio::Seq::Quality::new
>> /usr/lib/perl5/site_perl/5.8.8/Bio/Seq/Quality.pm:191
>> STACK: Bio::Seq::SeqFactory::create
>> /usr/lib/perl5/site_perl/5.8.8/Bio/Seq/SeqFactory.pm:116
>> STACK: Bio::SeqIO::fastq::next_seq
>> /usr/lib/perl5/site_perl/5.8.8/Bio/SeqIO/fastq.pm:151
>> STACK: fastQParser.pl:12
>>
>>
>>
>> On Tue, Jul 27, 2010 at 10:16 AM, Roy Chaudhuri<roy.chaudhuri at gmail.com>
>>  wrote:
>>>
>>> Hi Alan,
>>>
>>> Another case for the deobfuscator:
>>> http://bioperl.org/cgi-bin/deob_interface.cgi
>>>
>>> A Bio::Seq::Quality object is a Bio::PrimarySeq, so you can just say
>>> $seqqual->seq to get the sequence as a string.
>>>
>>> Cheers.
>>> Roy.
>>>
>>> On 27/07/2010 15:10, Alan Twaddle wrote:
>>>>
>>>> Hello,
>>>>
>>>>      I am curious as to how I am supposed to use SeqIO::fastq to read
>>>> in a fastq file and then obtain the nucleotide sequence from that. I
>>>> noticed that SeqIO::fastq returns a Seq::Quality object but I haven't
>>>> seen a method within that module that returns the nucleotide sequence.
>>>> Please, let me know if you have any suggestions!
>>>>
>>>> Thank you very much!!
>>>>
>>>
>>>
>>
>>
>>
>
>



-- 

Alan Twaddle, B.S.
MUC class of 2010



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