[Bioperl-l] Trouble with Bio::Graphics
michael watson (IAH-C)
michael.watson at bbsrc.ac.uk
Thu Aug 18 13:48:04 EDT 2005
Actually, more than likely they are transcription errors - I was running it on linux, my mail is on windows, sorry!
Somewhere "->primary_tag" is being called on a Location object...
From: Scott Cain [mailto:cain at cshl.edu]
Sent: Thu 18/08/2005 6:44 PM
To: michael watson (IAH-C)
Subject: Re: [Bioperl-l] Trouble with Bio::Graphics
I don't really know, but I just wanted to clarify the error message that
you put below. Is that a copy and paste, or did you retype it? The
reason I ask is there are a few things that are odd about it that might
point to a problem:
- it mentions "primary _tag" with a space between the y and _. Of
course there isn't a "primary _tag" method, as it is called
- It also references the file Bio/Graphics/processed_transcript.pm, but
that is not the right file path for that file; it should be in
Now, since you said this script works most of the time, these can't be
fatal problems, but perhaps these are related to what the problem is.
On Thu, 2005-08-18 at 17:03 +0100, michael watson (IAH-C) wrote:
> This is going to sound like a rather hard bug to track down but maybe
> someone can shed some light...
> I have a rather complicated script that takes a sequence, aligns it with
> other sequences, does some blast searching, then creates a whole load of
> features of the result for drawing with Bio::Graphics.
> I've used the script to create images of 2498 images.... But two fail...
> Both with the same error message, and this is it in it's entirety (there
> is no stack trace):
> Can't locate object method "primary _tag" via package
> "Bio::Location::Simple" at Bio/Graphics/processed_transcript.pm line 13,
> <GEN12> line 56.
> But of course it can't find that object method, and nor should it be...
> "processed_transcript" is my glyph of choice and as I said it has worked
> for 2498 of these jobs... But for some reason, on 2 of them, it's trying
> to find method primary_tag not on a feature object but on a location
> I am bemused.
> Any help appreciated.
> Bioperl-l mailing list
> Bioperl-l at portal.open-bio.org
Scott Cain, Ph. D. cain at cshl.edu
GMOD Coordinator (http://www.gmod.org/) 216-392-3087
Cold Spring Harbor Laboratory
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