[Bioperl-l] Trouble with Bio::Graphics

[michael watson (IAH-C)]

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...


-----Original Message-----
From:	Scott Cain [mailto:cain at cshl.edu]
Sent:	Thu 18/08/2005 6:44 PM
To:	michael watson (IAH-C)
Cc:	bioperl-l
Subject:	Re: [Bioperl-l] Trouble with Bio::Graphics

Mick,

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
"primary_tag".

- 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
Bio/Graphics/Glyph/processed_transcript.pm.

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.

Scott


On Thu, 2005-08-18 at 17:03 +0100, michael watson (IAH-C) wrote:
> Hi
> 
> 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
> object.
> 
> I am bemused.
> 
> Any help appreciated.
> 
> Mick
> 
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-- 
------------------------------------------------------------------------
Scott Cain, Ph. D.                                         cain at cshl.edu
GMOD Coordinator (http://www.gmod.org/)                     216-392-3087
Cold Spring Harbor Laboratory