[Bioperl-l] Bio::LocatableSeq warning

[Mark A. Jensen]

178 was the length of the sequence calculated by AlignIO and set with 
$seq->end(178). This number evidently ignores the 5 characters
*, 2, *, *, and 4.

Lseq ran interference, removing the gaps but not the special chars for the 
length calculation and came up with  183 = 178+5. It reset the end of the 
sequence to 183 and told you about it.

AlignIO::clustalw collects the end value by parsing a range in the sequence 
name, not by counting chars, as far as I can tell. So perhaps the alignment file 
is hosed.

I agree it's not too friendly.


----- Original Message ----- 
From: "Sendu Bala" <bix at sendu.me.uk>
To: "bioperl-l" <bioperl-l at lists.open-bio.org>
Sent: Wednesday, December 17, 2008 12:13 PM
Subject: [Bioperl-l] Bio::LocatableSeq warning


> I've just committed a test alignment file to bioperl-run t/data, and 
> Bio::LocatableSeq spurts up a warning about it:
>
> perl -MBio::AlignIO -e '$ai = Bio::AlignIO->new(-file => 
> "t/data/pal2nal.aln"); $aln = $ai->next_aln;'
>
> --------------------- WARNING ---------------------
> MSG: In sequence pseudogene residue count gives end value 183.
> Overriding value [178] with value 183 for Bio::LocatableSeq::end().
> ----LNCIVNDSQKMGIIRNGDLP*PQLKNKF2-FQRMTTPSSAEGKENLVFLIRKNWFSITEKNQPLKYIINLVVSRESKEPPQRPPFLD*SLGDALKRIEQLKLANKQDVFFTVGGSSVYKESMN*-DHFKLFVTWIMQDFQSDTFFS4EGDLEKYKLLPEYPQGVVSDVEEEKGIKYKFEVYEKND
> ---------------------------------------------------
>
>
> Is there simply something wrong with the alignment file (quite possible), and 
> this warning means something?
>
> Or is this just normal behaviour now for valid alignment files? What is this 
> warning supposed to mean to the user? What should I do about it? Why do I need 
> to see it?
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