[Bioperl-l] reading Quality files

shalu sharma sharmashalu.bio at gmail.com
Fri Feb 18 21:13:34 UTC 2011


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

and when i tried to read it with -format => 'qual' i got error message.
Can't locate object method "seq" via package "Bio::Seq::PrimaryQual" at
readQual.pl line 6, <GEN0> line 1

Do i have to call different methods when using quality files?

I will really appreciate your help.

Thanks
Shalu




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