galaxy-dist commit 9ee40043b826: rgHaploView tool version upgrade - now shows thumbnail of ld plots - galaxy-commits

20 Nov 2010

# HG changeset patch -- Bitbucket.org
# Project galaxy-dist
# URL http://bitbucket.org/galaxy/galaxy-dist/overview
# User Ross Lazarus ross.lazarus@gmail.com
# Date 1289322752 18000
# Node ID 9ee40043b826b3bc1e29f84996f9fe14dd119a45
# Parent  a77b2888759e94861252ca65437e11ec298b3058
rgHaploView tool version upgrade - now shows thumbnail of ld plots

--- a/tools/rgenetics/rgHaploView.xml
+++ b/tools/rgenetics/rgHaploView.xml
@@ -1,4 +1,4 @@
-<tool id="rgHaploView1" name="LD plots:" version="0.2">
+<tool id="rgHaploView1" name="LD plots:" version="0.3"><description>and comparisons with HapMap data</description>
--- a/test-data/rgtestouts/rgHaploView/rgHaploViewtest1.html
+++ b/test-data/rgtestouts/rgHaploView/rgHaploViewtest1.html
@@ -9,9 +9,11 @@
 </head><body><div class="document">
-<h4>rgenetics for Galaxy rgHaploView.py, wrapping HaploView</h4><br><div><hr><ul>
+<h4>rgenetics for Galaxy rgHaploView.py, wrapping HaploView</h4><table><tr><td><a href="allnup.pdf"><img src="allnup.png" alt="Main combined LD image" hspace="10" align="middle"></td><td>Click the thumbnail at left to download the main combined LD image <a href=allnup.pdf>allnup.pdf</a></td></tr></table>
+<br><div><hr><ul><li><a href="alljoin.pdf">alljoin.pdf - All pdf plots, each on a separate page</a></li><li><a href="allnup.pdf">allnup.pdf - All pdf plots on a single page</a></li>
+<li><a href="allnup.png">allnup.png - allnup.png</a></li><li><a href="1_rgHaploViewtest1.pdf">1_rgHaploViewtest1.pdf - 1_rgHaploViewtest1.pdf</a></li><li><a href="1_rgHaploViewtest1.png">1_rgHaploViewtest1.png - 1_rgHaploViewtest1.png</a></li><li><a href="2_HapMap_YRI_22.pdf">2_HapMap_YRI_22.pdf - Hapmap data</a></li>
@@ -33,7 +35,7 @@ Haploview 4.2	Java Version: 1.6.0_03
-Arguments:	-n	-pairwiseTagging	-pedfile	/opt/galaxy/test-data/rgtestouts/rgHaploView/rgHaploViewtest1.ped	-info	/opt/galaxy/test-data/rgtestouts/rgHaploView/rgHaploViewtest1.info	-tagrsqcounts	-tagrsqcutoff	0.8	-ldcolorscheme	RSQ	-maxDistance	200000	-compressedpng	-chromosome	22	
+Arguments:	-n	-pairwiseTagging	-pedfile	/tmp/foo/test-data/rgtestouts/rgHaploView/rgHaploViewtest1.ped	-info	/tmp/foo/test-data/rgtestouts/rgHaploView/rgHaploViewtest1.info	-tagrsqcounts	-tagrsqcutoff	0.8	-ldcolorscheme	RSQ	-maxDistance	200000	-compressedpng	-chromosome	22
@@ -41,9 +43,9 @@ Arguments:	-n	-pairwiseTagging	-pedfile
Max LD comparison distance = 200000kb
-Using data file: /opt/galaxy/test-data/rgtestouts/rgHaploView/rgHaploViewtest1.ped
+Using data file: /tmp/foo/test-data/rgtestouts/rgHaploView/rgHaploViewtest1.ped
-Using marker information file: /opt/galaxy/test-data/rgtestouts/rgHaploView/rgHaploViewtest1.info
+Using marker information file: /tmp/foo/test-data/rgtestouts/rgHaploView/rgHaploViewtest1.info
Writing output to rgHaploViewtest1.ped.LD.PNG
@@ -79,27 +81,37 @@ Downloading chromosome 22, analysis pane
Writing output to Chromosome22YRI.LD.PNG
-This is pdfjoin version 1.20
+          ----
-Reading site configuration from /etc/pdfnup.conf
+  pdfjam: This is pdfjam version 2.06.
-  Temporary LaTeX file for this job is /var/tmp/22578.tex
+  pdfjam: Reading any site-wide or user-specific defaults...
-  Calling pdflatex...
+          (none found)
-  Finished: output is /opt/galaxy/test-data/rgtestouts/rgHaploView/alljoin.pdf
+  pdfjam: Effective call for this run of pdfjam:
-This is pdfnup version 1.20
+          /usr/local/bin/pdfjam --fitpaper 'true' --rotateoversize 'true' --suffix joined --fitpaper 'true' --outfile alljoin.pdf -- 1_rgHaploViewtest1.pdf - 2_HapMap_YRI_22.pdf -
-Reading site configuration from /etc/pdfnup.conf
+  pdfjam: Calling pdflatex...
-Processing alljoin.pdf...
+  pdfjam: Finished.  Output was to 'alljoin.pdf'.
-  Temporary LaTeX file for this job is /var/tmp/22621-1.tex
+          ----
-  Calling pdflatex...
+  pdfjam: This is pdfjam version 2.06.
-  Finished: output is /opt/galaxy/test-data/rgtestouts/rgHaploView/allnup.pdf
+  pdfjam: Reading any site-wide or user-specific defaults...
+
+          (none found)
+
+  pdfjam: Effective call for this run of pdfjam:
+
+          /usr/local/bin/pdfjam --suffix nup --nup '2x1' --landscape --nup '1x2' --outfile allnup.pdf -- alljoin.pdf - 
+
+  pdfjam: Calling pdflatex...
+
+  pdfjam: Finished.  Output was to 'allnup.pdf'.
PATH=/usr/kerberos/bin:/usr/local/bin:/bin:/usr/bin:/home/rerla/bin
@@ -107,7 +119,7 @@ PATH=/usr/kerberos/bin:/usr/local/bin:/b
-## executing java -jar /opt/galaxy/tool-data/shared/jars/haploview.jar -n -memory 2048 -pairwiseTagging -pedfile /opt/galaxy/test-data/rgtestouts/rgHaploView/rgHaploViewtest1.ped -info /opt/galaxy/test-data/rgtestouts/rgHaploView/rgHaploViewtest1.info -tagrsqcounts -tagrsqcutoff 0.8 -ldcolorscheme RSQ -maxDistance 200000 -compressedpng -chromosome 22 returned 0
+## executing java -jar /opt/galaxy/tool-data/shared/jars/haploview.jar -n -memory 2048 -pairwiseTagging -pedfile /tmp/foo/test-data/rgtestouts/rgHaploView/rgHaploViewtest1.ped -info /tmp/foo/test-data/rgtestouts/rgHaploView/rgHaploViewtest1.info -tagrsqcounts -tagrsqcutoff 0.8 -ldcolorscheme RSQ -maxDistance 200000 -compressedpng -chromosome 22 returned 0
## executing mogrify -resize 800x400! *.PNG returned 0
@@ -123,7 +135,9 @@ PATH=/usr/kerberos/bin:/usr/local/bin:/b
## executing mogrify -format pdf -resize 800x400! *.png returned 0
-## executing pdfjoin "*.pdf" --fitpaper true --outfile alljoin.pdf returned 0
+## executing pdfjoin *.pdf --fitpaper true --outfile alljoin.pdf returned 0
## executing pdfnup alljoin.pdf --nup 1x2 --outfile allnup.pdf returned 0
+
+## executing convert -resize x300 allnup.pdf allnup.png returned 0
 </pre><hr></div></body></html>
Binary file test-data/rgtestouts/rgHaploView/alljoin.pdf has changed
Binary file test-data/rgtestouts/rgHaploView/2_HapMap_YRI_22.png has changed
Binary file test-data/rgtestouts/rgHaploView/1_rgHaploViewtest1.pdf has changed
Binary file test-data/rgtestouts/rgHaploView/2_HapMap_YRI_22.pdf has changed
Binary file test-data/rgtestouts/rgHaploView/1_rgHaploViewtest1.png has changed
--- a/test-data/rgtestouts/rgHaploView/rgHaploViewtest1.ped.TESTS
+++ b/test-data/rgtestouts/rgHaploView/rgHaploViewtest1.ped.TESTS
@@ -1,9 +1,9 @@
 rs2283804
 rs756632
-rs4820537
-rs3788347
-rs2283802
-rs4822363
 rs4820539
 rs16997606
+rs4822363
 rs2267000
+rs3788347
+rs4820537
+rs2283802
Binary file test-data/rgtestouts/rgHaploView/allnup.pdf has changed
--- a/tools/rgenetics/rgHaploView.py
+++ b/tools/rgenetics/rgHaploView.py
@@ -47,7 +47,7 @@ class ldPlot:
         self.args=argv
         self.parseArgs(argv=self.args)
         self.setupRegions()
-        
+                
     def parseArgs(self,argv=[]):
         """
         """
@@ -405,10 +405,10 @@ class ldPlot:
             p=subprocess.Popen(vcl,shell=True,cwd=self.outfpath,stderr=self.lf,stdout=self.lf)
             retval = p.wait()
             self.lf.write('## executing %s returned %d\n' % (vcl,retval))
-            #vcl = ['convert', 'allnup.pdf', 'allnup.png'] # this fails - bad pdf?
-            #p=subprocess.Popen(' '.join(vcl),shell=True,cwd=outfpath)
-            #retval = p.wait()
-            #lf.write('## executing %s returned %d\n' % (vcl,retval))
+            vcl = '%s -resize x300 allnup.pdf allnup.png' % (self.convert)
+            p=subprocess.Popen(vcl,shell=True,cwd=self.outfpath,stderr=self.lf,stdout=self.lf)
+            retval = p.wait()
+            self.lf.write('## executing %s returned %d\n' % (vcl,retval))
         ste.close() # temp file used to catch haploview blather
         hblather = open(blog,'r').readlines() # to catch the blather    
         os.unlink(blog)
@@ -425,20 +425,16 @@ class ldPlot:
         outf.write(galhtmlprefix % progname)
         s = '<h4>rgenetics for Galaxy %s, wrapping HaploView</h4>' % (progname)
         outf.write(s)
-        """
-        as at ashg 2009, convert fails on allnup.pdf - probably too complex...
         mainthumb = 'allnup.png'
         mainpdf = 'allnup.pdf'
-        if os.path.exists(mainpdf):
-            if not os.path.exists(mainthumb):
+        if os.path.exists(os.path.join(self.outfpath,mainpdf)):
+            if not os.path.exists(os.path.join(self.outfpath,mainthumb)):
                 outf.write('<table><tr><td colspan="3"><a href="%s">Main combined LD plot</a></td></tr></table>\n' % (mainpdf))
             else:
-                outf.write('<table><tr><td><a href="%s"><img src="%s" alt="Main combined LD image" hspace="10" align="middle">')
-                outf.write('</td><td>Click this thumbnail to display the main combined LD image</td></tr></table>\n' % (mainpdf,mainthumb))
+                outf.write('<table><tr><td><a href="%s"><img src="%s" alt="Main combined LD image" hspace="10" align="middle">' % (mainpdf,mainthumb))
+                outf.write('</td><td>Click the thumbnail at left to download the main combined LD image <a href=%s>%s</a></td></tr></table>\n' % (mainpdf,mainpdf))
         else:
             outf.write('(No main image was generated - this usually means a Haploview error connecting to Hapmap site - please try later)<br/>\n')
-        outf.write('## Called as %s' % sys.argv)
-        """
         outf.write('<br><div><hr><ul>\n')
         for i, data in enumerate( flist ):
             dn = os.path.split(data)[-1]
@@ -515,3 +511,4 @@ if __name__ == "__main__":
     ld.doPlots()
+
--- a/test-data/rgtestouts/rgHaploView/Log_rgHaploViewtest1.txt
+++ b/test-data/rgtestouts/rgHaploView/Log_rgHaploViewtest1.txt
@@ -3,12 +3,12 @@ Haploview 4.2	Java Version: 1.6.0_03
 *****************************************************
-Arguments:	-n	-pairwiseTagging	-pedfile	/opt/galaxy/test-data/rgtestouts/rgHaploView/rgHaploViewtest1.ped	-info	/opt/galaxy/test-data/rgtestouts/rgHaploView/rgHaploViewtest1.info	-tagrsqcounts	-tagrsqcutoff	0.8	-ldcolorscheme	RSQ	-maxDistance	200000	-compressedpng	-chromosome	22	
+Arguments:	-n	-pairwiseTagging	-pedfile	/tmp/foo/test-data/rgtestouts/rgHaploView/rgHaploViewtest1.ped	-info	/tmp/foo/test-data/rgtestouts/rgHaploView/rgHaploViewtest1.info	-tagrsqcounts	-tagrsqcutoff	0.8	-ldcolorscheme	RSQ	-maxDistance	200000	-compressedpng	-chromosome	22
Max LD comparison distance = 200000kb
-Using data file: /opt/galaxy/test-data/rgtestouts/rgHaploView/rgHaploViewtest1.ped
-Using marker information file: /opt/galaxy/test-data/rgtestouts/rgHaploView/rgHaploViewtest1.info
+Using data file: /tmp/foo/test-data/rgtestouts/rgHaploView/rgHaploViewtest1.ped
+Using marker information file: /tmp/foo/test-data/rgtestouts/rgHaploView/rgHaploViewtest1.info
 Writing output to rgHaploViewtest1.ped.LD.PNG
 Starting tagging.
 Writing output to rgHaploViewtest1.ped.TAGS
@@ -26,21 +26,26 @@ Arguments:	-n	-chromosome	22	-panel	YRI	
 Max LD comparison distance = 200000kb
 Downloading chromosome 22, analysis panel YRI, 21784..21905 from HapMap release 21.
 Writing output to Chromosome22YRI.LD.PNG
-This is pdfjoin version 1.20
-Reading site configuration from /etc/pdfnup.conf
-  Temporary LaTeX file for this job is /var/tmp/22578.tex
-  Calling pdflatex...
-  Finished: output is /opt/galaxy/test-data/rgtestouts/rgHaploView/alljoin.pdf
-This is pdfnup version 1.20
-Reading site configuration from /etc/pdfnup.conf
-Processing alljoin.pdf...
-  Temporary LaTeX file for this job is /var/tmp/22621-1.tex
-  Calling pdflatex...
-  Finished: output is /opt/galaxy/test-data/rgtestouts/rgHaploView/allnup.pdf
+          ----
+  pdfjam: This is pdfjam version 2.06.
+  pdfjam: Reading any site-wide or user-specific defaults...
+          (none found)
+  pdfjam: Effective call for this run of pdfjam:
+          /usr/local/bin/pdfjam --fitpaper 'true' --rotateoversize 'true' --suffix joined --fitpaper 'true' --outfile alljoin.pdf -- 1_rgHaploViewtest1.pdf - 2_HapMap_YRI_22.pdf - 
+  pdfjam: Calling pdflatex...
+  pdfjam: Finished.  Output was to 'alljoin.pdf'.
+          ----
+  pdfjam: This is pdfjam version 2.06.
+  pdfjam: Reading any site-wide or user-specific defaults...
+          (none found)
+  pdfjam: Effective call for this run of pdfjam:
+          /usr/local/bin/pdfjam --suffix nup --nup '2x1' --landscape --nup '1x2' --outfile allnup.pdf -- alljoin.pdf - 
+  pdfjam: Calling pdflatex...
+  pdfjam: Finished.  Output was to 'allnup.pdf'.
 PATH=/usr/kerberos/bin:/usr/local/bin:/bin:/usr/bin:/home/rerla/bin
 ## rgHaploView.py looking for 10 rs (['rs2283802', 'rs2267000', 'rs16997606', 'rs4820537', 'rs3788347'])## rgHaploView.py: wrote 10 markers, 40 subjects for region
-## executing java -jar /opt/galaxy/tool-data/shared/jars/haploview.jar -n -memory 2048 -pairwiseTagging -pedfile /opt/galaxy/test-data/rgtestouts/rgHaploView/rgHaploViewtest1.ped -info /opt/galaxy/test-data/rgtestouts/rgHaploView/rgHaploViewtest1.info -tagrsqcounts -tagrsqcutoff 0.8 -ldcolorscheme RSQ -maxDistance 200000 -compressedpng -chromosome 22 returned 0
+## executing java -jar /opt/galaxy/tool-data/shared/jars/haploview.jar -n -memory 2048 -pairwiseTagging -pedfile /tmp/foo/test-data/rgtestouts/rgHaploView/rgHaploViewtest1.ped -info /tmp/foo/test-data/rgtestouts/rgHaploView/rgHaploViewtest1.info -tagrsqcounts -tagrsqcutoff 0.8 -ldcolorscheme RSQ -maxDistance 200000 -compressedpng -chromosome 22 returned 0
 ## executing mogrify -resize 800x400! *.PNG returned 0
 ## executing convert -resize 800x400! rgHaploViewtest1.ped.LD.PNG rgHaploViewtest1.tmp.png returned 0
 ## executing convert -pointsize 25 -fill maroon -draw "text 10,300 'rgHaploViewtest1'" rgHaploViewtest1.tmp.png 1_rgHaploViewtest1.png returned 0
@@ -48,5 +53,6 @@ PATH=/usr/kerberos/bin:/usr/local/bin:/b
 ## executing convert -pointsize 25 -fill maroon -draw "text 10,300 'HapMap YRI'" rgHaploViewtest1.tmp.png 2_HapMap_YRI_22.png returned 0
 ### nimages=2
 ## executing mogrify -format pdf -resize 800x400! *.png returned 0
-## executing pdfjoin "*.pdf" --fitpaper true --outfile alljoin.pdf returned 0
+## executing pdfjoin *.pdf --fitpaper true --outfile alljoin.pdf returned 0
 ## executing pdfnup alljoin.pdf --nup 1x2 --outfile allnup.pdf returned 0
+## executing convert -resize x300 allnup.pdf allnup.png returned 0
--- a/test-data/rgtestouts/rgHaploView/rgHaploViewtest1.ped.TAGS
+++ b/test-data/rgtestouts/rgHaploView/rgHaploViewtest1.ped.TAGS
@@ -14,12 +14,12 @@ rs2267006	rs2283804	1.0
 rs4822363	rs4822363	1.0
Test	Alleles Captured
-rs2283804	rs2283804,rs2267006
+rs2283804	rs2267006,rs2283804
 rs756632	rs756632
-rs4820537	rs4820537
-rs3788347	rs3788347
-rs2283802	rs2283802
-rs4822363	rs4822363
 rs4820539	rs4820539
 rs16997606	rs16997606
+rs4822363	rs4822363
 rs2267000	rs2267000
+rs3788347	rs3788347
+rs4820537	rs4820537
+rs2283802	rs2283802
Binary file test-data/rgtestouts/rgHaploView/rgHaploViewtest1.ped.LD.PNG has changed

    