[hg] galaxy 3572: Fixed a file name in the GLM test outputs

16 Apr 2010

details:   http://www.bx.psu.edu/hg/galaxy/rev/b8689cf28fa7
changeset: 3572:b8689cf28fa7
user:      fubar: ross Lazarus at gmail period com
date:      Fri Mar 26 16:46:44 2010 -0400
description:
Fixed a file name in the GLM test outputs
Fixed a stoopid typo in the QC marker report call (how did that get there?)
Raised the lines_diff count for rgManQQ tests so they pass

diffstat:

 test-data/rgGLM_GLM_topTable.gff      |  26 --------------------------
 test-data/rgGLMtest1_GLM_topTable.gff |  26 ++++++++++++++++++++++++++
 tools/rgenetics/rgManQQ.xml           |   2 +-
 tools/rgenetics/rgQC.py               |  21 ++++++++++++---------
 tools/rgenetics/rgQC.xml              |   2 +-
 5 files changed, 40 insertions(+), 37 deletions(-)

diffs (148 lines):

diff -r d8e1a56b3415 -r b8689cf28fa7 test-data/rgGLM_GLM_topTable.gff

--- a/test-data/rgGLM_GLM_topTable.gff	Fri Mar 26 14:43:27 2010 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,26 +0,0 @@
-track name=rgGLM_TopTable description="rgGLMtest1" visibility=2 useScore=1 color=0,60,120
-chr22	rgGLM	variation	21784622	21784822	455	.	.	rs2283802 logp=0.75
-chr22	rgGLM	variation	21785266	21785466	152	.	.	rs2267000 logp=0.25
-chr22	rgGLM	variation	21794654	21794854	230	.	.	rs16997606 logp=0.38
-chr22	rgGLM	variation	21794710	21794910	107	.	.	rs4820537 logp=0.18
-chr22	rgGLM	variation	21797704	21797904	28	.	.	rs3788347 logp=0.05
-chr22	rgGLM	variation	21799818	21800018	45	.	.	rs756632 logp=0.08
-chr22	rgGLM	variation	21807870	21808070	151	.	.	rs4820539 logp=0.25
-chr22	rgGLM	variation	21820235	21820435	723	.	.	rs2283804 logp=1.19
-chr22	rgGLM	variation	21820890	21821090	723	.	.	rs2267006 logp=1.19
-chr22	rgGLM	variation	21820900	21821100	340	.	.	rs4822363 logp=0.56
-chr22	rgGLM	variation	21827574	21827774	337	.	.	rs5751592 logp=0.55
-chr22	rgGLM	variation	21832608	21832808	563	.	.	rs5759608 logp=0.92
-chr22	rgGLM	variation	21833070	21833270	563	.	.	rs5759612 logp=0.92
-chr22	rgGLM	variation	21860068	21860268	455	.	.	rs2267009 logp=0.75
-chr22	rgGLM	variation	21864266	21864466	391	.	.	rs2267010 logp=0.64
-chr22	rgGLM	variation	21868598	21868798	95	.	.	rs5759636 logp=0.16
-chr22	rgGLM	variation	21871388	21871588	455	.	.	rs2071436 logp=0.75
-chr22	rgGLM	variation	21875779	21875979	32	.	.	rs2267013 logp=0.05
-chr22	rgGLM	variation	21889706	21889906	125	.	.	rs6003566 logp=0.21
-chr22	rgGLM	variation	21892791	21892991	32	.	.	rs2256725 logp=0.05
-chr22	rgGLM	variation	21892825	21893025	127	.	.	rs12160770 logp=0.21
-chr22	rgGLM	variation	21895919	21896119	126	.	.	rs5751611 logp=0.21
-chr22	rgGLM	variation	21898758	21898958	446	.	.	rs762601 logp=0.73
-chr22	rgGLM	variation	21898963	21899163	446	.	.	rs2156921 logp=0.73
-chr22	rgGLM	variation	21905542	21905742	446	.	.	rs4822375 logp=0.73
diff -r d8e1a56b3415 -r b8689cf28fa7 test-data/rgGLMtest1_GLM_topTable.gff
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/rgGLMtest1_GLM_topTable.gff	Fri Mar 26 16:46:44 2010 -0400
@@ -0,0 +1,26 @@
+track name=rgGLM_TopTable description="rgGLMtest1" visibility=2 useScore=1 color=0,60,120
+chr22	rgGLM	variation	21784622	21784822	455	.	.	rs2283802 logp=0.75
+chr22	rgGLM	variation	21785266	21785466	152	.	.	rs2267000 logp=0.25
+chr22	rgGLM	variation	21794654	21794854	230	.	.	rs16997606 logp=0.38
+chr22	rgGLM	variation	21794710	21794910	107	.	.	rs4820537 logp=0.18
+chr22	rgGLM	variation	21797704	21797904	28	.	.	rs3788347 logp=0.05
+chr22	rgGLM	variation	21799818	21800018	45	.	.	rs756632 logp=0.08
+chr22	rgGLM	variation	21807870	21808070	151	.	.	rs4820539 logp=0.25
+chr22	rgGLM	variation	21820235	21820435	723	.	.	rs2283804 logp=1.19
+chr22	rgGLM	variation	21820890	21821090	723	.	.	rs2267006 logp=1.19
+chr22	rgGLM	variation	21820900	21821100	340	.	.	rs4822363 logp=0.56
+chr22	rgGLM	variation	21827574	21827774	337	.	.	rs5751592 logp=0.55
+chr22	rgGLM	variation	21832608	21832808	563	.	.	rs5759608 logp=0.92
+chr22	rgGLM	variation	21833070	21833270	563	.	.	rs5759612 logp=0.92
+chr22	rgGLM	variation	21860068	21860268	455	.	.	rs2267009 logp=0.75
+chr22	rgGLM	variation	21864266	21864466	391	.	.	rs2267010 logp=0.64
+chr22	rgGLM	variation	21868598	21868798	95	.	.	rs5759636 logp=0.16
+chr22	rgGLM	variation	21871388	21871588	455	.	.	rs2071436 logp=0.75
+chr22	rgGLM	variation	21875779	21875979	32	.	.	rs2267013 logp=0.05
+chr22	rgGLM	variation	21889706	21889906	125	.	.	rs6003566 logp=0.21
+chr22	rgGLM	variation	21892791	21892991	32	.	.	rs2256725 logp=0.05
+chr22	rgGLM	variation	21892825	21893025	127	.	.	rs12160770 logp=0.21
+chr22	rgGLM	variation	21895919	21896119	126	.	.	rs5751611 logp=0.21
+chr22	rgGLM	variation	21898758	21898958	446	.	.	rs762601 logp=0.73
+chr22	rgGLM	variation	21898963	21899163	446	.	.	rs2156921 logp=0.73
+chr22	rgGLM	variation	21905542	21905742	446	.	.	rs4822375 logp=0.73
diff -r d8e1a56b3415 -r b8689cf28fa7 tools/rgenetics/rgManQQ.xml
--- a/tools/rgenetics/rgManQQ.xml	Fri Mar 26 14:43:27 2010 -0400
+++ b/tools/rgenetics/rgManQQ.xml	Fri Mar 26 16:46:44 2010 -0400
@@ -39,7 +39,7 @@
  <param name='pval_col' value='5,7' />
  <param name='chrom_col' value='1' />
  <param name='offset_col' value='2' />
- <output name='out_html' file='rgtestouts/rgManQQ/rgManQQtest1.html' ftype='html' lines_diff='10'>
+ <output name='out_html' file='rgtestouts/rgManQQ/rgManQQtest1.html' ftype='html' lines_diff='17'>
    <extra_files type="file" name='Allelep_manhattan.png' value='rgtestouts/rgManQQ/Allelep_manhattan.png' compare="sim_size"   
      delta = "100" />
    <extra_files type="file" name='Allelep_qqplot.png' value='rgtestouts/rgManQQ/Allelep_qqplot.png' compare="sim_size"   
diff -r d8e1a56b3415 -r b8689cf28fa7 tools/rgenetics/rgQC.py
--- a/tools/rgenetics/rgQC.py	Fri Mar 26 14:43:27 2010 -0400
+++ b/tools/rgenetics/rgQC.py	Fri Mar 26 16:46:44 2010 -0400
@@ -294,8 +294,7 @@
     outfnames = [os.path.join(newfpath,ploturls[x]) for x in range(nplots)]
     ordoutfnames = [os.path.join(newfpath,ordploturls[x]) for x in range(nplots)]
     datasources = [markers,markers,markers,markers,subjects,subjects,subjects] # use this table
-    titles = ["Marker HWE","Marker Missing Genotype",
-        "Marker MAF","Marker Mendel",
+    titles = ["Marker HWE","Marker Missing Genotype", "Marker MAF","Marker Mendel",
         "Subject Missing Genotype","Subject Mendel",'Subject F Statistic']
     html = []
     pdflist = []
@@ -630,8 +629,7 @@
     outfnames = [os.path.join(newfpath,ploturls[x]) for x in range(nplots)]
     ordoutfnames = [os.path.join(newfpath,ordploturls[x]) for x in range(nplots)]
     datasources = [markers,markers,markers,markers,subjects,subjects,subjects] # use this table
-    titles = ["Marker HWE","Marker Missing Genotype",
-        "Marker MAF","Marker Mendel",
+    titles = ["Marker HWE","Marker Missing Genotype", "Marker MAF","Marker Mendel",
         "Subject Missing Genotype","Subject Mendel",'Subject F Statistic']
     html = []
     pdflist = []
@@ -1148,7 +1146,7 @@
         except:
             inmend = 'NA'
         try:
-            fhweall = '%f' % float(hwe_unaff[1]) # the log value
+            fhweall = '%f' % float(hwe_all[1]) # the log value
         except:
             fhweall = 'NA'
         try:
@@ -1263,7 +1261,7 @@
     repout = os.path.join(newfpath,basename)
     subjects,subjectTops = subjectRep(froot=repout,outfname=asubjf,newfpath=newfpath,
                 logf=alogf) # writes the subject_froot.xls file
-    markers,markerTops = markerRep(froot=newfpath,outfname=amarkf,newfpath=newfpath,
+    markers,markerTops = markerRep(froot=repout,outfname=amarkf,newfpath=newfpath,
                 logf=alogf) # marker_froot.xls
     nbreaks = 100
     s = '## starting plotpage, newfpath=%s,m=%s,s=%s/n' % (newfpath,markers[:2],subjects[:2])
@@ -1283,9 +1281,14 @@
     html.append('<tr><td colspan="3"><a href="%s" type="application/vnd.ms-excel">%s</a>%s tab delimited</td></tr>' % \
                 (asubjf,'Click here to download the Subject QC Detail report file',size))
     for (title,url,ofname) in plotpage:
-        dat = subjectTops.get(title,None)
+        ttitle = 'Ranked %s' % title
+        dat = subjectTops.get(ttitle,None)
         if not dat:
-            dat = markerTops.get(title,None)
+            dat = markerTops.get(ttitle,None)
+        if not dat:
+            print '## iterating plotpage - cannot find title=%s/ttitle=%s' % (title,ttitle)
+        else:
+            print '## iterating plotpage - found title=%s/ttitle=%s' % (title,ttitle)
         imghref = '%s.jpg' % os.path.splitext(url)[0] # removes .pdf
         thumbnail = os.path.join(newfpath,imghref)
         if not os.path.exists(thumbnail): # for multipage pdfs, mogrify makes multiple jpgs - fugly hack
@@ -1297,7 +1300,7 @@
             html.append('<tr><td><a href="%s"><img src="%s" alt="%s" hspace="10" align="middle">' \
                     % (url,imghref,title))
             if dat: # one or the other - write as an extra file and make a link here
-                t = '%s.xls' % (title.replace(' ','_'))
+                t = '%s.xls' % (ttitle.replace(' ','_'))
                 fname = os.path.join(newfpath,t)
                 f = file(fname,'w')
                 f.write('\n'.join(['\t'.join(x) for x in dat])) # the report
diff -r d8e1a56b3415 -r b8689cf28fa7 tools/rgenetics/rgQC.xml
--- a/tools/rgenetics/rgQC.xml	Fri Mar 26 14:43:27 2010 -0400
+++ b/tools/rgenetics/rgQC.xml	Fri Mar 26 16:46:44 2010 -0400
@@ -1,4 +1,4 @@
-<tool id="rgqc1" name="QC reports:">
+<tool id="rgQC1" name="QC reports:">
     <code file="rgQC_code.py"/>
 
     <description>Marker and Subject measures</description>

    

Greg Von Kuster

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