[Bioperl-l] help needed: EXCEPTION error

[Jason Stajich]

You're passing in
"QAQITGRPEWIWLALGTALMGLGTLYFLVKGMGVSDPDAKKFYAITTLVPAIAFTMYLSMLLGYGLTMVPFGGEQ
NPIYWARYADWLFTTPLLLLDLALLVDADQGTILALVGADGIMIGTGLVGALTKVYSYRFVWWAISTAAMLYILYV
LFFGFTSKAESMRPEVASTFKVLRNVTVVLWSAYPVVWLIGSEGAGIVPLNIETLLFMVLDVSAKVGFGLILLRSR
AIFGEAEAPEPSAGDGAAATS"
rather than
">seq1
QAQITGRPEWIWLALGTALMGLGTLYFLVKGMGVSDPDAKKFYAITTLVPAIAFTMYLSMLLGYGLTMVPFGGEQ
NPIYWARYADWLFTTPLLLLDLALLVDADQGTILALVGADGIMIGTGLVGALTKVYSYRFVWWAISTAAMLYILYV
LFFGFTSKAESMRPEVASTFKVLRNVTVVLWSAYPVVWLIGSEGAGIVPLNIETLLFMVLDVSAKVGFGLILLRSR
AIFGEAEAPEPSAGDGAAATS"


to the fasta parser.  That is not valid fasta format.


On Tue, 22 Jan 2002, Beth Kidd wrote:

>  I have created a web interface for the PDB website as part of a larger
>  project and I am using BioPerl for parts of this process. It seems to work
>  fine from the web page. But when I run the same thing at the command line I
>  am getting errors from the package. Here are the errors:
>
>  -------------------- EXCEPTION --------------------
>
>  MSG: Can't parse entry
>
> [QAQITGRPEWIWLALGTALMGLGTLYFLVKGMGVSDPDAKKFYAITTLVPAIAFTMYLSMLLGYGLTMVPFGGEQ
>
> NPIYWARYADWLFTTPLLLLDLALLVDADQGTILALVGADGIMIGTGLVGALTKVYSYRFVWWAISTAAMLYILYV
>
> LFFGFTSKAESMRPEVASTFKVLRNVTVVLWSAYPVVWLIGSEGAGIVPLNIETLLFMVLDVSAKVGFGLILLRSR
>  AIFGEAEAPEPSAGDGAAATS]
>
>  STACK Bio::SeqIO::fasta::next_primary_seq
>  /usr/lib/perl5/site_perl/5.6.0/i386-linux/Bio/SeqIO/fasta.pm:110
>
>  STACK Bio::SeqIO::fasta::next_seq
>  /usr/lib/perl5/site_perl/5.6.0/i386-linux/Bio/SeqIO/fasta.pm:85
>
>  STACK toplevel ./run_blast_remote.pl:121-
>
>  Can anyone translate for me? The brackets originate from the error message,
>  not input. Why would I be getting this error message? It doesn't make sense
>  that the problem would be with the sequence and it only happens at the
>  command line. I am only trying to submit only one sequence. Please forgive
> me if this seems simple or unclear. I'm new to this project.
>
>  Beth Kidd
>
>
>
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-- 
Jason Stajich
Duke University
jason@cgt.mc.duke.edu