Re: [base] Base1PluginExecutor
Hi Nick,
It is correct that reporterlists isn't imported by the
Base1PluginExecuter. I have added a ticket, http://base.thep.lu.se/ticket/943
.
There is no workaround.
/Johan
On 7 mar 2008, at 15.41, Nick Loman wrote:
Bob MacCallum wrote:
The tricks are (in no particular order)
* share the plugin definition and configuration to everyone
* configure the plugin using the the config files in
Root's /BASE 1 plugin configuration files folder.
Hi
Thanks for replies Bob/Nicklas.
I had to make the following changes to the MGH stuff so far and have
got
a little further.
BASE was getting upset because the first entry in the definition
was missing the 'maxChannels' parameter. Therefore, I deleted all
the BASEfile definitions apart from the last one which has a value
for 'maxChannels' and managed to configure the plugin successfully.
I had to make the following change to basefile-genelist.pl and
basefile-general.pl to get it to read the BASEfile correctly.
89c86
elsif($currentsection eq BASEfile) {
---
elsif($currentsection eq BASEfile or $currentsection eq
'settings') {
93d89
Now although the PNG files are created correctly and copied to the
folder, the actual reporterlist information is not being imported
into BASE.
The stdout output from the script is as follows:
BASEfile
sectiontabreporterlist
columnstabreporterIdtabscore
ECs4755 0.256762034483983
ECs3012 0.119996549971508
ECs2479 0.286847065875626
...
Now, looking at the BASE 2.5.0 sourcecode, there is no case in
importData() which handles a reporterlist section. So perhaps I
should
not be surprised no data is being imported?
Can anyone confirm whether this is the case, and whether there is any
workaround?
Many thanks
Nick.
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Re: [base] Base1PluginExecuter parameter xml
Hi Bob, Just wanted to tell you that I've successfully executed the clustering from Base1. As you mentioned the export wrote the external id wrong. It should be reporterId. It has been fixed in the Base2.4 branch. /Johan 12 sep 2007 kl. 13.36 skrev Bob MacCallum: [note: minor bug report buried deep in this email] Now I'm just having some problems with the BASE1/BASE2 column names. At last google and the mailing list help me out: http://www.mail-archive.com/basedb-users@lists.sourceforge.net/ msg00725.html It looks like I just have to create an extra value column called ratio1_2 actually I need a formula exactly as the mail suggests. But I'm still getting a problem: Status Error: /usr/local/base_dir/base2dev_plugins/base1plugins/ basehclust: Missing reporterId/assayData columns or ratio field Job parameters Assay distance metric Pearson New cluster point center of mass Gene distance metric Pearson Plugin directory /home/maccallr/Analysis Hierarchical clustering ratioColumn ratio1_2 section clustering settings Bioassay set background subtracted medians Plugin configuration parameters Parameter version 7 (7) execName clusteringscript Plugin executables path /usr/local/base_dir/base2dev_plugins/ base1plugins geneAverages true jobParameters [snip: imported from working base1 instance - no changes made] leaveStdintrue leaveStdout false maxChannels 2 minChannels 2 serialFormat false usedColumns reporterId usedFieldsratio1_2 versionNumber 1.1 Since Base1PluginExecuter uses BioAssaySetExporter.exportBaseFileMatrix to create a BASEfile, I tried to do this manually and get columns externalId assayData rather than columns reporterId assayData which I guess the basehclust binary is expecting? Here's a snippet of the BASEfile I manually exported. See how the ratio1_2 column is all present and correct (thanks to the formula). BASEfile section assays count 12 columns id nameGeneration OrganismPart annotationColumns Generation OrganismPart % 263 carcass_g1-cy3_SR-cy5 1 carcass 264 carcass_g1-cy5_SR-cy3 1 carcass 265 carcass_g3-cy5_SR-cy3 3 carcass 266 head_g1-cy3_SR-cy5 1 head 267 head_g1-cy5_SR-cy3 1 head 268 head_g3-cy5_SR-cy3 3 head 269 midgut_g1-cy3_SR-cy51 midgut 270 midgut_g1-cy5_SR-cy31 midgut 271 midgut_g3-cy5_SR-cy33 midgut 272 ovaries_g1-cy3_SR-cy5 1 ovaries 273 ovaries_g1-cy5_SR-cy3 1 ovaries 274 ovaries_g3-cy5_SR-cy3 3 ovaries section spots channels 2 assayFields ratio1_2 columns externalId assayData assays263 264 265 266 267 268 269 270 271 272 273 274 count 21100 % 4A3B-AAB-A-06 5.7225670458895 3.1218635882757 3.0588992108785 0.2639156720298 4.0223276353137 6.675902576748 3.4137582490339 2.3933277183965 2.7949516801256 2.7989004774074 2.481474953736 2.9725981696501 4A3B-AAB-A-12 2.6034823374857 1.8699111228203 2.1851485479522 0.46444012021543 1.5953635012332 2.6418038900175 1.1084148689112 0.81114689236237 1.2586586018848 1.3185744749523 1.3753473626496 1.0045607051797 4A3B-AAB-C-06 2.1968544953519 1.9939638540184 ... I then tried to create a reporterId formula in the same way, but this caused an uncaught exception (in the tomcat logs) when I try to view the column in experiment explorer: 12:05:43,237 ERROR [jsp]:253 - Servlet.service() for servlet jsp threw exception java.lang.ClassCastException: java.lang.String cannot be cast to java.lang.Number at net.sf.basedb.util.formatter.NumberFormatter.format (NumberFormatter.java:35) at net.sf.basedb.clients.web.taglib.table.Cell.doEndTag (Cell.java:231) at org.apache.jsp.views.experiments.explorer.view.view_jsp._jspService (view_jsp.java:1450) Not surprisingly a text column doesn't work too well in a formula. It looks like I should recompile basehclust to look for externalId instead of reporterId. This seems trivial having grepped the source code. Any thoughts? cheers, Bob. cheers, Bob. Johan Enell writes: Hj Bob, The clustering from Base1 will not work in Base2. Or more precisely, you will be able to run the plugin but you wont be able to se the result. The visualization page in Base1 was a specific php page for that plugin and we didn't want a solution like that in Base2. When you configure Base1 plugins you should always start of from a base1 plugin configuration file. From the plugin page in Base1 you will find an export link with each plugin. Use that file to configure the Base1PluginExecuter. /Johan 11 sep 2007 kl. 16.58 skrev Bob MacCallum: Hi, I
Re: [base] Base1PluginExecuter parameter xml
Hj Bob, The clustering from Base1 will not work in Base2. Or more precisely, you will be able to run the plugin but you wont be able to se the result. The visualization page in Base1 was a specific php page for that plugin and we didn't want a solution like that in Base2. When you configure Base1 plugins you should always start of from a base1 plugin configuration file. From the plugin page in Base1 you will find an export link with each plugin. Use that file to configure the Base1PluginExecuter. /Johan 11 sep 2007 kl. 16.58 skrev Bob MacCallum: Hi, I was trying to find out if base1's hierarchical clustering would run under base2 - and got to the point where I need to provide parameter settings as XML. I could spend an hour figuring this out by hand (e.g. from the examples on the BASE2 demo server) but I'm convinced there's an easier way. I've searched the plugin site for documentation. Could someone help please? Since the hierarchical clustering isn't on the BASE2 demo server, does that mean it doesn't work? We know that there won't be any display tools available in BASE2 for this, but we can work with the PNGs and assorted text files. many thanks, Bob. -- Bob MacCallum | VectorBase Developer | Kafatos/Christophides Groups | Division of Cell and Molecular Biology | Imperial College London | Phone +442075941945 | Email [EMAIL PROTECTED] -- --- This SF.net email is sponsored by: Microsoft Defy all challenges. Microsoft(R) Visual Studio 2005. http://clk.atdmt.com/MRT/go/vse012070mrt/direct/01/ ___ The BASE general discussion mailing list basedb-users@lists.sourceforge.net unsubscribe: send a mail with subject unsubscribe to [EMAIL PROTECTED] - This SF.net email is sponsored by: Microsoft Defy all challenges. Microsoft(R) Visual Studio 2005. http://clk.atdmt.com/MRT/go/vse012070mrt/direct/01/ ___ The BASE general discussion mailing list basedb-users@lists.sourceforge.net unsubscribe: send a mail with subject unsubscribe to [EMAIL PROTECTED]
Re: [base] base2 and Base1PluginExecuter - the parameter order is ignored and results in an invalid basefile
Hi Chad, This is correct. According to the specification (http://base1.thep.lu.se/documentation/development/plugins.txt) the order of the headers has no requirement. I suggest that you write your plug-in so it is independent of the order of the headers. /Johan Chad Matsalla wrote: Greetings, I'm trying to run a base1 plugin using the Base1PluginExecuter in base-2.3.1. In the 'Job Parameters' section of the configuration for this plugin, I have this[1]. The basefile that is generated should have a 'parameter' section. I would expect it to look like this[2]. Instead it looks like this[3]. Apparently, the 'position' is being ignored. In this case the position of the 'section\tparameter' is critical: it *must* be first. The order of items in the 'parameter' section does not change if I move the order of 'parameter' elements in the xml. Can you help? Chad Matsalla National Research Council of Canada Plant Biotechnology Institute [1] jobparameters parameter position=1 type=h namesection/name commonname/commonname options6/options defaultvalueparameter/defaultvalue /parameter parameter position=2 type=e namewindowcol/name commonnameIntensity to use/commonname options0/options defaultvaluemedian/defaultvalue enumoptions value key=medianMedian/value value key=meanMean/value /enumoptions /parameter !-- a total of ten parameters are in this file. I only included two, for brevity -- /jobparameters [2] BASEfile endwindow 32768 backgroundcol none section parameter startwindow16384 saturated 0 reportyes scale log2 replacefrom32768 originals leave pluginDirectory /home/root/projects for people/maureen/wt vs. tga1 (shearer)/Transformation PMT Merging windowcol median % [3] BASEfile section parameter endwindow 32768 backgroundcol none startwindow16384 saturated 0 reportyes scale log2 replacefrom32768 originals leave pluginDirectory /home/root/projects for people/maureen/wt vs. tga1 (shearer)/Transformation PMT Merging windowcol median % - This SF.net email is sponsored by DB2 Express Download DB2 Express C - the FREE version of DB2 express and take control of your XML. No limits. Just data. Click to get it now. http://sourceforge.net/powerbar/db2/ ___ The BASE general discussion mailing list basedb-users@lists.sourceforge.net unsubscribe: send a mail with subject unsubscribe to [EMAIL PROTECTED] - This SF.net email is sponsored by DB2 Express Download DB2 Express C - the FREE version of DB2 express and take control of your XML. No limits. Just data. Click to get it now. http://sourceforge.net/powerbar/db2/ ___ The BASE general discussion mailing list basedb-users@lists.sourceforge.net unsubscribe: send a mail with subject unsubscribe to [EMAIL PROTECTED]
Re: [base] Réplicates in base 2
I think I should answer this. There is still some features in the
Base1PluginExecuter to be done. It tries to simulate the plug-in
execution of BASE 1.2.17 and that process was a little bit more complex
then I first thought.
Q1?
-Why 3 Bioassay sets are created by this plugin ? (I clicked only 1
time)
A1-
There is only one BioAssaySet created, "Something after".
"Something---" is you transformation and JE_nbrOfElemets is a extra
value created by the plug-in.
Q2?
-Why those strange names: Something---, Something after (OK, it is not
a serious pb, except that I'm afraid it is the sign of something wong
in the process)
A2-
The names is because the plug-in (Base1PluginExecuter) is still in
development. It will of course change to be a useful name instead.
Q3?
-Why, in the Bioassay set Something after, are there 77148 Spots and 0
Reporters?
A3-
This is a known issue and of course it's wrong and will be corrected.
Q4?
-Why an extra value called JE_nbrOfElements is created as a last stuff ?
A3-
This is an extra value created by the plug-in. This value is the number
of spots the new merged spot was created from.
/Johan
Emmanuel Courcelle wrote:
I don't know much about the BASE 1 plugins. What do you think is buggy?
/Nicklas
Sorry, the html copy-and-paste was not clear; here is a hand-made
copy-and-paste:
Name
Spots/Values Reporters
Plugin
Median FG
Formula intensity
calculator
Mediane
80640 6229
Filter: raw('flags') ==
0
JEP filter plugin
Filtered Mediane
77148 6158
Normalization: Median
ratio
Normalization: Median ratio
Filtered normalized Mediane
77148 6158
Something---
Base1PluginExecuter
Something after
77148 0
JE_nbrOfElements
77148
Base1PluginExecuter
So, the things I don't understand (buggy or not buggy, that is the
question):
-Why 3 Bioassay sets are created by this plugin ? (I clicked only 1
time)
-Why those strange names: Something---, Something after (OK, it is not
a serious pb, except that I'm afraid it is the sign of something wong
in the process)
-Why, in the Bioassay set Something after, are there 77148 Spots and 0
Reporters ?
-Why an extra value called JE_nbrOfElements is created as a last stuff ?
--
Emmanuel COURCELLE[EMAIL PROTECTED]
L.I.P.M. (UMR CNRS-INRA 2594/441) tel (33) 5-61-28-54-50
B.P.52627 - 31326 CASTANET TOLOSAN Cedex - FRANCE
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Re: [base] filtering/analysis tips please
Missed to answer you other questions... You use the gene filter In # of Assays Exampel: You have 4 assays and you want to filter out the spots with ratio greater then 2 in at least 3 assays. You need two criterias for this. The spot filter ratio 2 and the and the gene filter In # Assays 2 /Johan Bob MacCallum wrote: Hi all, In the analysis steps part of BASE 1.2.x, is there a way to create a reporter list such that X out of Y assays satisfy some filter condition, where 1 X Y ? I already know how to do it where X=1 or X=Y. For example: 1. Reporters where at least one assay has a twofold change Filter on ratio not between 0.5, 2, create reporter list R with results, then filter original set on reporter list present in R. 2. Reporters where *all* assays have max intensity = 100: Filter on max(Ch1,Ch2) 100, create reporter list S with results, then filter original set on reporter list absent in S. Quite often you want to filter somewhere in between, i.e. at least half of the assays should show X-fold changes, or whatever. It would not be hard to write a plugin to do this, but I haven't written any plugins yet. So I wondered if there were any GUI tricks I had missed. Failing that I'll write a pseudo-plugin (a script which takes a custom BASE file and dumps a reporter list) and worry about configuring it as a plugin at a later date. Also, if anyone has an 'averaging over replicates' plugin (based on a specified sample annotation), I would be very grateful. Installing such a plugin would help me figure out how to write one. cheers, Bob. - Take Surveys. Earn Cash. Influence the Future of IT Join SourceForge.net's Techsay panel and you'll get the chance to share your opinions on IT business topics through brief surveys -- and earn cash http://www.techsay.com/default.php?page=join.phpp=sourceforgeCID=DEVDEV ___ The BASE general discussion mailing list basedb-users@lists.sourceforge.net unsubscribe: send a mail with subject unsubscribe to [EMAIL PROTECTED]
[base] Problems with RawDataImporter
Hi Pablo, This is the errors I found: Data header regexp: You should write Block\tColumn.* (this will match any line starting with BlockColumn) or Block\tColumn\tID (this will math a line Block ColumnID. Header regexp: Should something like ?(.+)=(.*)? so the header lines are matched. /Johan Pablo Lemos Ochandio wrote: Hi Everybody!! I have a problem (again!) with a .gpr file. I have configure a RAW data importer to parser GenePix .gpr file. The plugin configuration is: Block \Block\ Column\Column\ Data footer Data header Block\tColumn Data splitter \t HeaderATF\t1.0 Ignore Max data columns MetaGridX MetaGridY Min data columns CV Background pixels Channel 1 background mean Channel 1 background median Channel 1 background standard deviation Channel 1 foreground mean Channel 1 foreground median Channel 1 foreground standard deviation Percent saturated pixels Percent pixels within 1 standard deviation Percent pixels within 2 standard deviations Channel 2 background mean Channel 2 background median Channel 2 background standard deviation Channel 2 foreground mean Channel 2 foreground median Channel 2 foreground standard deviation Percent saturated pixels Percent pixels within 1 standard deviation Percent pixels within 2 standard deviations Spot diameter Foreground pixels Flags M value Standard deviation of ratios Rgn R2 Rgn ratio Raw data type genepix Reporter ID \ID\ Row Remove quotes true X Y I minimize the file to some columns (Block, Column, ID) to try to debug the plugin. Base2 give me the next error advise: Error: File 'File[id=31; name=prueba9.gpr]' cannot be imported by this plugin. InvalidDataException: File 'File[id=31; name=prueba9.gpr]' cannot be imported by this plugin. The .gpr file that im using is: ATF1.0 311 Type=GenePix Results 3 DateTime=2005/02/26 13:51:20 Settings=1.26.10.gps GalFile=Impresion3gal27enero04.gal PixelSize=10 Wavelengths=635532 ImageFiles=1.26.10_750_760 24h-4.tif 21.26.10_750_760 24h-4.tif 3 NormalizationMethod=None NormalizationFactors=11 JpegImage=1.26.10.jpg StdDev=Type 1 RatioFormulations=W1/W2 (635/532) Barcode= BackgroundSubtraction=LocalFeature ImageOrigin=1640, 4240 JpegOrigin=1640, 4240 Creator=GenePix Pro 4.1.1.4 Scanner=GenePix 4000B [92593] FocusPosition=5 Temperature=27.79 LinesAveraged=2 Comment= PMTGain=750760 ScanPower=100100 LaserPower=3.541.82 LaserOnTime=65326557 Filters= ScanRegion=164,424,2000,5952 Supplier=BioRobotics ArrayerSoftwareName=TAS Application Suite (MicroGrid II) ArrayerSoftwareVersion=2.4.0.2 BlockColumnID 11cal2 12cal2 Could someone help me? Could someone send me a test .gpr file or a valid configuration plugin? Thanks a lot -- Pablo Lemos Ochandio - Analista de Sistemas Fisicos Instituto Valenciano de Investigaciones Agrarias (IVIA) Crta Moncada - Naquera Km 4.5 46113 - Moncada Valencia Spain - Take Surveys. Earn Cash. Influence the Future of IT Join SourceForge.net's Techsay panel and you'll get the chance to share your opinions on IT business topics through brief surveys -- and earn cash http://www.techsay.com/default.php?page=join.phpp=sourceforgeCID=DEVDEV ___ The BASE general discussion mailing list basedb-users@lists.sourceforge.net unsubscribe: send a mail with subject unsubscribe to [EMAIL PROTECTED] - Take Surveys. Earn Cash. Influence the Future of IT Join SourceForge.net's Techsay panel and you'll get the chance to share your opinions on IT business topics through brief surveys -- and earn cash http://www.techsay.com/default.php?page=join.phpp=sourceforgeCID=DEVDEV ___ The BASE general discussion mailing list basedb-users@lists.sourceforge.net unsubscribe: send a mail with subject unsubscribe to [EMAIL PROTECTED]
Re: [base] remote servers
Hi Charles, On the plug-ins page in the Analyzq data menu you should find what you are looking for. Just below the table and above the line where you adjust the permission levels you should find a line where you can activate or deactivate the plug-ins you have selected in the table on your avalible servers. /Johan 16 jan 2006 kl. 17.06 skrev charles girardot: Hi all, We just added remote computers to our BASE installation to run plugins. It works fine given that we had to set the proper server id to be used by the plugin *manually* in the base db (I mean by issuing : update ProgramServer set computationServer = 3 where program = 10 ) We never managed to find how to set up this using the web interface. Did we miss something ? Thanks Cheers Charles --- This SF.net email is sponsored by: Splunk Inc. Do you grep through log files for problems? Stop! Download the new AJAX search engine that makes searching your log files as easy as surfing the web. DOWNLOAD SPLUNK! http://ads.osdn.com/?ad_id=7637alloc_id=16865op=click ___ The BASE general discussion mailing list basedb-users@lists.sourceforge.net unsubscribe: send a mail with subject unsubscribe to [EMAIL PROTECTED] --- This SF.net email is sponsored by: Splunk Inc. Do you grep through log files for problems? Stop! Download the new AJAX search engine that makes searching your log files as easy as surfing the web. DOWNLOAD SPLUNK! http://ads.osdn.com/?ad_id=7637alloc_id=16865op=click ___ The BASE general discussion mailing list basedb-users@lists.sourceforge.net unsubscribe: send a mail with subject unsubscribe to [EMAIL PROTECTED]
