[Bioperl-l] [Gmod-gbrowse] xyplot data alignment problem?

Chris Fields cjfields at uiuc.edu
Sat Dec 16 01:10:07 EST 2006


We could feasibly have regular point releases of the 1.5 dev. series  
for bug fixes; I guess it just depends on how often these should come  
out and what critical tests must pass for a release to go forward.   
Sendu's already done a ton of work towards getting BioPerl switched  
over to Module::Build and Test::More, and fixing bugs.  As Hilmar has  
pointed out in the past, this is a developer's series, so not every  
test needs to pass before a release goes out.

When would you like this to go out?

chris

On Dec 15, 2006, at 10:02 AM, Lincoln Stein wrote:

> This is very embarassing for me, particularly since I spent a lot  
> of time
> validating that Bio::Graphics was working properly before the 1.5.2  
> release
> went out. How long before there is a 1.5.3 release? How about a  
> 1.5.2.1release?
>
> Lincoln
>
> On 12/14/06, Lincoln Stein <lincoln.stein at gmail.com> wrote:
>>
>> Hi All,
>>
>> I'm afraid that the xyplot glyph that is in the recent bioperl  
>> release has
>> an error that causes the content to be printed to the right of the  
>> correct
>> position. Unfortunately this wasn't caught before the release  
>> because the
>> glyph was only tested on very large (whole genome) features.
>>
>> You will need to do a CVS update to get a fixed version from  
>> bioperl-live.
>> A future bugfix release of gbrowse will patch this glyph for you
>> automatically.
>>
>> Lincoln
>>
>> On 12/12/06, Kara Dolinski <kara at genomics.princeton.edu> wrote:
>>>
>>> Hi,
>>> I'm having a problem getting features and an xyplot properly  
>>> aligned in
>>> Gbrowse.  For example, see this page:
>>>
>>> http://tinyurl.com/ylbq3q
>>>
>>> The feature in the "CENPK SNPs" track should actually be around  
>>> the peak
>>> of the graph in the "CENPK prediction signal" xyplot  ie. the SNP
>>> feature is at position 79, and the xyplot axes and data should  
>>> span from
>>> 61 - 95.  However, as you can see, the data in the xyplot are oddly
>>> separated from the axes (which seem to be in the correct place),  
>>> with the
>>> data shifted over to about position 120-155.
>>> This occurs elsewhere, not just at the ends of the chromosomes.
>>>
>>> When I zoom to ~80 bp, all is well, see:
>>>
>>> http://tinyurl.com/yzav8k
>>>
>>> The relevant snippets from the GFF and the config files are below.
>>>
>>> Thanks!
>>> Kara
>>>
>>> GFF:
>>>
>>> chrI SNPScanner
>>> CENPK_GRAPH 61 95 41.9883 . .  
>>> ID=CENPK_all_peaks;Name=CENPK_peak0;PEAK=peak0;Note=score
>>> is 41.9883
>>> chrI SNPScanner
>>> CENPK_CALL 79 79 41.9883 . .  
>>> ID=CENPK_all_peaks;Name=CENPK_peak0;PEAK=peak0;Note=score
>>> is 41.9883
>>> chrI SNPScanner
>>> CENPK_SCORE 61 61 2.24506 . .  
>>> ID=CENPK_all_peaks;Name=chrI61;PEAK=peak0;Note=score
>>> is 2.24506
>>> chrI SNPScanner
>>> CENPK_SCORE 62 62 3.26837 . .  
>>> ID=CENPK_all_peaks;Name=chrI62;PEAK=peak0;Note=score
>>> is 3.26837
>>> chrI SNPScanner
>>> CENPK_SCORE 63 63 1.39938 . .  
>>> ID=CENPK_all_peaks;Name=chrI63;PEAK=peak0;Note=score
>>> is 1.39938
>>> chrI SNPScanner
>>> CENPK_SCORE 64 64 1.4039 . .  
>>> ID=CENPK_all_peaks;Name=chrI64;PEAK=peak0;Note=score
>>> is 1.4039
>>> chrI SNPScanner
>>> CENPK_SCORE 65 65 9.16134 . .  
>>> ID=CENPK_all_peaks;Name=chrI65;PEAK=peak0;Note=score
>>> is 9.16134
>>> chrI SNPScanner
>>> CENPK_SCORE 66 66 10.1413 . .  
>>> ID=CENPK_all_peaks;Name=chrI66;PEAK=peak0;Note=score
>>> is 10.1413
>>> chrI SNPScanner
>>> CENPK_SCORE 67 67 12.9256 . .  
>>> ID=CENPK_all_peaks;Name=chrI67;PEAK=peak0;Note=score
>>> is 12.9256
>>> chrI SNPScanner
>>> CENPK_SCORE 68 68 13.195 . .  
>>> ID=CENPK_all_peaks;Name=chrI68;PEAK=peak0;Note=score
>>> is 13.195
>>> chrI SNPScanner
>>> CENPK_SCORE 69 69 22.7127 . .  
>>> ID=CENPK_all_peaks;Name=chrI69;PEAK=peak0;Note=score
>>> is 22.7127
>>> chrI SNPScanner
>>> CENPK_SCORE 70 70 23.8289 . .  
>>> ID=CENPK_all_peaks;Name=chrI70;PEAK=peak0;Note=score
>>> is 23.8289
>>> chrI SNPScanner
>>> CENPK_SCORE 71 71 21.9123 . .  
>>> ID=CENPK_all_peaks;Name=chrI71;PEAK=peak0;Note=score
>>> is 21.9123
>>> chrI SNPScanner
>>> CENPK_SCORE 72 72 28.3344 . .  
>>> ID=CENPK_all_peaks;Name=chrI72;PEAK=peak0;Note=score
>>> is 28.3344
>>> chrI SNPScanner
>>> CENPK_SCORE 73 73 35.0436 . .  
>>> ID=CENPK_all_peaks;Name=chrI73;PEAK=peak0;Note=score
>>> is 35.0436
>>> chrI SNPScanner
>>> CENPK_SCORE 74 74 37.361 . .  
>>> ID=CENPK_all_peaks;Name=chrI74;PEAK=peak0;Note=score
>>> is 37.361
>>> chrI SNPScanner
>>> CENPK_SCORE 75 75 39.5408 . .  
>>> ID=CENPK_all_peaks;Name=chrI75;PEAK=peak0;Note=score
>>> is 39.5408
>>> chrI SNPScanner
>>> CENPK_SCORE 76 76 28.2008 . .  
>>> ID=CENPK_all_peaks;Name=chrI76;PEAK=peak0;Note=score
>>> is 28.2008
>>> chrI SNPScanner
>>> CENPK_SCORE 77 77 32.6254 . .  
>>> ID=CENPK_all_peaks;Name=chrI77;PEAK=peak0;Note=score
>>> is 32.6254
>>> chrI SNPScanner
>>> CENPK_SCORE 78 78 36.0832 . .  
>>> ID=CENPK_all_peaks;Name=chrI78;PEAK=peak0;Note=score
>>> is 36.0832
>>> chrI SNPScanner
>>> CENPK_SCORE 79 79 41.9883 . .  
>>> ID=CENPK_all_peaks;Name=chrI79;PEAK=peak0;Note=score
>>> is 41.9883
>>> chrI SNPScanner
>>> CENPK_SCORE 80 80 32.1205 . .  
>>> ID=CENPK_all_peaks;Name=chrI80;PEAK=peak0;Note=score
>>> is 32.1205
>>> chrI SNPScanner
>>> CENPK_SCORE 81 81 41.3048 . .  
>>> ID=CENPK_all_peaks;Name=chrI81;PEAK=peak0;Note=score
>>> is 41.3048
>>> chrI SNPScanner
>>> CENPK_SCORE 82 82 30.7975 . .  
>>> ID=CENPK_all_peaks;Name=chrI82;PEAK=peak0;Note=score
>>> is 30.7975
>>> chrI SNPScanner
>>> CENPK_SCORE 83 83 29.4282 . .  
>>> ID=CENPK_all_peaks;Name=chrI83;PEAK=peak0;Note=score
>>> is 29.4282
>>> chrI SNPScanner
>>> CENPK_SCORE 84 84 35.3586 . .  
>>> ID=CENPK_all_peaks;Name=chrI84;PEAK=peak0;Note=score
>>> is 35.3586
>>> chrI SNPScanner
>>> CENPK_SCORE 85 85 34.1426 . .  
>>> ID=CENPK_all_peaks;Name=chrI85;PEAK=peak0;Note=score
>>> is 34.1426
>>> chrI SNPScanner
>>> CENPK_SCORE 86 86 30.2966 . .  
>>> ID=CENPK_all_peaks;Name=chrI86;PEAK=peak0;Note=score
>>> is 30.2966
>>> chrI SNPScanner
>>> CENPK_SCORE 87 87 17.8402 . .  
>>> ID=CENPK_all_peaks;Name=chrI87;PEAK=peak0;Note=score
>>> is 17.8402
>>> chrI SNPScanner
>>> CENPK_SCORE 88 88 15.2637 . .  
>>> ID=CENPK_all_peaks;Name=chrI88;PEAK=peak0;Note=score
>>> is 15.2637
>>> chrI SNPScanner
>>> CENPK_SCORE 89 89 12.657 . .  
>>> ID=CENPK_all_peaks;Name=chrI89;PEAK=peak0;Note=score
>>> is 12.657
>>> chrI SNPScanner
>>> CENPK_SCORE 90 90 10.2033 . .  
>>> ID=CENPK_all_peaks;Name=chrI90;PEAK=peak0;Note=score
>>> is 10.2033
>>> chrI SNPScanner
>>> CENPK_SCORE 91 91 9.40143 . .  
>>> ID=CENPK_all_peaks;Name=chrI91;PEAK=peak0;Note=score
>>> is 9.40143
>>> chrI SNPScanner
>>> CENPK_SCORE 92 92 6.56273 . .  
>>> ID=CENPK_all_peaks;Name=chrI92;PEAK=peak0;Note=score
>>> is 6.56273
>>> chrI SNPScanner
>>> CENPK_SCORE 93 93 3.66211 . .  
>>> ID=CENPK_all_peaks;Name=chrI93;PEAK=peak0;Note=score
>>> is 3.66211
>>> chrI SNPScanner
>>> CENPK_SCORE 94 94 0.394194 . .  
>>> ID=CENPK_all_peaks;Name=chrI94;PEAK=peak0;Note=score
>>> is 0.394194
>>>
>>> CONFIG:
>>>
>>>
>>> GRAPH_CENPK{CENPK_SCORE/CENPK_GRAPH}
>>>
>>> [CENPK_all_scores_graph]
>>> feature = GRAPH_CENPK:SNPScanner
>>> glyph = xyplot
>>> graph_type = boxes
>>> fgcolor = purple
>>> bgcolor = purple
>>> height = 100
>>> min_score = 0
>>> max_score = 110
>>> label = 0
>>> key = CENPK prediction signal
>>> link =
>>> category = SNPs: signal graphs
>>>
>>>
>>>
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>>>
>>>
>>
>>
>> --
>> Lincoln D. Stein
>> Cold Spring Harbor Laboratory
>> 1 Bungtown Road
>> Cold Spring Harbor, NY 11724
>> (516) 367-8380 (voice)
>> (516) 367-8389 (fax)
>> FOR URGENT MESSAGES & SCHEDULING,
>> PLEASE CONTACT MY ASSISTANT,
>> SANDRA MICHELSEN, AT michelse at cshl.edu
>>
>
>
>
> -- 
> Lincoln D. Stein
> Cold Spring Harbor Laboratory
> 1 Bungtown Road
> Cold Spring Harbor, NY 11724
> (516) 367-8380 (voice)
> (516) 367-8389 (fax)
> FOR URGENT MESSAGES & SCHEDULING,
> PLEASE CONTACT MY ASSISTANT,
> SANDRA MICHELSEN, AT michelse at cshl.edu
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l

Christopher Fields
Postdoctoral Researcher
Lab of Dr. Robert Switzer
Dept of Biochemistry
University of Illinois Urbana-Champaign





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