[Gmod-help] Re: [Gmod-gbrowse] Problems displaying a wiggle track for .wig data in gbrowse 2.01
Jeff Bowes
bowes at ucalgary.ca
Fri Apr 9 14:04:07 EDT 2010
Hi Dave,
I got the track to display. It may well have been the hyphens in the SO
name that were the problem. However, there is another problem. While
I have values ranging from 1 to 198 the line graph seems to cut off at
about 13. Color density graphs seem to have a similar cut off. I'll
post this as a separate problem.
Jeff
Dave Clements, GMOD Help Desk wrote:
> Hi Jeff,
>
> You have probably got this resolved by now, but ...
>
> I don't know if there restrictions on hyphens in the SO terms. The GFF3 doc
> doesn't mention any. However, the current version of SO does not have any
> names with hyphens in them, so the ban may be implied.
>
> Sorry for the delayed response - I've been traveling recently.
>
> Dave C.
>
> On Thu, Mar 25, 2010 at 2:43 PM, Jeff Bowes <bowes at ucalgary.ca> wrote:
>
>
>> Hi Dave,
>>
>> That did not help. Are hyphens also problematic in the SO feature
>> names in the GFF3 for gbrowse?
>>
>> Thanks,
>>
>>
>> Jeff
>>
>>
>>
>>
>> Dave Clements, GMOD Help Desk wrote:
>>
>>> Hi Jeff,
>>>
>>> GBrowse does not like hyphens in track names. From the GBrowse Admin
>>> Tutorial:
>>>
>>> This is a "stanza" that describes one of the tracks displayed by GBrowse.
>>> The track has an internal name of "ExampleFeatures" which you can use in
>>>
>> the
>>
>>> URL to turn the track on. The internal name is enclosed by square
>>>
>> brackets.
>>
>>> Names can be any combination of printable characters and whitespace, but
>>>
>> can
>>
>>> not contain the hyphen ("-") character (you can use the underscore "_"
>>> character instead).
>>>
>>> Try that and let the list know if that helps. If not, we'll look for
>>>
>> other
>>
>>> problems.
>>>
>>> Dave C
>>>
>>> On Tue, Mar 23, 2010 at 4:17 PM, Jeff Bowes <bowes at ucalgary.ca> wrote:
>>>
>>>
>>>
>>>> Hi,
>>>>
>>>> We have received som Chip-seq methylation data in .wig format and we are
>>>> currently having trouble displaying this data. No glyphs appear under
>>>>
>> the
>>
>>>> wiggle track. I am not sure what I might be doing wrong. We are using
>>>> Gbrowse 2.01.
>>>>
>>>> The .wig file I received open as follows.
>>>>
>>>> browser position scaffold_163:520000-690000
>>>> track type=wiggle_0 name=H3K27me3_animal_ChIP-seq_st10-12
>>>> maxHeightPixels=64:64:11 color=254,196,79 visibility=full
>>>> fixedStep chrom=scaffold_1 start=321 step=10 span=10
>>>> 1
>>>> 1
>>>> 1
>>>>
>>>> The scores range from 1 to 198,
>>>>
>>>> I created gff3 for this file with wiggle2gff3. The binaries were all
>>>> created in a directory that is readable by apache. All the .wib files
>>>>
>> are
>>
>>>> readable by apache. The gff3 file reads
>>>>
>>>> ##gff-version 3
>>>>
>>>> scaffold_1 H3K27me3_animal_ChIP-seq_st10-12_xenTro2
>>>> Chip-seq 321 7792370 . . .
>>>>
>>>>
>> Name=H3K27me3_animal_ChIP-seq_st10-12;wigfile=/data/gbrowse/wiggle_data/H3K27me3_animal_ChIP-seq_st10-12_xenTro2.wig/track_001.scaffold_1.1269301611.wib
>>
>>>> This wiggle file was loaded into mysql using the bp_seqfeature_load.pl
>>>>
>> .
>>
>>>> The load did not seem to produce any errors.
>>>>
>>>> The last track definition I tried in the config file was:
>>>>
>>>> [H3K27me3_animal_ChIP-seq_st10-12_xenTro2 WIG]
>>>> feature = H3K27me3_animal_ChIP-seq_st10-12_xenTro2
>>>> glyph = wiggle_xyplot
>>>> min_score = 1
>>>> max_score = 198
>>>> key = H3K27 animal ChiP-seq_Xenopus Tropicalis stages 10 to 12
>>>>
>>>> The key appears but no glyphs appear under the key on that track.
>>>>
>>>> Here is a error_log output from an attempt to view a section that should
>>>> have had wiggle data. There was an "uninitialized value in
>>>>
>> concatenation
>>
>>>> (.) or string" error but nothing specific to the wiggle track that I
>>>>
>> can
>>
>>>> see: That error and the line retrieving the methylation wiggle track
>>>>
>> are
>>
>>>> bolded.
>>>>
>>>> Thanks,
>>>>
>>>> Jeff
>>>>
>>>> error_log output follows:
>>>>
>>>> [Tue Mar 23 13:50:25 2010] [error] [client 136.159.4.22] [2538] RUN():
>>>> POST:
>>>>
>>>>
>> http://xtropicalis.cpsc.ucalgary.ca/cgi-bin/gb2/gbrowse/Xenopus_tropicalis_4_1_mysql/force_submit=0;plugin_find=0;name=scaffold_165%3A82942..88271;Search=Search
>>
>>>> at
>>>>
>>>>
>> /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/Bio/Graphics/Browser2/Render.pm
>>
>>>> line 160., referer:
>>>>
>>>>
>> http://xtropicalis.cpsc.ucalgary.ca/cgi-bin/gb2/gbrowse/Xenopus_tropicalis_4_1_mysql/?name=id:1198108;dbid=scaffolds:database
>>
>>>> [Tue Mar 23 13:50:25 2010] [error] [client 136.159.4.22] [2538]
>>>> add_user_tracks() at
>>>>
>>>>
>> /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/Bio/Graphics/Browser2/Render.pm
>>
>>>> line 167., referer:
>>>>
>>>>
>> http://xtropicalis.cpsc.ucalgary.ca/cgi-bin/gb2/gbrowse/Xenopus_tropicalis_4_1_mysql/?name=id:1198108;dbid=scaffolds:database
>>
>>>> [Tue Mar 23 13:50:25 2010] [error] [client 136.159.4.22] [2538] testing
>>>>
>> for
>>
>>>> asynchronous event() at
>>>>
>>>>
>> /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/Bio/Graphics/Browser2/Render.pm
>>
>>>> line 178., referer:
>>>>
>>>>
>> http://xtropicalis.cpsc.ucalgary.ca/cgi-bin/gb2/gbrowse/Xenopus_tropicalis_4_1_mysql/?name=id:1198108;dbid=scaffolds:database
>>
>>>> [Tue Mar 23 13:50:25 2010] [error] [client 136.159.4.22] [2538] init()
>>>>
>> at
>>
>> /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/Bio/Graphics/Browser2/Render.pm
>>
>>>> line 185., referer:
>>>>
>>>>
>> http://xtropicalis.cpsc.ucalgary.ca/cgi-bin/gb2/gbrowse/Xenopus_tropicalis_4_1_mysql/?name=id:1198108;dbid=scaffolds:database
>>
>>>> [Tue Mar 23 13:50:25 2010] [error] [client 136.159.4.22] [2538]
>>>> update_state() at
>>>>
>>>>
>> /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/Bio/Graphics/Browser2/Render.pm
>>
>>>> line 188., referer:
>>>>
>>>>
>> http://xtropicalis.cpsc.ucalgary.ca/cgi-bin/gb2/gbrowse/Xenopus_tropicalis_4_1_mysql/?name=id:1198108;dbid=scaffolds:database
>>
>>>> [Tue Mar 23 13:50:25 2010] [error] [client 136.159.4.22] [2538] render()
>>>>
>> at
>>
>> /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/Bio/Graphics/Browser2/Render.pm
>>
>>>> line 195., referer:
>>>>
>>>>
>> http://xtropicalis.cpsc.ucalgary.ca/cgi-bin/gb2/gbrowse/Xenopus_tropicalis_4_1_mysql/?name=id:1198108;dbid=scaffolds:database
>>
>>>> [Tue Mar 23 13:50:25 2010] [error] [client 136.159.4.22] *Use of
>>>> uninitialized value in concatenation (.) or string at
>>>>
>>>>
>> /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/Bio/Graphics/Browser2/Render/HTML.pm
>>
>>>> line 139.*, referer:
>>>>
>>>>
>> http://xtropicalis.cpsc.ucalgary.ca/cgi-bin/gb2/gbrowse/Xenopus_tropicalis_4_1_mysql/?name=id:1198108;dbid=scaffolds:database
>>
>>>> [Tue Mar 23 13:50:26 2010] [error] [client 136.159.4.22] [2538] cleanup
>>>>
>> at
>>
>> /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/Bio/Graphics/Browser2/Render.pm
>>
>>>> line 199., referer:
>>>>
>>>>
>> http://xtropicalis.cpsc.ucalgary.ca/cgi-bin/gb2/gbrowse/Xenopus_tropicalis_4_1_mysql/?name=id:1198108;dbid=scaffolds:database
>>
>>>> [Tue Mar 23 13:50:26 2010] [error] [client 136.159.4.22] [2538] session
>>>> flush at
>>>>
>>>>
>> /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/Bio/Graphics/Browser2/Render.pm
>>
>>>> line 203., referer:
>>>>
>>>>
>> http://xtropicalis.cpsc.ucalgary.ca/cgi-bin/gb2/gbrowse/Xenopus_tropicalis_4_1_mysql/?name=id:1198108;dbid=scaffolds:database
>>
>>>> [Tue Mar 23 13:50:26 2010] [error] [client 136.159.4.22] [2538]
>>>>
>> synchronous
>>
>>>> exit at
>>>>
>>>>
>> /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/Bio/Graphics/Browser2/Render.pm
>>
>>>> line 205., referer:
>>>>
>>>>
>> http://xtropicalis.cpsc.ucalgary.ca/cgi-bin/gb2/gbrowse/Xenopus_tropicalis_4_1_mysql/?name=id:1198108;dbid=scaffolds:database
>>
>>>> [Tue Mar 23 13:50:31 2010] [error] [client 136.159.4.22] [2541] RUN():
>>>> POST:
>>>>
>>>>
>> http://xtropicalis.cpsc.ucalgary.ca/cgi-bin/gb2/gbrowse/Xenopus_tropicalis_4_1_mysql/action=navigate;navigate=left%200at
>>
>> /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/Bio/Graphics/Browser2/Render.pm
>>
>>>> line 160., referer:
>>>>
>>>>
>> http://xtropicalis.cpsc.ucalgary.ca/cgi-bin/gb2/gbrowse/Xenopus_tropicalis_4_1_mysql/?name=id:1198108;dbid=scaffolds:database
>>
>>>> [Tue Mar 23 13:50:31 2010] [error] [client 136.159.4.22] [2541]
>>>> add_user_tracks() at
>>>>
>>>>
>> /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/Bio/Graphics/Browser2/Render.pm
>>
>>>> line 167., referer:
>>>>
>>>>
>> http://xtropicalis.cpsc.ucalgary.ca/cgi-bin/gb2/gbrowse/Xenopus_tropicalis_4_1_mysql/?name=id:1198108;dbid=scaffolds:database
>>
>>>> [Tue Mar 23 13:50:31 2010] [error] [client 136.159.4.22] [2541] testing
>>>>
>> for
>>
>>>> asynchronous event() at
>>>>
>>>>
>> /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/Bio/Graphics/Browser2/Render.pm
>>
>>>> line 178., referer:
>>>>
>>>>
>> http://xtropicalis.cpsc.ucalgary.ca/cgi-bin/gb2/gbrowse/Xenopus_tropicalis_4_1_mysql/?name=id:1198108;dbid=scaffolds:database
>>
>>>> [Tue Mar 23 13:50:31 2010] [error] [client 136.159.4.22] [2541]
>>>> asynchronous exit at
>>>>
>>>>
>> /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/Bio/Graphics/Browser2/Render.pm
>>
>>>> line 180., referer:
>>>>
>>>>
>> http://xtropicalis.cpsc.ucalgary.ca/cgi-bin/gb2/gbrowse/Xenopus_tropicalis_4_1_mysql/?name=id:1198108;dbid=scaffolds:database
>>
>>>> [Tue Mar 23 13:50:32 2010] [error] [client 136.159.4.22] [2549] RUN():
>>>> POST:
>>>>
>>>>
>> http://xtropicalis.cpsc.ucalgary.ca/cgi-bin/gb2/gbrowse/Xenopus_tropicalis_4_1_mysql/action=update_sections;section_names=page_title;section_names=span;section_names=galaxy_form;section_names=search_form_objects
>>
>>>> at
>>>>
>>>>
>> /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/Bio/Graphics/Browser2/Render.pm
>>
>>>> line 160., referer:
>>>>
>>>>
>> http://xtropicalis.cpsc.ucalgary.ca/cgi-bin/gb2/gbrowse/Xenopus_tropicalis_4_1_mysql/?name=id:1198108;dbid=scaffolds:database
>>
>>>> [Tue Mar 23 13:50:32 2010] [error] [client 136.159.4.22] [2549]
>>>> add_user_tracks() at
>>>>
>>>>
>> /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/Bio/Graphics/Browser2/Render.pm
>>
>>>> line 167., referer:
>>>>
>>>>
>> http://xtropicalis.cpsc.ucalgary.ca/cgi-bin/gb2/gbrowse/Xenopus_tropicalis_4_1_mysql/?name=id:1198108;dbid=scaffolds:database
>>
>>>> [Tue Mar 23 13:50:32 2010] [error] [client 136.159.4.22] [2549] testing
>>>>
>> for
>>
>>>> asynchronous event() at
>>>>
>>>>
>> /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/Bio/Graphics/Browser2/Render.pm
>>
>>>> line 178., referer:
>>>>
>>>>
>> http://xtropicalis.cpsc.ucalgary.ca/cgi-bin/gb2/gbrowse/Xenopus_tropicalis_4_1_mysql/?name=id:1198108;dbid=scaffolds:database
>>
>>>> [Tue Mar 23 13:50:32 2010] [error] [client 136.159.4.22] [2549]
>>>> asynchronous exit at
>>>>
>>>>
>> /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/Bio/Graphics/Browser2/Render.pm
>>
>>>> line 180., referer:
>>>>
>>>>
>> http://xtropicalis.cpsc.ucalgary.ca/cgi-bin/gb2/gbrowse/Xenopus_tropicalis_4_1_mysql/?name=id:1198108;dbid=scaffolds:database
>>
>>>> *[Tue Mar 23 13:50:33 2010] [error] [client 136.159.4.22] [2550] RUN():
>>>> POST:
>>>>
>>>>
>> http://xtropicalis.cpsc.ucalgary.ca/cgi-bin/gb2/gbrowse/Xenopus_tropicalis_4_1_mysql/action=retrieve_multiple;track_ids=DNA%2FGC%20Content;track_ids=Xenbase_XT_Gene_4.1;track_ids=Jgi_XT_Gene_4.1;track_ids=Jgi_XT_Mrna_4.1;track_ids=Ensembl_XT_Gene_4.1;track_ids=Gurdon_xt7.1_est;track_ids=%20H3K27me3_animal_ChIP-seq_st10-12_xenTro2%20WIG;tk_DNA%2FGC%20Content=63cc431bb4a3ae7ef5e6b6d708ee71c1;tk_Xenbase_XT_Gene_4.1=012653797c6e2ddd07ce56cfef2d3884;tk_Jgi_XT_Gene_4.1=4e7b66bd0c6f1a1416073694fef6352f;tk_Jgi_XT_Mrna_4.1=95da4a70614a3b23606e182662b0e4c4;tk_Ensembl_XT_Gene_4.1=c3b31b5e53cd8773545a5a2f6c77ce0e;tk_Gurdon_xt7.1_est=d73f47066f8f6d4e868d20ffa3c59148;tk_%20H3K27me3_animal_ChIP-seq_st10-12_xenTro2%20WIG=2a2bafb7bfe61a0489ccef1d400aeee0
>>
>>>> at
>>>>
>>>>
>> /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/Bio/Graphics/Browser2/Render.pm
>>
>>>> line 160., referer:
>>>>
>>>>
>> http://xtropicalis.cpsc.ucalgary.ca/cgi-bin/gb2/gbrowse/Xenopus_tropicalis_4_1_mysql/?name=id:1198108;dbid=scaffolds:database
>>
>>>> *
>>>> [Tue Mar 23 13:50:33 2010] [error] [client 136.159.4.22] [2550]
>>>> add_user_tracks() at
>>>>
>>>>
>> /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/Bio/Graphics/Browser2/Render.pm
>>
>>>> line 167., referer:
>>>>
>>>>
>> http://xtropicalis.cpsc.ucalgary.ca/cgi-bin/gb2/gbrowse/Xenopus_tropicalis_4_1_mysql/?name=id:1198108;dbid=scaffolds:database
>>
>>>> [Tue Mar 23 13:50:33 2010] [error] [client 136.159.4.22] [2550] testing
>>>>
>> for
>>
>>>> asynchronous event() at
>>>>
>>>>
>> /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/Bio/Graphics/Browser2/Render.pm
>>
>>>> line 178., referer:
>>>>
>>>>
>> http://xtropicalis.cpsc.ucalgary.ca/cgi-bin/gb2/gbrowse/Xenopus_tropicalis_4_1_mysql/?name=id:1198108;dbid=scaffolds:database
>>
>>>> [Tue Mar 23 13:50:34 2010] [error] [client 136.159.4.22] [2550]
>>>> asynchronous exit at
>>>>
>>>>
>> /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/Bio/Graphics/Browser2/Render.pm
>>
>>>> line 180., referer:
>>>>
>>>>
>> http://xtropicalis.cpsc.ucalgary.ca/cgi-bin/gb2/gbrowse/Xenopus_tropicalis_4_1_mysql/?name=id:1198108;dbid=scaffolds:database
>>
>>>> Jeff Bowes M.Sc.
>>>> Technical Director, Xenbase
>>>> Department of Biological Sciences
>>>> University of Calgary
>>>> Calgary, Alberta T2N 1N4
>>>> CANADA
>>>> Tel: (403) 220-2824
>>>> Fax: (403) 284-4707
>>>>
>>>>
>>>>
>>>>
>>>>
>>>>
>>>>
>> ------------------------------------------------------------------------------
>>
>>>> Download Intel® Parallel Studio Eval
>>>> Try the new software tools for yourself. Speed compiling, find bugs
>>>> proactively, and fine-tune applications for parallel performance.
>>>> See why Intel Parallel Studio got high marks during beta.
>>>> http://p.sf.net/sfu/intel-sw-dev
>>>> _______________________________________________
>>>> Gmod-gbrowse mailing list
>>>> Gmod-gbrowse at lists.sourceforge.net
>>>> https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse
>>>>
>>>>
>>>>
>>>>
>>>
>>>
>> --
>> Jeff Bowes M.Sc.
>> Technical Director, Xenbase
>> Department of Biological Sciences
>> University of Calgary
>> Calgary, Alberta T2N 1N4
>> CANADA
>> Tel: (403) 220-2824
>> Fax: (403) 284-4707
>>
>>
>>
>>
>>
>> ------------------------------------------------------------------------------
>> Download Intel® Parallel Studio Eval
>> Try the new software tools for yourself. Speed compiling, find bugs
>> proactively, and fine-tune applications for parallel performance.
>> See why Intel Parallel Studio got high marks during beta.
>> http://p.sf.net/sfu/intel-sw-dev
>> _______________________________________________
>> Gmod-gbrowse mailing list
>> Gmod-gbrowse at lists.sourceforge.net
>> https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse
>>
>>
>
>
>
>
--
Jeff Bowes M.Sc.
Technical Director, Xenbase
Department of Biological Sciences
University of Calgary
Calgary, Alberta T2N 1N4
CANADA
Tel: (403) 220-2824
Fax: (403) 284-4707
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