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Re^2: Reading in Qual File Using Bio::SeqIO

by twaddlac (Novice)
on Jul 06, 2010 at 19:09 UTC ( #848300=note: print w/ replies, xml ) Need Help??


in reply to Re: Reading in Qual File Using Bio::SeqIO
in thread Reading in Qual File Using Bio::SeqIO

Well I have unfortunately encountered another error. I read the qual file in like a fastA file and put it into a hash and I can't write it like a qual file for some reason.. is there some sort of parsing that I have to do that the BioPerl modules won't do for me?

--------------------- WARNING --------------------- MSG: seq doesn't validate, mismatch is 4040404040404040404040404040404 +040404040404040404040404040404040404040393737373737373737373737373737 +373737373535353535353030302828283030323235373737373737373737373737373 +737373737373737373737373737373535353737343232323232323230161515152427 +2626131313232313131317212121212119211618171918 --------------------------------------------------- ------------- EXCEPTION: Bio::Root::Exception ------------- MSG: Attempting to set the sequence to [404040404040404040404040404040 +404040404040404040404040404040404040404039373737373737373737373737373 +737373737353535353535303030282828303032323537373737373737373737373737 +373737373737373737373737373737353535373734323232323232323016151515242 +72626131313232313131317212121212119211618171918] 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/Primary +Seq.pm:270 STACK: Bio::PrimarySeq::new /usr/lib/perl5/site_perl/5.8.8/Bio/Primary +Seq.pm:221 STACK: Bio::Seq::new /usr/lib/perl5/site_perl/5.8.8/Bio/Seq.pm:484 STACK: tagfinder.pl:227


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