[Bioperl-l] reading Quality files

[Florent Angly]

On 19/02/11 07:13, shalu sharma wrote:
> Hi ,
>       Can i read quality files just as the same way i read fasta files (by
> using Bio::SeqIO) ?
> I tried reading with using -format =>  'fasta' but as the output all the
> spaces between the quality scores are deleted.
>   ex:
>> 1508:1:1:2228:1817_55bp_47.8_0.74
> 3939383938393935393939393936383735393533383338382735233838333835381135353838383836173536362735383838353835353638353636293835383238293838403939314040357241596965596364474950225467646314607056636769717175707161732538333520353735382029254040294037392036393229253535371940403537353540402940423137423737223540222227202220
>
Yes, that is not correct. There is a specific IO module for quality 
scores: Bio::SeqIO::qual

> and when i tried to read it with -format =>  'qual'
That is good: see 
http://search.cpan.org/~cjfields/BioPerl-1.6.1/Bio/SeqIO/qual.pm 
<http://search.cpan.org/%7Ecjfields/BioPerl-1.6.1/Bio/SeqIO/qual.pm>
Once you have initialized a Bio::SeqIO object, you can call next_seq() 
to get the next Bio::Seq::Quality object.

> i got error message.
> Can't locate object method "seq" via package "Bio::Seq::PrimaryQual" at
> readQual.pl line 6,<GEN0>  line 1
Once you have a Bio::Seq::Quality object, you can use the qual() method 
on it. See 
http://search.cpan.org/~cjfields/BioPerl-1.6.1/Bio/Seq/Quality.pm 
<http://search.cpan.org/%7Ecjfields/BioPerl-1.6.1/Bio/Seq/Quality.pm>

> Do i have to call different methods when using quality files?
>
> I will really appreciate your help.
>
> Thanks
> Shalu
>
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