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>