[Bioperl-l] Suppress warnings for Bio:.LocatableSeq:.end()

Jun Yin jun.yin at ucd.ie
Tue Dec 14 06:23:59 EST 2010

Hi, Kevin,

The warning is because Bio::LocatableSeq::end() is using this formula to
check the end coordinate:

It is possible that the start and end assigned by Ensembl does not fit this

For turning off warnings, I found this comment from one of Chris Fields' old

If you want to turn off warnings for any bioperl class,  you can set the
object to $obj->verbose(-1), or pass it to the constructor:

my $seqio = Bio::SeqIO->new(‘-file’ => $infile, ‘-format’ => ‘fasta’,
-verbose => -1);

Jun Yin
Ph.D. student in U.C.D.

Bioinformatics Laboratory
Conway Institute
University College Dublin

-----Original Message-----
From: bioperl-l-bounces at lists.open-bio.org
[mailto:bioperl-l-bounces at lists.open-bio.org] On Behalf Of Kevin L. Keys
Sent: Tuesday, December 14, 2010 10:16 AM
To: bioperl-l at lists.open-bio.org
Subject: [Bioperl-l] Suppress warnings for Bio:.LocatableSeq:.end()


I am using BioPerl to download multiple alignments from the Ensembl
databases. I keep getting the following message:

--------------------- WARNING ---------------------
MSG: In sequence $(...) residue count gives end value (####).
Overriding value [####] with value (####) for Bio::LocatableSeq::end().

where $(...) is an Ensembl transcript ID and the #'s represent digits.

I suspect that BioPerl is complaining about varying sequence lengths.
For my project, this is no concern of mine since I control for it
after downloading. Is there a way to suppress this warning so that it
doesn't clog my terminal feed?

many thanks,
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