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April 2010
- 37 participants
- 148 discussions
15 Apr '10
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>
1
0
15 Apr '10
details: http://www.bx.psu.edu/hg/galaxy/rev/d8e1a56b3415
changeset: 3571:d8e1a56b3415
user: fubar: ross Lazarus at gmail period com
date: Fri Mar 26 14:43:27 2010 -0400
description:
Adding images for manhattan plot tool help
diffstat:
static/images/Armitagep_manhattan.png | 0
static/images/Armitagep_qqplot.png | 0
2 files changed, 0 insertions(+), 0 deletions(-)
diffs (4 lines):
diff -r cc8a30a0669f -r d8e1a56b3415 static/images/Armitagep_manhattan.png
Binary file static/images/Armitagep_manhattan.png has changed
diff -r cc8a30a0669f -r d8e1a56b3415 static/images/Armitagep_qqplot.png
Binary file static/images/Armitagep_qqplot.png has changed
1
0
details: http://www.bx.psu.edu/hg/galaxy/rev/cc8a30a0669f
changeset: 3570:cc8a30a0669f
user: fubar: ross Lazarus at gmail period com
date: Fri Mar 26 14:42:15 2010 -0400
description:
Adding rg test outputs and updated tools
diffstat:
.hgignore | 4 +
test-data/rgCaCotest1_CaCo.xls | 26 +
test-data/rgCaCotest1_CaCo_log.txt | 46 +
test-data/rgCaCotest1_CaCo_topTable.gff | 26 +
test-data/rgGLM_GLM_topTable.gff | 26 +
test-data/rgGLMtest1_GLM.xls | 26 +
test-data/rgGLMtest1_GLM_log.txt | 58 +
test-data/rgQQtest1.pdf | 384 ++
test-data/rgTDTtest1_TDT.xls | 25 +
test-data/rgTDTtest1_TDT_log.txt | 53 +
test-data/rgTDTtest1_TDT_topTable.gff | 25 +
test-data/rgtestouts/rgClean/rgCleantest1.bed | 1 +
test-data/rgtestouts/rgClean/rgCleantest1.bim | 25 +
test-data/rgtestouts/rgClean/rgCleantest1.fam | 40 +
test-data/rgtestouts/rgClean/rgCleantest1.log | 66 +
test-data/rgtestouts/rgClean/rgCleantest1.pbed | 19 +
test-data/rgtestouts/rgEigPCA/Rplots.pdf | 59 +
test-data/rgtestouts/rgEigPCA/rgEigPCAtest1.R | 19 +
test-data/rgtestouts/rgEigPCA/rgEigPCAtest1.html | 160 +
test-data/rgtestouts/rgEigPCA/rgEigPCAtest1.txt | 40 +
test-data/rgtestouts/rgEigPCA/rgEigPCAtest1_PCAPlot.pdf | 454 +++
test-data/rgtestouts/rgEigPCA/rgEigPCAtest1_PCAPlot.pdf.png | 0
test-data/rgtestouts/rgEigPCA/rgEigPCAtest1_eigensoftplot.pdf.pdf | 0
test-data/rgtestouts/rgEigPCA/rgEigPCAtest1_eigensoftplot.pdf.ps | 502 +++
test-data/rgtestouts/rgEigPCA/rgEigPCAtest1_eigensoftplot.pdf.xtxt | 7 +
test-data/rgtestouts/rgEigPCA/rgEigPCAtest1_eval.xls | 39 +
test-data/rgtestouts/rgEigPCA/rgEigPCAtest1_log.txt | 128 +
test-data/rgtestouts/rgEigPCA/rgEigPCAtest1_pca.xls | 45 +
test-data/rgtestouts/rgEigPCA/rgEigPCAtest1_pca.xls.evec | 40 +
test-data/rgtestouts/rgEigPCA/rgEigPCAtest1_pca.xls.par | 11 +
test-data/rgtestouts/rgGRR/Log_rgGRRtest1.txt | 23 +
test-data/rgtestouts/rgGRR/rgGRRtest1.html | 65 +
test-data/rgtestouts/rgGRR/rgGRRtest1.svg | 770 +++++
test-data/rgtestouts/rgGRR/rgGRRtest1_table.xls | 781 +++++
test-data/rgtestouts/rgHaploView/1_rgHaploViewtest1.pdf | 0
test-data/rgtestouts/rgHaploView/1_rgHaploViewtest1.png | 0
test-data/rgtestouts/rgHaploView/2_HapMap_YRI_22.pdf | 0
test-data/rgtestouts/rgHaploView/2_HapMap_YRI_22.png | 0
test-data/rgtestouts/rgHaploView/Chromosome22YRI.LD.PNG | 0
test-data/rgtestouts/rgHaploView/Log_rgHaploViewtest1.txt | 50 +
test-data/rgtestouts/rgHaploView/alljoin.pdf | 0
test-data/rgtestouts/rgHaploView/allnup.pdf | 0
test-data/rgtestouts/rgHaploView/rgHaploViewtest1.html | 124 +
test-data/rgtestouts/rgHaploView/rgHaploViewtest1.ped.LD.PNG | 0
test-data/rgtestouts/rgHaploView/rgHaploViewtest1.ped.TAGS | 25 +
test-data/rgtestouts/rgHaploView/rgHaploViewtest1.ped.TESTS | 9 +
test-data/rgtestouts/rgLDIndep/rgLDIndeptest1.bed | 1 +
test-data/rgtestouts/rgLDIndep/rgLDIndeptest1.bim | 3 +
test-data/rgtestouts/rgLDIndep/rgLDIndeptest1.fam | 40 +
test-data/rgtestouts/rgLDIndep/rgLDIndeptest1.log | 169 +
test-data/rgtestouts/rgLDIndep/rgLDIndeptest1.map | 3 +
test-data/rgtestouts/rgLDIndep/rgLDIndeptest1.pbed | 22 +
test-data/rgtestouts/rgLDIndep/rgLDIndeptest1.ped | 40 +
test-data/rgtestouts/rgLDIndep/rgLDIndeptest1.prune.in | 3 +
test-data/rgtestouts/rgLDIndep/rgLDIndeptest1.prune.out | 22 +
test-data/rgtestouts/rgManQQ/Allelep_manhattan.png | 0
test-data/rgtestouts/rgManQQ/Allelep_qqplot.png | 0
test-data/rgtestouts/rgManQQ/Armitagep_manhattan.png | 0
test-data/rgtestouts/rgManQQ/Armitagep_qqplot.png | 0
test-data/rgtestouts/rgManQQ/rgManQQtest1.R | 150 +
test-data/rgtestouts/rgManQQ/rgManQQtest1.html | 61 +
test-data/rgtestouts/rgPedSub/rgPedSubtest1.log | 12 +
test-data/rgtestouts/rgPedSub/rgPedSubtest1.lped | 17 +
test-data/rgtestouts/rgPedSub/tinywga.map | 10 +
test-data/rgtestouts/rgPedSub/tinywga.ped | 40 +
test-data/rgtestouts/rgQC/FQNormtinywga_s_het_cum.jpg | 0
test-data/rgtestouts/rgQC/FQNormtinywga_s_het_cum.pdf | 373 ++
test-data/rgtestouts/rgQC/MarkerDetails_rgQCtest1.xls | 1 +
test-data/rgtestouts/rgQC/Ranked_Subject_Missing_Genotype.xls | 21 +
test-data/rgtestouts/rgQC/SubjectDetails_rgQCtest1.xls | 41 +
test-data/rgtestouts/rgQC/ldp_tinywga.bed | 1 +
test-data/rgtestouts/rgQC/ldp_tinywga.bim | 14 +
test-data/rgtestouts/rgQC/ldp_tinywga.fam | 40 +
test-data/rgtestouts/rgQC/ldp_tinywga.log | 48 +
test-data/rgtestouts/rgQC/rgQCtest1.html | 576 ++++
test-data/rgtestouts/rgQC/tinywga.fmendel | 14 +
test-data/rgtestouts/rgQC/tinywga.frq | 26 +
test-data/rgtestouts/rgQC/tinywga.het | 41 +
test-data/rgtestouts/rgQC/tinywga.hwe | 76 +
test-data/rgtestouts/rgQC/tinywga.imendel | 40 +
test-data/rgtestouts/rgQC/tinywga.imiss | 41 +
test-data/rgtestouts/rgQC/tinywga.lmendel | 26 +
test-data/rgtestouts/rgQC/tinywga.lmiss | 26 +
test-data/rgtestouts/rgQC/tinywga.log | 48 +
test-data/rgtestouts/rgQC/tinywga.mendel | 1 +
test-data/rgtestouts/rgQC/tinywga.prune.in | 14 +
test-data/rgtestouts/rgQC/tinywga.prune.out | 11 +
test-data/rgtestouts/rgQC/tinywga.sexcheck | 41 +
test-data/rgtestouts/rgQC/tinywga_All_3x3.jpg | 0
test-data/rgtestouts/rgQC/tinywga_All_3x3.pdf | 0
test-data/rgtestouts/rgQC/tinywga_All_Paged-0.jpg | 0
test-data/rgtestouts/rgQC/tinywga_All_Paged-1.jpg | 0
test-data/rgtestouts/rgQC/tinywga_All_Paged-2.jpg | 0
test-data/rgtestouts/rgQC/tinywga_All_Paged-3.jpg | 0
test-data/rgtestouts/rgQC/tinywga_All_Paged-4.jpg | 0
test-data/rgtestouts/rgQC/tinywga_All_Paged.pdf | 0
test-data/rgtestouts/rgQC/tinywga_fracmiss.jpg | 0
test-data/rgtestouts/rgQC/tinywga_fracmiss.pdf | 333 ++
test-data/rgtestouts/rgQC/tinywga_fracmiss_cum.jpg | 0
test-data/rgtestouts/rgQC/tinywga_fracmiss_cum.pdf | 369 ++
test-data/rgtestouts/rgQC/tinywga_s_het.jpg | 0
test-data/rgtestouts/rgQC/tinywga_s_het.pdf | 344 ++
test-data/rgtestouts/rgQC/tinywga_s_het_cum.jpg | 0
test-data/rgtestouts/rgQC/tinywga_s_het_cum.pdf | 379 ++
test-data/rgtestouts/rgfakePed/rgfakePedtest1.lped | 16 +
test-data/rgtestouts/rgfakePed/rgfakePedtest1.map | 10 +
test-data/rgtestouts/rgfakePed/rgfakePedtest1.ped | 40 +
test-data/rgtestouts/rgfakePhe/rgfakePhetest1.pphe | 41 +
test-data/rgtestouts/rgfakePhe/script_file | 7 +
tools/rgenetics/listFiles.py | 227 +
tools/rgenetics/plinkbinJZ.py | 868 ++++++
tools/rgenetics/rgCaCo.py | 282 ++
tools/rgenetics/rgCaCo.xml | 101 +
tools/rgenetics/rgCaCo_code.py | 45 +
tools/rgenetics/rgClean.py | 160 +
tools/rgenetics/rgClean.xml | 155 +
tools/rgenetics/rgClean_code.py | 28 +
tools/rgenetics/rgEigPCA.py | 385 ++
tools/rgenetics/rgEigPCA.xml | 142 +
tools/rgenetics/rgEigPCA_code.py | 27 +
tools/rgenetics/rgGLM.py | 286 ++
tools/rgenetics/rgGLM.xml | 139 +
tools/rgenetics/rgGLM_code.py | 59 +
tools/rgenetics/rgGRR.py | 1092 ++++++++
tools/rgenetics/rgGRR.xml | 94 +
tools/rgenetics/rgGRR_code.py | 23 +
tools/rgenetics/rgGTOOL.py | 58 +
tools/rgenetics/rgGTOOL.xml | 54 +
tools/rgenetics/rgGTOOL_code.py | 19 +
tools/rgenetics/rgHaploView.py | 521 +++
tools/rgenetics/rgHaploView.xml | 153 +
tools/rgenetics/rgHaploView_code.py | 84 +
tools/rgenetics/rgLDIndep.py | 182 +
tools/rgenetics/rgLDIndep.xml | 157 +
tools/rgenetics/rgLDIndep_code.py | 25 +
tools/rgenetics/rgManQQ.py | 223 +
tools/rgenetics/rgManQQ.xml | 117 +
tools/rgenetics/rgManQQ_code.py | 50 +
tools/rgenetics/rgPedSub.py | 305 ++
tools/rgenetics/rgPedSub.xml | 143 +
tools/rgenetics/rgPedSub_code.py | 78 +
tools/rgenetics/rgQC.py | 1334 ++++++++++
tools/rgenetics/rgQC.xml | 109 +
tools/rgenetics/rgQC_code.py | 38 +
tools/rgenetics/rgQQ.py | 365 ++
tools/rgenetics/rgQQ.xml | 99 +
tools/rgenetics/rgQQ_code.py | 72 +
tools/rgenetics/rgRegion.py | 80 +
tools/rgenetics/rgRegion.xml | 60 +
tools/rgenetics/rgRegion_code.py | 47 +
tools/rgenetics/rgTDT.py | 263 +
tools/rgenetics/rgTDT.xml | 84 +
tools/rgenetics/rgTDT_code.py | 43 +
tools/rgenetics/rgfakePed.py | 535 ++++
tools/rgenetics/rgfakePed.xml | 111 +
tools/rgenetics/rgfakePed_code.py | 53 +
tools/rgenetics/rgfakePhe.py | 469 +++
tools/rgenetics/rgfakePhe.xml | 132 +
tools/rgenetics/rgfakePhe_code.py | 46 +
tools/rgenetics/rgutils.py | 281 ++
160 files changed, 18356 insertions(+), 0 deletions(-)
diffs (truncated from 18957 to 3000 lines):
diff -r 4906f2302c85 -r cc8a30a0669f .hgignore
--- a/.hgignore Fri Mar 26 14:14:40 2010 -0400
+++ b/.hgignore Fri Mar 26 14:42:15 2010 -0400
@@ -1,3 +1,7 @@
+syntax: regexp
+
+\.svn$
+
syntax: glob
.hg*
diff -r 4906f2302c85 -r cc8a30a0669f test-data/rgCaCotest1_CaCo.xls
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/rgCaCotest1_CaCo.xls Fri Mar 26 14:42:15 2010 -0400
@@ -0,0 +1,26 @@
+rs Chr Offset Genop log10Genop Armitagep log10Armitagep Allelep log10Allelep Domp log10Domp
+rs2283802 22 21784722 1.000 0.000000 1.000 -0.000000 1.000 -0.000000 1.000 0.000000
+rs2267000 22 21785366 1.000 0.000000 0.893 0.049197 0.896 0.047450 1.000 0.000000
+rs16997606 22 21794754 1.000 0.000000 0.512 0.290815 0.540 0.267606 1.000 0.000000
+rs4820537 22 21794810 1.000 0.000000 0.266 0.575935 0.238 0.623423 1.000 0.000000
+rs3788347 22 21797804 1.000 0.000000 0.528 0.276955 0.518 0.285251 1.000 0.000000
+rs756632 22 21799918 1.000 0.000000 0.847 0.072014 0.838 0.076704 1.000 0.000000
+rs4820539 22 21807970 1.000 0.000000 0.663 0.178618 0.669 0.174704 1.000 0.000000
+rs2283804 22 21820335 1.000 0.000000 0.888 0.051636 0.891 0.049927 1.000 0.000000
+rs2267006 22 21820990 1.000 0.000000 0.888 0.051636 0.891 0.049927 1.000 0.000000
+rs4822363 22 21821000 1.000 0.000000 0.609 0.215311 0.624 0.204815 1.000 0.000000
+rs5751592 22 21827674 1.000 0.000000 0.426 0.370998 0.470 0.328272 1.000 0.000000
+rs5759608 22 21832708 1.000 0.000000 1.000 -0.000000 1.000 -0.000000 1.000 0.000000
+rs5759612 22 21833170 1.000 0.000000 1.000 -0.000000 1.000 -0.000000 1.000 0.000000
+rs2267009 22 21860168 1.000 0.000000 1.000 -0.000000 1.000 -0.000000 1.000 0.000000
+rs2267010 22 21864366 1.000 0.000000 0.729 0.137332 0.734 0.134304 1.000 0.000000
+rs5759636 22 21868698 1.000 0.000000 0.215 0.667360 0.228 0.642256 1.000 0.000000
+rs2071436 22 21871488 1.000 0.000000 1.000 -0.000000 1.000 -0.000000 1.000 0.000000
+rs2267013 22 21875879 1.000 0.000000 0.512 0.290815 0.540 0.267606 1.000 0.000000
+rs6003566 22 21889806 1.000 0.000000 0.361 0.442132 0.389 0.409604 1.000 0.000000
+rs2256725 22 21892891 1.000 0.000000 0.512 0.290815 0.540 0.267606 1.000 0.000000
+rs12160770 22 21892925 1.000 0.000000 0.594 0.225921 0.597 0.224098 1.000 0.000000
+rs5751611 22 21896019 1.000 0.000000 0.893 0.049246 0.894 0.048565 1.000 0.000000
+rs762601 22 21898858 1.000 0.000000 0.897 0.047111 0.893 0.049051 1.000 0.000000
+rs2156921 22 21899063 1.000 0.000000 0.897 0.047111 0.893 0.049051 1.000 0.000000
+rs4822375 22 21905642 1.000 0.000000 0.897 0.047111 0.893 0.049051 1.000 0.000000
diff -r 4906f2302c85 -r cc8a30a0669f test-data/rgCaCotest1_CaCo_log.txt
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/rgCaCotest1_CaCo_log.txt Fri Mar 26 14:42:15 2010 -0400
@@ -0,0 +1,46 @@
+
+@----------------------------------------------------------@
+| PLINK! | v1.06 | 24/Apr/2009 |
+|----------------------------------------------------------|
+| (C) 2009 Shaun Purcell, GNU General Public License, v2 |
+|----------------------------------------------------------|
+| For documentation, citation & bug-report instructions: |
+| http://pngu.mgh.harvard.edu/purcell/plink/ |
+@----------------------------------------------------------@
+
+Skipping web check... [ --noweb ]
+Writing this text to log file [ rgCaCotest1.log ]
+Analysis started: Thu Mar 25 21:01:31 2010
+
+Options in effect:
+ --noweb
+ --bfile /opt/galaxy/test-data/tinywga
+ --out rgCaCotest1
+ --model
+
+Reading map (extended format) from [ /opt/galaxy/test-data/tinywga.bim ]
+25 markers to be included from [ /opt/galaxy/test-data/tinywga.bim ]
+Reading pedigree information from [ /opt/galaxy/test-data/tinywga.fam ]
+40 individuals read from [ /opt/galaxy/test-data/tinywga.fam ]
+40 individuals with nonmissing phenotypes
+Assuming a disease phenotype (1=unaff, 2=aff, 0=miss)
+Missing phenotype value is also -9
+10 cases, 30 controls and 0 missing
+21 males, 19 females, and 0 of unspecified sex
+Reading genotype bitfile from [ /opt/galaxy/test-data/tinywga.bed ]
+Detected that binary PED file is v1.00 SNP-major mode
+Before frequency and genotyping pruning, there are 25 SNPs
+27 founders and 13 non-founders found
+Total genotyping rate in remaining individuals is 0.995
+0 SNPs failed missingness test ( GENO > 1 )
+0 SNPs failed frequency test ( MAF < 0 )
+After frequency and genotyping pruning, there are 25 SNPs
+After filtering, 10 cases, 30 controls and 0 missing
+After filtering, 21 males, 19 females, and 0 of unspecified sex
+Full-model association tests, minimum genotype count: --cell 5
+Writing full model association results to [ rgCaCotest1.model ]
+
+Analysis finished: Thu Mar 25 21:01:31 2010
+
+###maxp=0.667360,minp=-0.000000,prange=1.167360,scalefact=856.633772
+Rgenetics V000.1 April 2007 http://rgenetics.org Galaxy Tools, rgCaCo.py started 25/03/2010 21:01:31
diff -r 4906f2302c85 -r cc8a30a0669f test-data/rgCaCotest1_CaCo_topTable.gff
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/rgCaCotest1_CaCo_topTable.gff Fri Mar 26 14:42:15 2010 -0400
@@ -0,0 +1,26 @@
+track name=rgGLM_TopTable description="rgCaCotest1" visibility=2 useScore=1 color=0,60,120
+chr22 rgGLM variation 21784622 21784822 0 . . rs2283802 logp=-0.00
+chr22 rgGLM variation 21785266 21785466 42 . . rs2267000 logp=0.05
+chr22 rgGLM variation 21794654 21794854 249 . . rs16997606 logp=0.29
+chr22 rgGLM variation 21794710 21794910 493 . . rs4820537 logp=0.58
+chr22 rgGLM variation 21797704 21797904 237 . . rs3788347 logp=0.28
+chr22 rgGLM variation 21799818 21800018 61 . . rs756632 logp=0.07
+chr22 rgGLM variation 21807870 21808070 153 . . rs4820539 logp=0.18
+chr22 rgGLM variation 21820235 21820435 44 . . rs2283804 logp=0.05
+chr22 rgGLM variation 21820890 21821090 44 . . rs2267006 logp=0.05
+chr22 rgGLM variation 21820900 21821100 184 . . rs4822363 logp=0.22
+chr22 rgGLM variation 21827574 21827774 317 . . rs5751592 logp=0.37
+chr22 rgGLM variation 21832608 21832808 0 . . rs5759608 logp=-0.00
+chr22 rgGLM variation 21833070 21833270 0 . . rs5759612 logp=-0.00
+chr22 rgGLM variation 21860068 21860268 0 . . rs2267009 logp=-0.00
+chr22 rgGLM variation 21864266 21864466 117 . . rs2267010 logp=0.14
+chr22 rgGLM variation 21868598 21868798 571 . . rs5759636 logp=0.67
+chr22 rgGLM variation 21871388 21871588 0 . . rs2071436 logp=-0.00
+chr22 rgGLM variation 21875779 21875979 249 . . rs2267013 logp=0.29
+chr22 rgGLM variation 21889706 21889906 378 . . rs6003566 logp=0.44
+chr22 rgGLM variation 21892791 21892991 249 . . rs2256725 logp=0.29
+chr22 rgGLM variation 21892825 21893025 193 . . rs12160770 logp=0.23
+chr22 rgGLM variation 21895919 21896119 42 . . rs5751611 logp=0.05
+chr22 rgGLM variation 21898758 21898958 40 . . rs762601 logp=0.05
+chr22 rgGLM variation 21898963 21899163 40 . . rs2156921 logp=0.05
+chr22 rgGLM variation 21905542 21905742 40 . . rs4822375 logp=0.05
diff -r 4906f2302c85 -r cc8a30a0669f test-data/rgGLM_GLM_topTable.gff
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/rgGLM_GLM_topTable.gff Fri Mar 26 14:42:15 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 4906f2302c85 -r cc8a30a0669f test-data/rgGLMtest1_GLM.xls
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/rgGLMtest1_GLM.xls Fri Mar 26 14:42:15 2010 -0400
@@ -0,0 +1,26 @@
+rs chrom offset ADD_stat ADD_p ADD_log10p
+rs2283802 22 21784722 1.369 0.1789 0.747390
+rs2267000 22 21785366 0.5866 0.5609 0.251115
+rs16997606 22 21794754 -0.8178 0.4185 0.378305
+rs4820537 22 21794810 0.4346 0.6663 0.176330
+rs3788347 22 21797804 -0.1292 0.8979 0.046772
+rs756632 22 21799918 0.202 0.841 0.075204
+rs4820539 22 21807970 0.5836 0.563 0.249492
+rs2283804 22 21820335 -1.902 0.0648 1.188425
+rs2267006 22 21820990 -1.902 0.0648 1.188425
+rs4822363 22 21821000 1.105 0.2761 0.558934
+rs5751592 22 21827674 1.099 0.2788 0.554707
+rs5759608 22 21832708 -1.596 0.1189 0.924818
+rs5759612 22 21833170 -1.596 0.1189 0.924818
+rs2267009 22 21860168 1.369 0.1789 0.747390
+rs2267010 22 21864366 -1.227 0.2276 0.642828
+rs5759636 22 21868698 0.3942 0.6957 0.157578
+rs2071436 22 21871488 1.369 0.1789 0.747390
+rs2267013 22 21875879 -0.1449 0.8855 0.052811
+rs6003566 22 21889806 -0.4952 0.6233 0.205303
+rs2256725 22 21892891 -0.1449 0.8855 0.052811
+rs12160770 22 21892925 0.5031 0.618 0.209012
+rs5751611 22 21896019 0.5008 0.6195 0.207959
+rs762601 22 21898858 1.35 0.1849 0.733063
+rs2156921 22 21899063 1.35 0.1849 0.733063
+rs4822375 22 21905642 1.35 0.1849 0.733063
diff -r 4906f2302c85 -r cc8a30a0669f test-data/rgGLMtest1_GLM_log.txt
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/rgGLMtest1_GLM_log.txt Fri Mar 26 14:42:15 2010 -0400
@@ -0,0 +1,58 @@
+rgGLM.py called with ['/opt/galaxy/tools/rgenetics/rgGLM.py', '/opt/galaxy/test-data/tinywga', '/opt/galaxy/test-data/tinywga', 'rgGLMtest1', 'c1', '', '/opt/galaxy/test-data/rgGLMtest1_GLM.xls', '/opt/galaxy/test-data/rgGLMtest1_GLM_log.txt', 'tinywga', '', '', '', '1', '1', '0', '0', '/opt/galaxy/test-data/rgGLM_GLM_topTable.gff']
+vcl=['plink', '--noweb', '--bfile', '/opt/galaxy/test-data/tinywga', '--pheno-name', '"c1"', '--pheno', '/opt/galaxy/test-data/tinywga.pphe', '--out', 'tinywga', '--mind 1', '--geno 1', '--maf 0', '--linear']
+xformQassoc got resf=/tmp/tmpCB6CwWrgGLM/tinywga.assoc.linear, outfname=/opt/galaxy/test-data/rgGLMtest1_GLM.xls
+###maxp=1.188425,minp=0.046772,prange=1.641653,scalefact=609.142127
+
+
+@----------------------------------------------------------@
+| PLINK! | v1.06 | 24/Apr/2009 |
+|----------------------------------------------------------|
+| (C) 2009 Shaun Purcell, GNU General Public License, v2 |
+|----------------------------------------------------------|
+| For documentation, citation & bug-report instructions: |
+| http://pngu.mgh.harvard.edu/purcell/plink/ |
+@----------------------------------------------------------@
+
+Skipping web check... [ --noweb ]
+Writing this text to log file [ tinywga.log ]
+Analysis started: Thu Mar 25 21:01:31 2010
+
+Options in effect:
+ --noweb
+ --bfile /opt/galaxy/test-data/tinywga
+ --pheno-name c1
+ --pheno /opt/galaxy/test-data/tinywga.pphe
+ --out tinywga
+ --mind 1
+ --geno 1
+ --maf 0
+ --linear
+
+Reading map (extended format) from [ /opt/galaxy/test-data/tinywga.bim ]
+25 markers to be included from [ /opt/galaxy/test-data/tinywga.bim ]
+Reading pedigree information from [ /opt/galaxy/test-data/tinywga.fam ]
+40 individuals read from [ /opt/galaxy/test-data/tinywga.fam ]
+40 individuals with nonmissing phenotypes
+Assuming a disease phenotype (1=unaff, 2=aff, 0=miss)
+Missing phenotype value is also -9
+10 cases, 30 controls and 0 missing
+21 males, 19 females, and 0 of unspecified sex
+Reading genotype bitfile from [ /opt/galaxy/test-data/tinywga.bed ]
+Detected that binary PED file is v1.00 SNP-major mode
+Reading alternate phenotype from [ /opt/galaxy/test-data/tinywga.pphe ]
+40 individuals with non-missing alternate phenotype
+Assuming a quantitative trait
+Missing phenotype value is -9
+Before frequency and genotyping pruning, there are 25 SNPs
+27 founders and 13 non-founders found
+Total genotyping rate in remaining individuals is 0.995
+0 SNPs failed missingness test ( GENO > 1 )
+0 SNPs failed frequency test ( MAF < 0 )
+After frequency and genotyping pruning, there are 25 SNPs
+After filtering, 40 individuals with non-missing status
+After filtering, 21 males, 19 females, and 0 of unspecified sex
+Converting data to Individual-major format
+Writing linear model association results to [ tinywga.assoc.linear ]
+
+Analysis finished: Thu Mar 25 21:01:31 2010
+
diff -r 4906f2302c85 -r cc8a30a0669f test-data/rgQQtest1.pdf
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diff -r 4906f2302c85 -r cc8a30a0669f test-data/rgTDTtest1_TDT.xls
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/rgTDTtest1_TDT.xls Fri Mar 26 14:42:15 2010 -0400
@@ -0,0 +1,25 @@
+rs chrom offset a1 a2 transmitted untransmitted TDTChiSq TDTp -log10TDTp AbsTDTOR TDTOR
+rs2283802 22 21784722 4 2 4 4 0 1 -0.000000 1 1
+rs2267000 22 21785366 4 2 4 5 0.1111 0.7389 0.131414 1.250000 0.8
+rs16997606 22 21794754 1 3 3 3 0 1 -0.000000 1 1
+rs4820537 22 21794810 1 3 3 6 1 0.3173 0.498530 2.000000 0.5
+rs3788347 22 21797804 3 1 5 4 0.1111 0.7389 0.131414 1.25 1.25
+rs756632 22 21799918 4 2 2 1 0.3333 0.5637 0.248952 2 2
+rs4820539 22 21807970 1 3 4 5 0.1111 0.7389 0.131414 1.250000 0.8
+rs2283804 22 21820335 1 2 5 3 0.5 0.4795 0.319211 1.667 1.667
+rs2267006 22 21820990 3 1 5 3 0.5 0.4795 0.319211 1.667 1.667
+rs4822363 22 21821000 4 2 1 1 0 1 -0.000000 1 1
+rs5751592 22 21827674 4 2 2 5 1.286 0.2568 0.590405 2.500000 0.4
+rs5759608 22 21832708 2 4 7 4 0.8182 0.3657 0.436875 1.75 1.75
+rs5759612 22 21833170 3 1 7 4 0.8182 0.3657 0.436875 1.75 1.75
+rs2267009 22 21860168 3 4 4 4 0 1 -0.000000 1 1
+rs2267010 22 21864366 3 1 1 1 0 1 -0.000000 1 1
+rs5759636 22 21868698 4 2 0 1 1 0.3173 0.498530 0 0
+rs2071436 22 21871488 4 2 4 4 0 1 -0.000000 1 1
+rs2267013 22 21875879 3 1 3 1 1 0.3173 0.498530 3 3
+rs6003566 22 21889806 3 1 3 2 0.2 0.6547 0.183958 1.5 1.5
+rs2256725 22 21892891 2 1 3 1 1 0.3173 0.498530 3 3
+rs5751611 22 21896019 2 4 8 5 0.6923 0.4054 0.392116 1.6 1.6
+rs762601 22 21898858 1 3 7 4 0.8182 0.3657 0.436875 1.75 1.75
+rs2156921 22 21899063 3 1 7 4 0.8182 0.3657 0.436875 1.75 1.75
+rs4822375 22 21905642 1 3 7 4 0.8182 0.3657 0.436875 1.75 1.75
diff -r 4906f2302c85 -r cc8a30a0669f test-data/rgTDTtest1_TDT_log.txt
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/rgTDTtest1_TDT_log.txt Fri Mar 26 14:42:15 2010 -0400
@@ -0,0 +1,53 @@
+
+@----------------------------------------------------------@
+| PLINK! | v1.06 | 24/Apr/2009 |
+|----------------------------------------------------------|
+| (C) 2009 Shaun Purcell, GNU General Public License, v2 |
+|----------------------------------------------------------|
+| For documentation, citation & bug-report instructions: |
+| http://pngu.mgh.harvard.edu/purcell/plink/ |
+@----------------------------------------------------------@
+
+Skipping web check... [ --noweb ]
+Writing this text to log file [ rgTDTtest1.log ]
+Analysis started: Thu Mar 25 21:01:31 2010
+
+Options in effect:
+ --noweb
+ --bfile /opt/galaxy/test-data/tinywga
+ --out rgTDTtest1
+ --mind 0.5
+ --tdt
+
+Reading map (extended format) from [ /opt/galaxy/test-data/tinywga.bim ]
+25 markers to be included from [ /opt/galaxy/test-data/tinywga.bim ]
+Reading pedigree information from [ /opt/galaxy/test-data/tinywga.fam ]
+40 individuals read from [ /opt/galaxy/test-data/tinywga.fam ]
+40 individuals with nonmissing phenotypes
+Assuming a disease phenotype (1=unaff, 2=aff, 0=miss)
+Missing phenotype value is also -9
+10 cases, 30 controls and 0 missing
+21 males, 19 females, and 0 of unspecified sex
+Reading genotype bitfile from [ /opt/galaxy/test-data/tinywga.bed ]
+Detected that binary PED file is v1.00 SNP-major mode
+Before frequency and genotyping pruning, there are 25 SNPs
+27 founders and 13 non-founders found
+0 of 40 individuals removed for low genotyping ( MIND > 0.5 )
+Total genotyping rate in remaining individuals is 0.995
+0 SNPs failed missingness test ( GENO > 1 )
+0 SNPs failed frequency test ( MAF < 0 )
+After frequency and genotyping pruning, there are 25 SNPs
+After filtering, 10 cases, 30 controls and 0 missing
+After filtering, 21 males, 19 females, and 0 of unspecified sex
+14 nuclear families, 1 founder singletons found
+13 non-founders with 2 parents in 13 nuclear families
+0 non-founders without 2 parents in 0 nuclear families
+10 affected offspring trios
+0 phenotypically discordant parent pairs found
+Converting data to Individual-major format
+0 Mendel errors detected in total
+Writing TDT results (asymptotic) to [ rgTDTtest1.tdt ]
+
+Analysis finished: Thu Mar 25 21:01:31 2010
+
+###maxp=0.590405,minp=-0.000000,prange=1.090405,scalefact=917.090439
diff -r 4906f2302c85 -r cc8a30a0669f test-data/rgTDTtest1_TDT_topTable.gff
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/rgTDTtest1_TDT_topTable.gff Fri Mar 26 14:42:15 2010 -0400
@@ -0,0 +1,25 @@
+track name=rgTDT_Top_Table description="rgTDTtest1" visibility=2 useScore=1 color=0,60,120
+chr22 rgGLM variation 21784622 21784822 0 . . rs2283802 logp=-0.00
+chr22 rgGLM variation 21785266 21785466 120 . . rs2267000 logp=0.13
+chr22 rgGLM variation 21794654 21794854 0 . . rs16997606 logp=-0.00
+chr22 rgGLM variation 21794710 21794910 457 . . rs4820537 logp=0.50
+chr22 rgGLM variation 21797704 21797904 120 . . rs3788347 logp=0.13
+chr22 rgGLM variation 21799818 21800018 228 . . rs756632 logp=0.25
+chr22 rgGLM variation 21807870 21808070 120 . . rs4820539 logp=0.13
+chr22 rgGLM variation 21820235 21820435 292 . . rs2283804 logp=0.32
+chr22 rgGLM variation 21820890 21821090 292 . . rs2267006 logp=0.32
+chr22 rgGLM variation 21820900 21821100 0 . . rs4822363 logp=-0.00
+chr22 rgGLM variation 21827574 21827774 541 . . rs5751592 logp=0.59
+chr22 rgGLM variation 21832608 21832808 400 . . rs5759608 logp=0.44
+chr22 rgGLM variation 21833070 21833270 400 . . rs5759612 logp=0.44
+chr22 rgGLM variation 21860068 21860268 0 . . rs2267009 logp=-0.00
+chr22 rgGLM variation 21864266 21864466 0 . . rs2267010 logp=-0.00
+chr22 rgGLM variation 21868598 21868798 457 . . rs5759636 logp=0.50
+chr22 rgGLM variation 21871388 21871588 0 . . rs2071436 logp=-0.00
+chr22 rgGLM variation 21875779 21875979 457 . . rs2267013 logp=0.50
+chr22 rgGLM variation 21889706 21889906 168 . . rs6003566 logp=0.18
+chr22 rgGLM variation 21892791 21892991 457 . . rs2256725 logp=0.50
+chr22 rgGLM variation 21895919 21896119 359 . . rs5751611 logp=0.39
+chr22 rgGLM variation 21898758 21898958 400 . . rs762601 logp=0.44
+chr22 rgGLM variation 21898963 21899163 400 . . rs2156921 logp=0.44
+chr22 rgGLM variation 21905542 21905742 400 . . rs4822375 logp=0.44
diff -r 4906f2302c85 -r cc8a30a0669f test-data/rgtestouts/rgClean/rgCleantest1.bed
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/rgtestouts/rgClean/rgCleantest1.bed Fri Mar 26 14:42:15 2010 -0400
@@ -0,0 +1,1 @@
+lÿëþ¿¾+êóª¿ü £ïªîþ¨êÿïªûÿÿÿÿÿÿþﮨª"ëú £ïªîþ¨ÿÿ»ÿÿïïþÿèÿþ"ÿ«ïªîþ¨:*ÿïêüº.«ë:*ÿïêüº.«ëÿÿÿÿ¯ÿ¿ïþ¿ÿþªÿ¯û¿ïþ¿:*»ïêìª,«À:*»ïêìª,«Àÿëþ¿¾+êóª¿ÿÿÿÿûÿúÿÿÿÿÿÿÿÿÿ¿þ¿ÿëþ¿¾+ê󪿺ûÿÿ¿»ÿÿþ¿êÿÿªûÿÿÿÿÿºûÿÿ¿»ÿÿþ¿mÿÿÿýÿÿÿÿÿ ú¢ª±«¯ü(:ú¢ÿ¿«¯ü(:ú¢ÿ¿«¯ü(:ú¢ÿ¿«¯ü(
\ No newline at end of file
diff -r 4906f2302c85 -r cc8a30a0669f test-data/rgtestouts/rgClean/rgCleantest1.bim
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/rgtestouts/rgClean/rgCleantest1.bim Fri Mar 26 14:42:15 2010 -0400
@@ -0,0 +1,25 @@
+22 rs2283802 0 21784722 4 2
+22 rs2267000 0 21785366 4 2
+22 rs16997606 0 21794754 1 3
+22 rs4820537 0 21794810 1 3
+22 rs3788347 0 21797804 3 1
+22 rs756632 0 21799918 4 2
+22 rs4820539 0 21807970 1 3
+22 rs2283804 0 21820335 1 2
+22 rs2267006 0 21820990 3 1
+22 rs4822363 0 21821000 4 2
+22 rs5751592 0 21827674 4 2
+22 rs5759608 0 21832708 2 4
+22 rs5759612 0 21833170 3 1
+22 rs2267009 0 21860168 3 4
+22 rs2267010 0 21864366 3 1
+22 rs5759636 0 21868698 4 2
+22 rs2071436 0 21871488 4 2
+22 rs2267013 0 21875879 3 1
+22 rs6003566 0 21889806 3 1
+22 rs2256725 0 21892891 2 1
+22 rs12160770 0 21892925 1 3
+22 rs5751611 0 21896019 2 4
+22 rs762601 0 21898858 1 3
+22 rs2156921 0 21899063 3 1
+22 rs4822375 0 21905642 1 3
diff -r 4906f2302c85 -r cc8a30a0669f test-data/rgtestouts/rgClean/rgCleantest1.fam
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/rgtestouts/rgClean/rgCleantest1.fam Fri Mar 26 14:42:15 2010 -0400
@@ -0,0 +1,40 @@
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+101 2 0 0 2 1
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+105 1 3 2 2 2
+105 2 0 0 2 1
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+112 1 3 2 1 2
+112 2 0 0 2 1
+112 3 0 0 1 1
+117 1 3 2 2 2
+117 2 0 0 2 1
+117 3 0 0 1 1
+12 1 3 2 1 2
+12 2 0 0 2 1
+12 3 0 0 1 1
+13 1 3 2 1 2
+13 2 0 0 2 1
+13 3 0 0 1 1
+1334 1 10 11 1 2
+1334 10 0 0 1 1
+1334 11 0 0 2 1
+1334 12 0 0 1 1
+1334 13 0 0 2 1
+1334 2 12 13 2 2
+1340 1 9 10 1 2
+1340 10 0 0 2 1
+1340 11 0 0 1 1
+1340 12 0 0 2 1
+1340 2 11 12 2 2
+1340 9 0 0 1 1
+1341 1 11 12 1 1
+1341 11 0 0 1 1
+1341 12 0 0 2 1
+1341 13 0 0 1 1
+1341 14 0 0 2 1
+1341 2 13 14 2 1
+1344 1 12 13 1 1
+1344 12 0 0 1 1
+1344 13 0 0 2 1
+1345 12 0 0 1 1
diff -r 4906f2302c85 -r cc8a30a0669f test-data/rgtestouts/rgClean/rgCleantest1.log
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/rgtestouts/rgClean/rgCleantest1.log Fri Mar 26 14:42:15 2010 -0400
@@ -0,0 +1,66 @@
+rgClean.py started, called as /opt/galaxy/tools/rgenetics/rgClean.py /opt/galaxy/test-data tinywga rgCleantest1 1 1 0 0 1 1 /opt/galaxy/test-data/rgtestouts/rgClean/rgCleantest1.pbed /opt/galaxy/test-data/rgtestouts/rgClean 0 0 0 0
+
+@----------------------------------------------------------@
+| PLINK! | v1.06 | 24/Apr/2009 |
+|----------------------------------------------------------|
+| (C) 2009 Shaun Purcell, GNU General Public License, v2 |
+|----------------------------------------------------------|
+| For documentation, citation & bug-report instructions: |
+| http://pngu.mgh.harvard.edu/purcell/plink/ |
+@----------------------------------------------------------@
+
+Skipping web check... [ --noweb ]
+Writing this text to log file [ /opt/galaxy/test-data/rgtestouts/rgClean/rgCleantest1.log ]
+Analysis started: Thu Mar 25 21:01:24 2010
+
+Options in effect:
+--noweb
+--bfile /opt/galaxy/test-data/tinywga
+--make-bed
+--out /opt/galaxy/test-data/rgtestouts/rgClean/rgCleantest1
+--set-hh-missing
+--mind 1
+--geno 1
+--maf 0
+--hwe 0
+--me 1 1
+
+Reading map (extended format) from [ /opt/galaxy/test-data/tinywga.bim ]
+25 markers to be included from [ /opt/galaxy/test-data/tinywga.bim ]
+Reading pedigree information from [ /opt/galaxy/test-data/tinywga.fam ]
+40 individuals read from [ /opt/galaxy/test-data/tinywga.fam ]
+40 individuals with nonmissing phenotypes
+Assuming a disease phenotype (1=unaff, 2=aff, 0=miss)
+Missing phenotype value is also -9
+10 cases, 30 controls and 0 missing
+21 males, 19 females, and 0 of unspecified sex
+Reading genotype bitfile from [ /opt/galaxy/test-data/tinywga.bed ]
+Detected that binary PED file is v1.00 SNP-major mode
+Before frequency and genotyping pruning, there are 25 SNPs
+27 founders and 13 non-founders found
+0 markers to be excluded based on HWE test ( p <= 0 )
+0 markers failed HWE test in cases
+0 markers failed HWE test in controls
+Total genotyping rate in remaining individuals is 0.995
+0 SNPs failed missingness test ( GENO > 1 )
+0 SNPs failed frequency test ( MAF < 0 )
+After frequency and genotyping pruning, there are 25 SNPs
+After filtering, 10 cases, 30 controls and 0 missing
+After filtering, 21 males, 19 females, and 0 of unspecified sex
+14 nuclear families, 1 founder singletons found
+13 non-founders with 2 parents in 13 nuclear families
+0 non-founders without 2 parents in 0 nuclear families
+10 affected offspring trios
+0 phenotypically discordant parent pairs found
+Converting data to Individual-major format
+Filtering SNPs/families for Mendel Error rates above 1, 1
+0 Mendel errors detected in total
+0 families ( 0 individuals ) removed due to Mendel errors
+0 markers removed due to Mendel errors, 25 remaining
+Writing pedigree information to [ /opt/galaxy/test-data/rgtestouts/rgClean/rgCleantest1.fam ]
+Writing map (extended format) information to [ /opt/galaxy/test-data/rgtestouts/rgClean/rgCleantest1.bim ]
+Writing genotype bitfile to [ /opt/galaxy/test-data/rgtestouts/rgClean/rgCleantest1.bed ]
+Using (default) SNP-major mode
+Converting data to SNP-major format
+
+Analysis finished: Thu Mar 25 21:01:24 2010
diff -r 4906f2302c85 -r cc8a30a0669f test-data/rgtestouts/rgClean/rgCleantest1.pbed
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/rgtestouts/rgClean/rgCleantest1.pbed Fri Mar 26 14:42:15 2010 -0400
@@ -0,0 +1,19 @@
+<?xml version="1.0" encoding="utf-8" ?>
+<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN" "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
+<html xmlns="http://www.w3.org/1999/xhtml" xml:lang="en" lang="en">
+<head>
+<meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
+<meta name="generator" content="Galaxy rgClean.py tool output - see http://g2.trac.bx.psu.edu/" />
+<title></title>
+<link rel="stylesheet" href="/static/style/base.css" type="text/css" />
+</head>
+<body>
+<div class="document">
+<ul>
+<li><a href="rgCleantest1.bed">rgCleantest1.bed</a></li>
+<li><a href="rgCleantest1.bim">rgCleantest1.bim</a></li>
+<li><a href="rgCleantest1.fam">rgCleantest1.fam</a></li>
+<li><a href="rgCleantest1.log">rgCleantest1.log</a></li>
+<li><a href="rgCleantest1.pbed">rgCleantest1.pbed</a></li>
+</ul>
+</ul></br></div></body></html>
\ No newline at end of file
diff -r 4906f2302c85 -r cc8a30a0669f test-data/rgtestouts/rgEigPCA/Rplots.pdf
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diff -r 4906f2302c85 -r cc8a30a0669f test-data/rgtestouts/rgEigPCA/rgEigPCAtest1.R
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/rgtestouts/rgEigPCA/rgEigPCAtest1.R Fri Mar 26 14:42:15 2010 -0400
@@ -0,0 +1,19 @@
+llist=c("Control","Case")
+glist=c(2,3)
+par(lab=c(10,10,10))
+par(mai=c(1,1,1,0.5))
+pdf("rgEigPCAtest1_PCAPlot.pdf",h=8,w=10)
+par(lab=c(10,10,10))
+pca1 = c(0.127600,0.027200,0.145200,0.088700,-0.002600,-0.245300,-0.241200,0.035800,0.290500,0.160700,0.167500,0.027200,0.027200,-0.087000,-0.063000,-0.188600,0.026800,-0.064300,0.092700,-0.241200,0.005600,0.026100,-0.160800,-0.160800,0.026100,0.074200,0.030200,-0.249300,0.183300,-0.102700,0.231200,-0.245300,-0.245300,-0.245300,0.301500,0.030200,0.030200,0.259300)
+pca2 = c(0.006000,-0.179400,0.266600,0.076500,-0.036700,-0.016500,0.253700,-0.176600,0.081100,-0.124700,0.041800,-0.179400,-0.179400,0.015400,-0.265600,-0.025100,-0.000800,0.041800,-0.221000,0.253700,-0.205100,-0.035400,-0.034900,-0.034900,-0.035400,0.081900,0.234800,-0.286700,0.120600,0.293900,-0.180800,-0.016500,-0.016500,-0.016500,0.215900,0.234800,0.234800,-0.191600)
+pgvec = c(2,2,3,2,2,3,2,2,3,2,2,3,2,2,3,2,2,3,2,2,2,2,3,2,2,2,3,2,2,2,2,2,2,2,2,2,2,2)
+plot(pca1,pca2,type='p',main='rgEigPCAtest1', ylab='Second ancestry eigenvector',xlab='First ancestry eigenvector',col=pgvec,cex=0.8,pch=pgvec)
+legend("top",legend=llist,pch=glist,col=glist,title="Sample")
+grid(nx = 10, ny = 10, col = "lightgray", lty = "dotted")
+dev.off()
+png("rgEigPCAtest1_PCAPlot.pdf.png",h=8,w=10,units="in",res=72)
+plot(pca1,pca2,type='p',main='rgEigPCAtest1', ylab='Second ancestry eigenvector',xlab='First ancestry eigenvector',col=pgvec,cex=0.8,pch=pgvec)
+legend("top",legend=llist,pch=glist,col=glist,title="Sample")
+grid(nx = 10, ny = 10, col = "lightgray", lty = "dotted")
+dev.off()
+#R script autogenerated by rgenetics/rgutils.py on 25/03/2010 21:01:25
diff -r 4906f2302c85 -r cc8a30a0669f test-data/rgtestouts/rgEigPCA/rgEigPCAtest1.html
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/rgtestouts/rgEigPCA/rgEigPCAtest1.html Fri Mar 26 14:42:15 2010 -0400
@@ -0,0 +1,160 @@
+<?xml version="1.0" encoding="utf-8" ?>
+<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN" "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
+<html xmlns="http://www.w3.org/1999/xhtml" xml:lang="en" lang="en">
+<head>
+<meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
+<meta name="generator" content="Galaxy rgEigPCA.py tool output - see http://g2.trac.bx.psu.edu/" />
+<title></title>
+<link rel="stylesheet" href="/static/style/base.css" type="text/css" />
+</head>
+<body>
+<div class="document">
+<h4>Output from rgEigPCA.py run at 25/03/2010 21:01:25<br/>
+</h4>
+newfilepath=/opt/galaxy/test-data/rgtestouts/rgEigPCA, rexe=R(click on the image below to see a much higher quality PDF version)<table border="0" cellpadding="10" cellspacing="10"><tr><td>
+<a href="rgEigPCAtest1_PCAPlot.pdf"><img src="rgEigPCAtest1_PCAPlot.pdf.png" alt="Samples plotted in first 2 eigenvector space" hspace="10" align="left" /></a></td></tr></table><br/>
+<div class="document">All Files:<ol><li><a href="rgEigPCAtest1_eval.xls">rgEigPCAtest1_eval.xls (507 B)</a></li>
+<li><a href="rgEigPCAtest1_pca.xls.par">rgEigPCAtest1_pca.xls.par (311 B)</a></li>
+<li><a href="rgEigPCAtest1_PCAPlot.pdf.png">rgEigPCAtest1_PCAPlot.pdf.png (27.1 KB)</a></li>
+<li><a href="rgEigPCAtest1_log.txt">rgEigPCAtest1_log.txt (6.0 KB)</a></li>
+<li><a href="rgEigPCAtest1.html">rgEigPCAtest1.html </a></li>
+<li><a href="rgEigPCAtest1_eigensoftplot.pdf.xtxt">rgEigPCAtest1_eigensoftplot.pdf.xtxt (257 B)</a></li>
+<li><a href="rgEigPCAtest1_eigensoftplot.pdf.ps">rgEigPCAtest1_eigensoftplot.pdf.ps (13.6 KB)</a></li>
+<li><a href="rgEigPCAtest1_pca.xls.evec">rgEigPCAtest1_pca.xls.evec (3.3 KB)</a></li>
+<li><a href="rgEigPCAtest1_pca.xls">rgEigPCAtest1_pca.xls (1.3 KB)</a></li>
+<li><a href="rgEigPCAtest1_PCAPlot.pdf">rgEigPCAtest1_PCAPlot.pdf (7.9 KB)</a></li>
+<li><a href="rgEigPCAtest1.txt">rgEigPCAtest1.txt (3.3 KB)</a></li>
+<li><a href="rgEigPCAtest1_eigensoftplot.pdf.pdf">rgEigPCAtest1_eigensoftplot.pdf.pdf (2.1 KB)</a></li>
+<li><a href="rgEigPCAtest1.R">rgEigPCAtest1.R (1.6 KB)</a></li>
+<li><a href="Rplots.pdf">Rplots.pdf (813 B)</a></li>
+</ol></div><div class="document">Log rgEigPCAtest1_log.txt contents follow below<p/><pre>parameter file: rgEigPCAtest1_pca.xls.par
+### THE INPUT PARAMETERS
+##PARAMETER NAME: VALUE
+genotypename: /opt/galaxy/test-data/tinywga.ped
+snpname: /opt/galaxy/test-data/tinywga.map
+indivname: /opt/galaxy/test-data/tinywga.ped
+evecoutname: rgEigPCAtest1_pca.xls.evec
+evaloutname: rgEigPCAtest1_eval.xls
+altnormstyle: NO
+numoutevec: 4
+numoutlieriter: 2
+numoutlierevec: 2
+outliersigmathresh: 2
+qtmode: 0
+## smartpca version: 8000
+norm used
+
+genetic distance set from physical distance
+genotype file processed
+number of samples used: 40 number of snps used: 25
+REMOVED outlier 1334:2 iter 1 evec 1 sigmage -2.329
+number of samples after outlier removal: 39
+
+## Tracy-Widom statistics: rows: 39 cols: 24
+ #N eigenvalue difference twstat p-value effect. n
+ 1 11.481974 NA -0.712 0.332198 8.854
+ 2 7.739771 -3.742203 -1.302 0.510496 8.388
+ 3 7.254586 -0.485185 -0.171 0.201072 7.095
+ 4 4.270950 -2.983636 -0.191 0.205302 8.005
+ 5 2.538320 -1.732630 -0.341 0.238117 9.118
+ 6 1.667964 -0.870356 -0.231 0.21376 9.910
+ 7 1.043403 -0.624560 -0.269 0.222042 11.590
+ 8 0.653401 -0.390003 NA NA NA
+ 9 0.391044 -0.262357 NA NA NA
+ 10 0.338164 -0.052880 NA NA NA
+ 11 0.263384 -0.074780 NA NA NA
+ 12 0.150750 -0.112634 NA NA NA
+ 13 0.085580 -0.065170 NA NA NA
+ 14 0.065301 -0.020279 NA NA NA
+ 15 0.048797 -0.016504 NA NA NA
+ 16 0.006611 -0.042186 NA NA NA
+ kurtosis snps indivs
+ eigenvector 1 1.926 2.122
+ eigenvector 2 2.599 2.148
+ eigenvector 3 2.593 2.873
+ eigenvector 4 3.165 2.831
+population: 0 Case 9
+population: 1 Control 30
+
+## Average divergence between populations:
+ Case Control popsize
+ Case 1.028 0.954 9
+ Control 0.954 0.972 30
+
+
+number of blocks for moving block jackknife: 1
+fst *1000:
+ C C
+ C 0 0
+ C 0 0
+
+s.dev * 1000000:
+ C C
+ C 0 0
+ C 0 0
+
+## Anova statistics for population differences along each eigenvector:
+ p-value
+ eigenvector_1_Case_Control_ 0.841067
+ eigenvector_2_Case_Control_ 0.758376
+ eigenvector_3_Case_Control_ 0.238793
+ eigenvector_4_Case_Control_ 0.678458
+
+## Statistical significance of differences beween populations:
+ pop1 pop2 chisq p-value |pop1| |pop2|
+popdifference: Case Control 1.810 0.77061 9 30
+
+eigbestsnp 1 rs762601 22 21898858 1.674
+eigbestsnp 1 rs2156921 22 21899063 1.674
+eigbestsnp 1 rs4822375 22 21905642 1.674
+eigbestsnp 1 rs5751611 22 21896019 1.635
+eigbestsnp 1 rs4820537 22 21794810 1.542
+eigbestsnp 1 rs3788347 22 21797804 1.413
+eigbestsnp 1 rs2267000 22 21785366 1.151
+eigbestsnp 1 rs4820539 22 21807970 1.141
+eigbestsnp 1 rs5751592 22 21827674 0.890
+eigbestsnp 1 rs2283804 22 21820335 0.815
+eigbestsnp 1 rs2267006 22 21820990 0.815
+eigbestsnp 2 rs5759608 22 21832708 2.197
+eigbestsnp 2 rs5759612 22 21833170 2.197
+eigbestsnp 2 rs2283804 22 21820335 1.643
+eigbestsnp 2 rs2267006 22 21820990 1.643
+eigbestsnp 2 rs2283802 22 21784722 1.283
+eigbestsnp 2 rs2267009 22 21860168 1.283
+eigbestsnp 2 rs2071436 22 21871488 1.283
+eigbestsnp 2 rs756632 22 21799918 0.942
+eigbestsnp 2 rs16997606 22 21794754 0.715
+eigbestsnp 2 rs6003566 22 21889806 0.645
+eigbestsnp 2 rs762601 22 21898858 0.545
+eigbestsnp 3 rs16997606 22 21794754 1.770
+eigbestsnp 3 rs6003566 22 21889806 1.725
+eigbestsnp 3 rs3788347 22 21797804 1.452
+eigbestsnp 3 rs2267000 22 21785366 1.386
+eigbestsnp 3 rs2283802 22 21784722 1.247
+eigbestsnp 3 rs2267009 22 21860168 1.247
+eigbestsnp 3 rs2071436 22 21871488 1.247
+eigbestsnp 3 rs4820537 22 21794810 1.168
+eigbestsnp 3 rs762601 22 21898858 1.153
+eigbestsnp 3 rs2156921 22 21899063 1.153
+eigbestsnp 3 rs4822375 22 21905642 1.153
+eigbestsnp 4 rs756632 22 21799918 2.146
+eigbestsnp 4 rs4820539 22 21807970 1.938
+eigbestsnp 4 rs2267013 22 21875879 1.917
+eigbestsnp 4 rs2256725 22 21892891 1.917
+eigbestsnp 4 rs2283804 22 21820335 1.336
+eigbestsnp 4 rs2267006 22 21820990 1.336
+eigbestsnp 4 rs6003566 22 21889806 1.000
+eigbestsnp 4 rs16997606 22 21794754 0.875
+eigbestsnp 4 rs5751611 22 21896019 0.823
+eigbestsnp 4 rs5759636 22 21868698 0.799
+eigbestsnp 4 rs2267000 22 21785366 0.584
+packedancestrymap output
+##end of smartpca run
+
+Correlation between eigenvector 1 (of 4) and Case/Control status is 0.033
+Correlation between eigenvector 2 (of 4) and Case/Control status is 0.051
+Correlation between eigenvector 3 (of 4) and Case/Control status is 0.193
+Correlation between eigenvector 4 (of 4) and Case/Control status is -0.069
+</pre></div>If you need to rerun this analysis, the command line used was
+smartpca.perl -i /opt/galaxy/test-data/tinywga.ped -a /opt/galaxy/test-data/tinywga.map -b /opt/galaxy/test-data/tinywga.ped -o rgEigPCAtest1_pca.xls -p rgEigPCAtest1_eigensoftplot.pdf -e rgEigPCAtest1_eval.xls -l rgEigPCAtest1_log.txt -k 4 -m 2 -t 2 -s 2
+<p/></div></body></html>
diff -r 4906f2302c85 -r cc8a30a0669f test-data/rgtestouts/rgEigPCA/rgEigPCAtest1.txt
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/rgtestouts/rgEigPCA/rgEigPCAtest1.txt Fri Mar 26 14:42:15 2010 -0400
@@ -0,0 +1,40 @@
+ #eigvals: 11.482 7.740 7.255 4.271
+ 101:1 0.1276 0.0060 0.1550 -0.3329 Case
+ 101:2 0.1276 0.0060 0.1550 -0.3329 Control
+ 101:3 0.0272 -0.1794 0.3241 -0.0243 Control
+ 105:1 0.1452 0.2666 -0.0845 -0.3446 Case
+ 105:2 0.0887 0.0765 0.0527 0.0326 Control
+ 105:3 -0.0026 -0.0367 -0.1333 -0.2045 Control
+ 112:1 -0.2453 -0.0165 -0.0856 0.0221 Case
+ 112:2 -0.2412 0.2537 0.0100 -0.0961 Control
+ 112:3 0.0358 -0.1766 -0.1010 0.1423 Control
+ 117:1 0.2905 0.0811 -0.0332 0.2245 Case
+ 117:2 0.1607 -0.1247 0.1495 0.0759 Control
+ 117:3 0.1675 0.0418 0.0449 0.2637 Control
+ 12:1 0.0272 -0.1794 0.3241 -0.0243 Case
+ 12:2 0.0272 -0.1794 0.3241 -0.0243 Control
+ 12:3 -0.0870 0.0154 0.2295 -0.1150 Control
+ 13:1 -0.0630 -0.2656 0.1607 -0.0055 Case
+ 13:2 -0.1886 -0.0251 -0.0558 -0.0102 Control
+ 13:3 0.0268 -0.0008 0.3404 -0.0369 Control
+ 1334:1 -0.0643 0.0418 0.0358 0.0343 Case
+ 1334:10 0.0927 -0.2210 -0.1938 -0.0651 Control
+ 1334:11 -0.2412 0.2537 0.0100 -0.0961 Control
+ 1334:12 0.0056 -0.2051 -0.2132 -0.1240 Control
+ 1334:13 0.0261 -0.0354 -0.0819 0.2399 Control
+ 1340:1 -0.1608 -0.0349 0.0222 0.1244 Case
+ 1340:10 -0.1608 -0.0349 0.0222 0.1244 Control
+ 1340:11 0.0261 -0.0354 -0.0819 0.2399 Control
+ 1340:12 0.0742 0.0819 -0.0833 -0.0528 Control
+ 1340:2 0.0302 0.2348 0.0136 0.1216 Case
+ 1340:9 -0.2493 -0.2867 -0.1811 0.1404 Control
+ 1341:1 0.1833 0.1206 -0.1248 -0.0491 Control
+ 1341:11 -0.1027 0.2939 -0.1091 -0.1832 Control
+ 1341:12 0.2312 -0.1808 -0.3129 -0.1522 Control
+ 1341:13 -0.2453 -0.0165 -0.0856 0.0221 Control
+ 1341:14 -0.2453 -0.0165 -0.0856 0.0221 Control
+ 1341:2 -0.2453 -0.0165 -0.0856 0.0221 Control
+ 1344:1 0.3015 0.2159 0.0173 0.3393 Control
+ 1344:12 0.0302 0.2348 0.0136 0.1216 Control
+ 1344:13 0.0302 0.2348 0.0136 0.1216 Control
+ 1345:12 0.2593 -0.1916 -0.2862 -0.1609 Control
diff -r 4906f2302c85 -r cc8a30a0669f test-data/rgtestouts/rgEigPCA/rgEigPCAtest1_PCAPlot.pdf
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
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diff -r 4906f2302c85 -r cc8a30a0669f test-data/rgtestouts/rgEigPCA/rgEigPCAtest1_eigensoftplot.pdf.pdf
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diff -r 4906f2302c85 -r cc8a30a0669f test-data/rgtestouts/rgEigPCA/rgEigPCAtest1_eigensoftplot.pdf.xtxt
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/rgtestouts/rgEigPCA/rgEigPCAtest1_eigensoftplot.pdf.xtxt Fri Mar 26 14:42:15 2010 -0400
@@ -0,0 +1,7 @@
+set terminal postscript color
+set title ""
+set xlabel "eigenvector 1"
+set ylabel "eigenvector 2"
+plot "rgEigPCAtest1_pca.xls.evec.1:2:Case" using 2:3 title "Case" , \
+ "rgEigPCAtest1_pca.xls.evec.1:2:Control" using 2:3 title "Control"
+## pause 9999
diff -r 4906f2302c85 -r cc8a30a0669f test-data/rgtestouts/rgEigPCA/rgEigPCAtest1_eval.xls
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/rgtestouts/rgEigPCA/rgEigPCAtest1_eval.xls Fri Mar 26 14:42:15 2010 -0400
@@ -0,0 +1,39 @@
+ 11.481974
+ 7.739771
+ 7.254586
+ 4.270950
+ 2.538320
+ 1.667964
+ 1.043403
+ 0.653401
+ 0.391044
+ 0.338164
+ 0.263384
+ 0.150750
+ 0.085580
+ 0.065301
+ 0.048797
+ 0.006611
+ 0.000000
+ 0.000000
+ 0.000000
+ 0.000000
+ 0.000000
+ 0.000000
+ 0.000000
+ 0.000000
+ 0.000000
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+ -0.000000
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+ -0.000000
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diff -r 4906f2302c85 -r cc8a30a0669f test-data/rgtestouts/rgEigPCA/rgEigPCAtest1_log.txt
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/rgtestouts/rgEigPCA/rgEigPCAtest1_log.txt Fri Mar 26 14:42:15 2010 -0400
@@ -0,0 +1,128 @@
+parameter file: rgEigPCAtest1_pca.xls.par
+### THE INPUT PARAMETERS
+##PARAMETER NAME: VALUE
+genotypename: /opt/galaxy/test-data/tinywga.ped
+snpname: /opt/galaxy/test-data/tinywga.map
+indivname: /opt/galaxy/test-data/tinywga.ped
+evecoutname: rgEigPCAtest1_pca.xls.evec
+evaloutname: rgEigPCAtest1_eval.xls
+altnormstyle: NO
+numoutevec: 4
+numoutlieriter: 2
+numoutlierevec: 2
+outliersigmathresh: 2
+qtmode: 0
+## smartpca version: 8000
+norm used
+
+genetic distance set from physical distance
+genotype file processed
+number of samples used: 40 number of snps used: 25
+REMOVED outlier 1334:2 iter 1 evec 1 sigmage -2.329
+number of samples after outlier removal: 39
+
+## Tracy-Widom statistics: rows: 39 cols: 24
+ #N eigenvalue difference twstat p-value effect. n
+ 1 11.481974 NA -0.712 0.332198 8.854
+ 2 7.739771 -3.742203 -1.302 0.510496 8.388
+ 3 7.254586 -0.485185 -0.171 0.201072 7.095
+ 4 4.270950 -2.983636 -0.191 0.205302 8.005
+ 5 2.538320 -1.732630 -0.341 0.238117 9.118
+ 6 1.667964 -0.870356 -0.231 0.21376 9.910
+ 7 1.043403 -0.624560 -0.269 0.222042 11.590
+ 8 0.653401 -0.390003 NA NA NA
+ 9 0.391044 -0.262357 NA NA NA
+ 10 0.338164 -0.052880 NA NA NA
+ 11 0.263384 -0.074780 NA NA NA
+ 12 0.150750 -0.112634 NA NA NA
+ 13 0.085580 -0.065170 NA NA NA
+ 14 0.065301 -0.020279 NA NA NA
+ 15 0.048797 -0.016504 NA NA NA
+ 16 0.006611 -0.042186 NA NA NA
+ kurtosis snps indivs
+ eigenvector 1 1.926 2.122
+ eigenvector 2 2.599 2.148
+ eigenvector 3 2.593 2.873
+ eigenvector 4 3.165 2.831
+population: 0 Case 9
+population: 1 Control 30
+
+## Average divergence between populations:
+ Case Control popsize
+ Case 1.028 0.954 9
+ Control 0.954 0.972 30
+
+
+number of blocks for moving block jackknife: 1
+fst *1000:
+ C C
+ C 0 0
+ C 0 0
+
+s.dev * 1000000:
+ C C
+ C 0 0
+ C 0 0
+
+## Anova statistics for population differences along each eigenvector:
+ p-value
+ eigenvector_1_Case_Control_ 0.841067
+ eigenvector_2_Case_Control_ 0.758376
+ eigenvector_3_Case_Control_ 0.238793
+ eigenvector_4_Case_Control_ 0.678458
+
+## Statistical significance of differences beween populations:
+ pop1 pop2 chisq p-value |pop1| |pop2|
+popdifference: Case Control 1.810 0.77061 9 30
+
+eigbestsnp 1 rs762601 22 21898858 1.674
+eigbestsnp 1 rs2156921 22 21899063 1.674
+eigbestsnp 1 rs4822375 22 21905642 1.674
+eigbestsnp 1 rs5751611 22 21896019 1.635
+eigbestsnp 1 rs4820537 22 21794810 1.542
+eigbestsnp 1 rs3788347 22 21797804 1.413
+eigbestsnp 1 rs2267000 22 21785366 1.151
+eigbestsnp 1 rs4820539 22 21807970 1.141
+eigbestsnp 1 rs5751592 22 21827674 0.890
+eigbestsnp 1 rs2283804 22 21820335 0.815
+eigbestsnp 1 rs2267006 22 21820990 0.815
+eigbestsnp 2 rs5759608 22 21832708 2.197
+eigbestsnp 2 rs5759612 22 21833170 2.197
+eigbestsnp 2 rs2283804 22 21820335 1.643
+eigbestsnp 2 rs2267006 22 21820990 1.643
+eigbestsnp 2 rs2283802 22 21784722 1.283
+eigbestsnp 2 rs2267009 22 21860168 1.283
+eigbestsnp 2 rs2071436 22 21871488 1.283
+eigbestsnp 2 rs756632 22 21799918 0.942
+eigbestsnp 2 rs16997606 22 21794754 0.715
+eigbestsnp 2 rs6003566 22 21889806 0.645
+eigbestsnp 2 rs762601 22 21898858 0.545
+eigbestsnp 3 rs16997606 22 21794754 1.770
+eigbestsnp 3 rs6003566 22 21889806 1.725
+eigbestsnp 3 rs3788347 22 21797804 1.452
+eigbestsnp 3 rs2267000 22 21785366 1.386
+eigbestsnp 3 rs2283802 22 21784722 1.247
+eigbestsnp 3 rs2267009 22 21860168 1.247
+eigbestsnp 3 rs2071436 22 21871488 1.247
+eigbestsnp 3 rs4820537 22 21794810 1.168
+eigbestsnp 3 rs762601 22 21898858 1.153
+eigbestsnp 3 rs2156921 22 21899063 1.153
+eigbestsnp 3 rs4822375 22 21905642 1.153
+eigbestsnp 4 rs756632 22 21799918 2.146
+eigbestsnp 4 rs4820539 22 21807970 1.938
+eigbestsnp 4 rs2267013 22 21875879 1.917
+eigbestsnp 4 rs2256725 22 21892891 1.917
+eigbestsnp 4 rs2283804 22 21820335 1.336
+eigbestsnp 4 rs2267006 22 21820990 1.336
+eigbestsnp 4 rs6003566 22 21889806 1.000
+eigbestsnp 4 rs16997606 22 21794754 0.875
+eigbestsnp 4 rs5751611 22 21896019 0.823
+eigbestsnp 4 rs5759636 22 21868698 0.799
+eigbestsnp 4 rs2267000 22 21785366 0.584
+packedancestrymap output
+##end of smartpca run
+
+Correlation between eigenvector 1 (of 4) and Case/Control status is 0.033
+Correlation between eigenvector 2 (of 4) and Case/Control status is 0.051
+Correlation between eigenvector 3 (of 4) and Case/Control status is 0.193
+Correlation between eigenvector 4 (of 4) and Case/Control status is -0.069
diff -r 4906f2302c85 -r cc8a30a0669f test-data/rgtestouts/rgEigPCA/rgEigPCAtest1_pca.xls
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/rgtestouts/rgEigPCA/rgEigPCAtest1_pca.xls Fri Mar 26 14:42:15 2010 -0400
@@ -0,0 +1,45 @@
+4
+11.4820
+7.7400
+7.2550
+4.2710
+ 0.3015 0.2159 0.0173 0.3393
+ -0.2453 -0.0165 -0.0856 0.0221
+ 0.0268 -0.0008 0.3404 -0.0369
+ 0.3015 0.2159 0.0173 0.3393
+ -0.2453 -0.0165 -0.0856 0.0221
+ 0.0268 -0.0008 0.3404 -0.0369
+ 0.3015 0.2159 0.0173 0.3393
+ -0.2453 -0.0165 -0.0856 0.0221
+ 0.0268 -0.0008 0.3404 -0.0369
+ 0.3015 0.2159 0.0173 0.3393
+ -0.2453 -0.0165 -0.0856 0.0221
+ 0.0268 -0.0008 0.3404 -0.0369
+ 0.3015 0.2159 0.0173 0.3393
+ -0.2453 -0.0165 -0.0856 0.0221
+ 0.0268 -0.0008 0.3404 -0.0369
+ 0.3015 0.2159 0.0173 0.3393
+ -0.2453 -0.0165 -0.0856 0.0221
+ 0.0268 -0.0008 0.3404 -0.0369
+ 0.3015 0.2159 0.0173 0.3393
+ -0.1608 -0.0349 0.0222 0.1244
+ -0.1027 0.2939 -0.1091 -0.1832
+ 0.2593 -0.1916 -0.2862 -0.1609
+ 0.0302 0.2348 0.0136 0.1216
+ -0.2453 -0.0165 -0.0856 0.0221
+ 0.3015 0.2159 0.0173 0.3393
+ -0.1608 -0.0349 0.0222 0.1244
+ -0.1027 0.2939 -0.1091 -0.1832
+ 0.2593 -0.1916 -0.2862 -0.1609
+ -0.2453 -0.0165 -0.0856 0.0221
+ -0.2493 -0.2867 -0.1811 0.1404
+ 0.3015 0.2159 0.0173 0.3393
+ -0.1027 0.2939 -0.1091 -0.1832
+ 0.2593 -0.1916 -0.2862 -0.1609
+ 0.0302 0.2348 0.0136 0.1216
+ -0.2453 -0.0165 -0.0856 0.0221
+ -0.2453 -0.0165 -0.0856 0.0221
+ 0.3015 0.2159 0.0173 0.3393
+ 0.2593 -0.1916 -0.2862 -0.1609
+ 0.0302 0.2348 0.0136 0.1216
+ 0.2593 -0.1916 -0.2862 -0.1609
diff -r 4906f2302c85 -r cc8a30a0669f test-data/rgtestouts/rgEigPCA/rgEigPCAtest1_pca.xls.evec
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/rgtestouts/rgEigPCA/rgEigPCAtest1_pca.xls.evec Fri Mar 26 14:42:15 2010 -0400
@@ -0,0 +1,40 @@
+ #eigvals: 11.482 7.740 7.255 4.271
+ 101:1 0.1276 0.0060 0.1550 -0.3329 Case
+ 101:2 0.1276 0.0060 0.1550 -0.3329 Control
+ 101:3 0.0272 -0.1794 0.3241 -0.0243 Control
+ 105:1 0.1452 0.2666 -0.0845 -0.3446 Case
+ 105:2 0.0887 0.0765 0.0527 0.0326 Control
+ 105:3 -0.0026 -0.0367 -0.1333 -0.2045 Control
+ 112:1 -0.2453 -0.0165 -0.0856 0.0221 Case
+ 112:2 -0.2412 0.2537 0.0100 -0.0961 Control
+ 112:3 0.0358 -0.1766 -0.1010 0.1423 Control
+ 117:1 0.2905 0.0811 -0.0332 0.2245 Case
+ 117:2 0.1607 -0.1247 0.1495 0.0759 Control
+ 117:3 0.1675 0.0418 0.0449 0.2637 Control
+ 12:1 0.0272 -0.1794 0.3241 -0.0243 Case
+ 12:2 0.0272 -0.1794 0.3241 -0.0243 Control
+ 12:3 -0.0870 0.0154 0.2295 -0.1150 Control
+ 13:1 -0.0630 -0.2656 0.1607 -0.0055 Case
+ 13:2 -0.1886 -0.0251 -0.0558 -0.0102 Control
+ 13:3 0.0268 -0.0008 0.3404 -0.0369 Control
+ 1334:1 -0.0643 0.0418 0.0358 0.0343 Case
+ 1334:10 0.0927 -0.2210 -0.1938 -0.0651 Control
+ 1334:11 -0.2412 0.2537 0.0100 -0.0961 Control
+ 1334:12 0.0056 -0.2051 -0.2132 -0.1240 Control
+ 1334:13 0.0261 -0.0354 -0.0819 0.2399 Control
+ 1340:1 -0.1608 -0.0349 0.0222 0.1244 Case
+ 1340:10 -0.1608 -0.0349 0.0222 0.1244 Control
+ 1340:11 0.0261 -0.0354 -0.0819 0.2399 Control
+ 1340:12 0.0742 0.0819 -0.0833 -0.0528 Control
+ 1340:2 0.0302 0.2348 0.0136 0.1216 Case
+ 1340:9 -0.2493 -0.2867 -0.1811 0.1404 Control
+ 1341:1 0.1833 0.1206 -0.1248 -0.0491 Control
+ 1341:11 -0.1027 0.2939 -0.1091 -0.1832 Control
+ 1341:12 0.2312 -0.1808 -0.3129 -0.1522 Control
+ 1341:13 -0.2453 -0.0165 -0.0856 0.0221 Control
+ 1341:14 -0.2453 -0.0165 -0.0856 0.0221 Control
+ 1341:2 -0.2453 -0.0165 -0.0856 0.0221 Control
+ 1344:1 0.3015 0.2159 0.0173 0.3393 Control
+ 1344:12 0.0302 0.2348 0.0136 0.1216 Control
+ 1344:13 0.0302 0.2348 0.0136 0.1216 Control
+ 1345:12 0.2593 -0.1916 -0.2862 -0.1609 Control
diff -r 4906f2302c85 -r cc8a30a0669f test-data/rgtestouts/rgEigPCA/rgEigPCAtest1_pca.xls.par
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/rgtestouts/rgEigPCA/rgEigPCAtest1_pca.xls.par Fri Mar 26 14:42:15 2010 -0400
@@ -0,0 +1,11 @@
+genotypename: /opt/galaxy/test-data/tinywga.ped
+snpname: /opt/galaxy/test-data/tinywga.map
+indivname: /opt/galaxy/test-data/tinywga.ped
+evecoutname: rgEigPCAtest1_pca.xls.evec
+evaloutname: rgEigPCAtest1_eval.xls
+altnormstyle: NO
+numoutevec: 4
+numoutlieriter: 2
+numoutlierevec: 2
+outliersigmathresh: 2
+qtmode: 0
diff -r 4906f2302c85 -r cc8a30a0669f test-data/rgtestouts/rgGRR/Log_rgGRRtest1.txt
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/rgtestouts/rgGRR/Log_rgGRRtest1.txt Fri Mar 26 14:42:15 2010 -0400
@@ -0,0 +1,23 @@
+Reading genotypes for 40 subjects and 25 markers
+Calculating 780 pairs, updating every 78 pairs...
+Estimated time is 0.00 to 0.00 seconds ...
+0.003503 sec at pair 78 of 780 (10.00%): 556652.337848 marker*pairs/sec
+0.005636 sec at pair 156 of 780 (20.00%): 691982.977283 marker*pairs/sec
+0.007769 sec at pair 234 of 780 (30.00%): 752982.213220 marker*pairs/sec
+0.009869 sec at pair 312 of 780 (40.00%): 790345.731265 marker*pairs/sec
+0.011900 sec at pair 390 of 780 (50.00%): 819314.887905 marker*pairs/sec
+0.013981 sec at pair 468 of 780 (60.00%): 836843.791886 marker*pairs/sec
+0.015971 sec at pair 546 of 780 (70.00%): 854664.262256 marker*pairs/sec
+0.017976 sec at pair 624 of 780 (80.00%): 867821.563192 marker*pairs/sec
+0.020017 sec at pair 702 of 780 (90.00%): 876748.317016 marker*pairs/sec
+T1: 0.00267601013184 T2: 0.0181350708008 T3: 0.000470638275146 TOT: 0.0224170684814 0 pairs with no (or not enough) comparable genotypes (0.0%)
+Relstate dupe: mean(mean)=nan sdev(mean)=0.00, mean(sdev)=nan sdev(sdev)=0.00
+Relstate parentchild: mean(mean)=1.68 sdev(mean)=0.19, mean(sdev)=0.39 sdev(sdev)=0.19
+Relstate sibpairs: mean(mean)=nan sdev(mean)=0.00, mean(sdev)=nan sdev(sdev)=0.00
+Relstate halfsibs: mean(mean)=nan sdev(mean)=0.00, mean(sdev)=nan sdev(sdev)=0.00
+Relstate parents: mean(mean)=1.46 sdev(mean)=0.25, mean(sdev)=0.55 sdev(sdev)=0.17
+Relstate unrelated: mean(mean)=1.44 sdev(mean)=0.21, mean(sdev)=0.58 sdev(sdev)=0.15
+Relstate unknown: mean(mean)=nan sdev(mean)=0.00, mean(sdev)=nan sdev(sdev)=0.00
+780 pairs are available of 780
+Outliers: 0
+Plotting ...
\ No newline at end of file
diff -r 4906f2302c85 -r cc8a30a0669f test-data/rgtestouts/rgGRR/rgGRRtest1.html
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/rgtestouts/rgGRR/rgGRRtest1.html Fri Mar 26 14:42:15 2010 -0400
@@ -0,0 +1,65 @@
+<?xml version="1.0" encoding="utf-8" ?>
+<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN" "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
+<html xmlns="http://www.w3.org/1999/xhtml" xml:lang="en" lang="en">
+<head>
+<meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
+<meta name="generator" content="Galaxy rgGRR.py tool output - see http://g2.trac.bx.psu.edu/" />
+<title></title>
+<link rel="stylesheet" href="/static/style/base.css" type="text/css" />
+</head>
+<body>
+<div class="document">
+<h4><div>Output from rgGRR.py run at 25/03/2010 21:01:24<br>
+</h4>
+If you need to rerun this analysis, the command line was
+<pre>'/opt/galaxy/tools/rgenetics/rgGRR.py' '/opt/galaxy/test-data/tinywga' 'tinywga' '/opt/galaxy/test-data/rgtestouts/rgGRR/rgGRRtest1.html' '/opt/galaxy/test-data/rgtestouts/rgGRR' 'rgGRRtest1' '100' '6'</pre>
+</div> <embed src="rgGRRtest1.svg" type="image/svg+xml" width="1150" height="600" /><div><h4>Click the links below to save output files and plots</h4><br><ol>
+<li><a href="rgGRRtest1.svg" type="image/svg+xml" >rgGRR Plot (requires SVG)</a></li>
+<li><a href="rgGRRtest1_table.xls">Mean by SD alleles shared - 780 rows</a></li>
+<li><a href="rgGRRtest1.html">rgGRRtest1.html</a></li>
+<li><a href="Log_rgGRRtest1.txt">Log_rgGRRtest1.txt</a></li>
+</ol></div><div><h2>Outliers in tab delimited files linked above are also listed below</h2></div><div><hr><h3>Log from this job (also stored in Log_rgGRRtest1.txt)</h3><pre>Reading genotypes for 40 subjects and 25 markers
+
+Calculating 780 pairs, updating every 78 pairs...
+
+Estimated time is 0.00 to 0.00 seconds ...
+
+0.003503 sec at pair 78 of 780 (10.00%): 556652.337848 marker*pairs/sec
+
+0.005636 sec at pair 156 of 780 (20.00%): 691982.977283 marker*pairs/sec
+
+0.007769 sec at pair 234 of 780 (30.00%): 752982.213220 marker*pairs/sec
+
+0.009869 sec at pair 312 of 780 (40.00%): 790345.731265 marker*pairs/sec
+
+0.011900 sec at pair 390 of 780 (50.00%): 819314.887905 marker*pairs/sec
+
+0.013981 sec at pair 468 of 780 (60.00%): 836843.791886 marker*pairs/sec
+
+0.015971 sec at pair 546 of 780 (70.00%): 854664.262256 marker*pairs/sec
+
+0.017976 sec at pair 624 of 780 (80.00%): 867821.563192 marker*pairs/sec
+
+0.020017 sec at pair 702 of 780 (90.00%): 876748.317016 marker*pairs/sec
+
+T1: 0.00267601013184 T2: 0.0181350708008 T3: 0.000470638275146 TOT: 0.0224170684814 0 pairs with no (or not enough) comparable genotypes (0.0%)
+
+Relstate dupe: mean(mean)=nan sdev(mean)=0.00, mean(sdev)=nan sdev(sdev)=0.00
+
+Relstate parentchild: mean(mean)=1.68 sdev(mean)=0.19, mean(sdev)=0.39 sdev(sdev)=0.19
+
+Relstate sibpairs: mean(mean)=nan sdev(mean)=0.00, mean(sdev)=nan sdev(sdev)=0.00
+
+Relstate halfsibs: mean(mean)=nan sdev(mean)=0.00, mean(sdev)=nan sdev(sdev)=0.00
+
+Relstate parents: mean(mean)=1.46 sdev(mean)=0.25, mean(sdev)=0.55 sdev(sdev)=0.17
+
+Relstate unrelated: mean(mean)=1.44 sdev(mean)=0.21, mean(sdev)=0.58 sdev(sdev)=0.15
+
+Relstate unknown: mean(mean)=nan sdev(mean)=0.00, mean(sdev)=nan sdev(sdev)=0.00
+
+780 pairs are available of 780
+
+Outliers: 0
+
+Plotting ...</pre><hr></div></body></html>
diff -r 4906f2302c85 -r cc8a30a0669f test-data/rgtestouts/rgGRR/rgGRRtest1.svg
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/rgtestouts/rgGRR/rgGRRtest1.svg Fri Mar 26 14:42:15 2010 -0400
@@ -0,0 +1,770 @@
+<?xml version="1.0" standalone="no"?>
+<!DOCTYPE svg PUBLIC "-//W3C//DTD SVG 1.2//EN" "http://www.w3.org/Graphics/SVG/1.2/DTD/svg12.dtd">
+
+<svg width="1280" height="800"
+ xmlns="http://www.w3.org/2000/svg" version="1.2"
+ xmlns:xlink="http://www.w3.org/1999/xlink" viewBox="0 0 1280 800" onload="init()">
+
+ <script type="text/ecmascript" xlink:href="/static/scripts/tools/rgenetics/checkbox_and_radiobutton.js"/>
+ <script type="text/ecmascript" xlink:href="/static/scripts/tools/rgenetics/helper_functions.js"/>
+ <script type="text/ecmascript" xlink:href="/static/scripts/tools/rgenetics/timer.js"/>
+ <script type="text/ecmascript">
+ <![CDATA[
+ var checkBoxes = new Array();
+ var radioGroupBandwidth;
+ var colours = ['cyan','dodgerblue','mediumpurple','forestgreen','lightgreen','gold','gray'];
+ function init() {
+ var style = {"font-family":"Arial,Helvetica", "fill":"black", "font-size":12};
+ var dist = 12;
+ var yOffset = 4;
+
+ //A checkBox for each relationship type dupe,parentchild,sibpair,halfsib,parents,unrel,unkn
+ checkBoxes["dupe"] = new checkBox("dupe","checkboxes",20,40,"cbRect","cbCross",true,"Duplicate",style,dist,yOffset,undefined,hideShowLayer);
+ checkBoxes["parentchild"] = new checkBox("parentchild","checkboxes",20,60,"cbRect","cbCross",true,"Parent-Child",style,dist,yOffset,undefined,hideShowLayer);
+ checkBoxes["sibpairs"] = new checkBox("sibpairs","checkboxes",20,80,"cbRect","cbCross",true,"Sib-pairs",style,dist,yOffset,undefined,hideShowLayer);
+ checkBoxes["halfsibs"] = new checkBox("halfsibs","checkboxes",20,100,"cbRect","cbCross",true,"Half-sibs",style,dist,yOffset,undefined,hideShowLayer);
+ checkBoxes["parents"] = new checkBox("parents","checkboxes",20,120,"cbRect","cbCross",true,"Parents",style,dist,yOffset,undefined,hideShowLayer);
+ checkBoxes["unrelated"] = new checkBox("unrelated","checkboxes",20,140,"cbRect","cbCross",true,"Unrelated",style,dist,yOffset,undefined,hideShowLayer);
+ checkBoxes["unknown"] = new checkBox("unknown","checkboxes",20,160,"cbRect","cbCross",true,"Unknown",style,dist,yOffset,undefined,hideShowLayer);
+
+ }
+
+ function hideShowLayer(id, status, label) {
+ var vis = "hidden";
+ if (status) {
+ vis = "visible";
+ }
+ document.getElementById(id).setAttributeNS(null, 'visibility', vis);
+ }
+
+ function showBTT(evt, rel, mm, dm, md, dd, n, mg, dg, lg, hg) {
+ var x = parseInt(evt.pageX)-250;
+ var y = parseInt(evt.pageY)-110;
+ switch(rel) {
+ case 0:
+ fill = colours[rel];
+ relt = "dupe";
+ break;
+ case 1:
+ fill = colours[rel];
+ relt = "parentchild";
+ break;
+ case 2:
+ fill = colours[rel];
+ relt = "sibpairs";
+ break;
+ case 3:
+ fill = colours[rel];
+ relt = "halfsibs";
+ break;
+ case 4:
+ fill = colours[rel];
+ relt = "parents";
+ break;
+ case 5:
+ fill = colours[rel];
+ relt = "unrelated";
+ break;
+ case 6:
+ fill = colours[rel];
+ relt = "unknown";
+ break;
+ default:
+ fill = "cyan";
+ relt = "ERROR_CODE: "+rel;
+ }
+
+ document.getElementById("btRel").textContent = "GROUP: "+relt;
+ document.getElementById("btMean").textContent = "mean="+mm+" +/- "+dm;
+ document.getElementById("btSdev").textContent = "sdev="+dm+" +/- "+dd;
+ document.getElementById("btPair").textContent = "npairs="+n;
+ document.getElementById("btGeno").textContent = "ngenos="+mg+" +/- "+dg+" (min="+lg+", max="+hg+")";
+ document.getElementById("btHead").setAttribute('fill', fill);
+
+ var tt = document.getElementById("btTip");
+ tt.setAttribute("transform", "translate("+x+","+y+")");
+ tt.setAttribute('visibility', 'visible');
+ }
+
+ function showOTT(evt, rel, s1, s2, mean, sdev, ngeno, rmean, rsdev) {
+ var x = parseInt(evt.pageX)-150;
+ var y = parseInt(evt.pageY)-180;
+
+ switch(rel) {
+ case 0:
+ fill = colours[rel];
+ relt = "dupe";
+ break;
+ case 1:
+ fill = colours[rel];
+ relt = "parentchild";
+ break;
+ case 2:
+ fill = colours[rel];
+ relt = "sibpairs";
+ break;
+ case 3:
+ fill = colours[rel];
+ relt = "halfsibs";
+ break;
+ case 4:
+ fill = colours[rel];
+ relt = "parents";
+ break;
+ case 5:
+ fill = colours[rel];
+ relt = "unrelated";
+ break;
+ case 6:
+ fill = colours[rel];
+ relt = "unknown";
+ break;
+ default:
+ fill = "cyan";
+ relt = "ERROR_CODE: "+rel;
+ }
+
+ document.getElementById("otRel").textContent = "PAIR: "+relt;
+ document.getElementById("otS1").textContent = "s1="+s1;
+ document.getElementById("otS2").textContent = "s2="+s2;
+ document.getElementById("otMean").textContent = "mean="+mean;
+ document.getElementById("otSdev").textContent = "sdev="+sdev;
+ document.getElementById("otGeno").textContent = "ngenos="+ngeno;
+ document.getElementById("otRmean").textContent = "relmean="+rmean;
+ document.getElementById("otRsdev").textContent = "relsdev="+rsdev;
+ document.getElementById("otHead").setAttribute('fill', fill);
+
+ var tt = document.getElementById("otTip");
+ tt.setAttribute("transform", "translate("+x+","+y+")");
+ tt.setAttribute('visibility', 'visible');
+ }
+
+ function hideBTT(evt) {
+ document.getElementById("btTip").setAttributeNS(null, 'visibility', 'hidden');
+ }
+
+ function hideOTT(evt) {
+ document.getElementById("otTip").setAttributeNS(null, 'visibility', 'hidden');
+ }
+
+ ]]>
+ </script>
+ <defs>
+ <!-- symbols for check boxes -->
+ <symbol id="cbRect" overflow="visible">
+ <rect x="-5" y="-5" width="10" height="10" fill="white" stroke="dimgray" stroke-width="1" cursor="pointer"/>
+ </symbol>
+ <symbol id="cbCross" overflow="visible">
+ <g pointer-events="none" stroke="black" stroke-width="1">
+ <line x1="-3" y1="-3" x2="3" y2="3"/>
+ <line x1="3" y1="-3" x2="-3" y2="3"/>
+ </g>
+ </symbol>
+ </defs>
+
+<desc>Developer Works Dynamic Scatter Graph Scaling Example</desc>
+
+<!-- Now Draw the main X and Y axis -->
+<g style="stroke-width:1.0; stroke:black; shape-rendering:crispEdges">
+ <!-- X Axis top and bottom -->
+ <path d="M 100 100 L 1250 100 Z"/>
+ <path d="M 100 700 L 1250 700 Z"/>
+
+ <!-- Y Axis left and right -->
+ <path d="M 100 100 L 100 700 Z"/>
+ <path d="M 1250 100 L 1250 700 Z"/>
+</g>
+
+<g transform="translate(100,100)">
+
+ <!-- Grid Lines -->
+ <g style="fill:none; stroke:#dddddd; stroke-width:1; stroke-dasharray:2,2; text-anchor:end; shape-rendering:crispEdges">
+
+ <!-- Vertical grid lines -->
+ <line x1="125" y1="0" x2="115" y2="600" />
+ <line x1="230" y1="0" x2="230" y2="600" />
+ <line x1="345" y1="0" x2="345" y2="600" />
+ <line x1="460" y1="0" x2="460" y2="600" />
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+ <line x1="805" y1="0" x2="805" y2="600" />
+ <line x1="920" y1="0" x2="920" y2="600" />
+ <line x1="1035" y1="0" x2="1035" y2="600" />
+
+ <!-- Horizontal grid lines -->
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+ <line x1="0" y1="120" x2="1150" y2="120" />
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+ <line x1="0" y1="480" x2="1150" y2="480" />
+ <line x1="0" y1="540" x2="1150" y2="540" />
+ </g>
+
+ <!-- Legend -->
+ <g style="fill:black; stroke:none" font-size="12" font-family="Arial" transform="translate(25,25)">
+ <rect width="160" height="270" style="fill:none; stroke:black; shape-rendering:crispEdges" />
+ <text x="5" y="20" style="fill:black; stroke:none;" font-size="13" font-weight="bold">Given Pair Relationship</text>
+ <rect x="120" y="35" width="10" height="10" fill="cyan" stroke="cyan" stroke-width="1" cursor="pointer"/>
+ <rect x="120" y="55" width="10" height="10" fill="dodgerblue" stroke="dodgerblue" stroke-width="1" cursor="pointer"/>
+ <rect x="120" y="75" width="10" height="10" fill="mediumpurple" stroke="mediumpurple" stroke-width="1" cursor="pointer"/>
+ <rect x="120" y="95" width="10" height="10" fill="forestgreen" stroke="forestgreen" stroke-width="1" cursor="pointer"/>
+ <rect x="120" y="115" width="10" height="10" fill="lightgreen" stroke="lightgreen" stroke-width="1" cursor="pointer"/>
+ <rect x="120" y="135" width="10" height="10" fill="gold" stroke="gold" stroke-width="1" cursor="pointer"/>
+ <rect x="120" y="155" width="10" height="10" fill="gray" stroke="gray" stroke-width="1" cursor="pointer"/>
+ <text x="15" y="195" style="fill:black; stroke:none" font-size="12" font-family="Arial" >Zscore gt 15</text>
+ <circle cx="125" cy="192" r="6" style="stroke:red; fill:gold; fill-opacity:1.0; stroke-width:1;"/>
+ <text x="15" y="215" style="fill:black; stroke:none" font-size="12" font-family="Arial" >Zscore 4 to 15</text>
+ <circle cx="125" cy="212" r="3" style="stroke:gold; fill:gold; fill-opacity:1.0; stroke-width:1;"/>
+ <text x="15" y="235" style="fill:black; stroke:none" font-size="12" font-family="Arial" >Zscore lt 4</text>
+ <circle cx="125" cy="232" r="2" style="stroke:gold; fill:gold; fill-opacity:1.0; stroke-width:1;"/>
+ <g id="checkboxes">
+ </g>
+ </g>
+
+
+ <g style='fill:black; stroke:none' font-size="17" font-family="Arial">
+ <!-- X Axis Labels -->
+ <text x="480" y="660">Mean Alleles Shared</text>
+ <text x="0" y="630" >1.0</text>
+ <text x="277" y="630" >1.25</text>
+ <text x="564" y="630" >1.5</text>
+ <text x="842" y="630" >1.75</text>
+ <text x="1140" y="630" >2.0</text>
+ </g>
+
+ <g transform="rotate(270)" style="fill:black; stroke:none" font-size="17" font-family="Arial">
+ <!-- Y Axis Labels -->
+ <text x="-350" y="-40">SD Alleles Shared</text>
+ <text x="-20" y="-10" >1.0</text>
+ <text x="-165" y="-10" >0.75</text>
+ <text x="-310" y="-10" >0.5</text>
+ <text x="-455" y="-10" >0.25</text>
+ <text x="-600" y="-10" >0.0</text>
+ </g>
+
+<!-- Plot Title -->
+<g style="fill:black; stroke:none" font-size="18" font-family="Arial">
+ <text x="425" y="-30">rgGRRtest1 (40 subjects, 25 snp)</text>
+</g>
+
+<!-- One group/layer of points for each relationship type -->
+<g id="unrelated" style="stroke:gold; fill:gold; fill-opacity:1.0; stroke-width:1;" cursor="pointer">
+<circle cx="276" cy="202" r="2"
+ onmouseover="showBTT(evt, 5, 1.24, 0.00, 0.66, 0.00, 2, 2, 0, 2, 2)"
+ onmouseout="hideBTT(evt)" />
+<circle cx="479" cy="134" r="2"
+ onmouseover="showBTT(evt, 5, 1.42, 0.00, 0.78, 0.00, 2, 2, 0, 2, 2)"
+ onmouseout="hideBTT(evt)" />
+<circle cx="874" cy="338" r="2"
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+ onmouseout="hideBTT(evt)" />
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+ onmouseover="showBTT(evt, 5, 1.32, 0.00, 0.63, 0.00, 3, 2, 0, 2, 2)"
+ onmouseout="hideBTT(evt)" />
+<circle cx="275" cy="132" r="2"
+ onmouseover="showBTT(evt, 5, 1.24, 0.00, 0.78, 0.00, 2, 2, 0, 2, 2)"
+ onmouseout="hideBTT(evt)" />
+<circle cx="287" cy="235" r="2"
+ onmouseover="showBTT(evt, 5, 1.25, 0.00, 0.61, 0.00, 2, 2, 0, 2, 2)"
+ onmouseout="hideBTT(evt)" />
+<circle cx="644" cy="296" r="2"
+ onmouseover="showBTT(evt, 5, 1.56, 0.00, 0.51, 0.00, 2, 2, 0, 2, 2)"
+ onmouseout="hideBTT(evt)" />
+<circle cx="368" cy="185" r="2"
+ onmouseover="showBTT(evt, 5, 1.32, 0.00, 0.69, 0.00, 9, 2, 0, 2, 2)"
+ onmouseout="hideBTT(evt)" />
+<circle cx="828" cy="325" r="2"
+ onmouseover="showBTT(evt, 5, 1.72, 0.00, 0.46, 0.00, 4, 2, 0, 2, 2)"
+ onmouseout="hideBTT(evt)" />
+<circle cx="958" cy="371" r="2" onmouseover="showOTT(evt, 5, '1340,12,0,0', '1341,1,11,12', 1.83, 0.38, 24, 1.44, 0.58)" onmouseout="hideOTT(evt)" />
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+<circle cx="239" cy="205" r="2"
+ onmouseover="showBTT(evt, 5, 1.21, 0.00, 0.66, 0.00, 2, 2, 0, 2, 2)"
+ onmouseout="hideBTT(evt)" />
+<circle cx="450" cy="206" r="2"
+ onmouseover="showBTT(evt, 5, 1.39, 0.00, 0.66, 0.00, 3, 2, 0, 2, 2)"
+ onmouseout="hideBTT(evt)" />
+<circle cx="368" cy="223" r="2"
+ onmouseover="showBTT(evt, 5, 1.32, 0.00, 0.63, 0.00, 4, 2, 0, 2, 2)"
+ onmouseout="hideBTT(evt)" />
+<circle cx="643" cy="250" r="2"
+ onmouseover="showBTT(evt, 5, 1.56, 0.00, 0.58, 0.00, 5, 2, 0, 2, 2)"
+ onmouseout="hideBTT(evt)" />
+<circle cx="782" cy="314" r="2"
+ onmouseover="showBTT(evt, 5, 1.68, 0.00, 0.48, 0.00, 9, 2, 0, 2, 2)"
+ onmouseout="hideBTT(evt)" />
+<circle cx="229" cy="253" r="2"
+ onmouseover="showBTT(evt, 5, 1.20, 0.00, 0.58, 0.00, 3, 2, 0, 2, 2)"
+ onmouseout="hideBTT(evt)" />
+<circle cx="506" cy="250" r="2"
+ onmouseover="showBTT(evt, 5, 1.44, 0.00, 0.58, 0.00, 2, 2, 0, 2, 2)"
+ onmouseout="hideBTT(evt)" />
+<circle cx="950" cy="367" r="2"
+ onmouseover="showBTT(evt, 5, 1.83, 0.00, 0.39, 0.00, 2, 2, 0, 2, 2)"
+ onmouseout="hideBTT(evt)" />
+<circle cx="184" cy="89" r="2"
+ onmouseover="showBTT(evt, 5, 1.16, 0.00, 0.85, 0.00, 3, 2, 0, 2, 2)"
+ onmouseout="hideBTT(evt)" />
+<circle cx="736" cy="306" r="2"
+ onmouseover="showBTT(evt, 5, 1.64, 0.00, 0.49, 0.00, 7, 2, 0, 2, 2)"
+ onmouseout="hideBTT(evt)" />
+<circle cx="383" cy="217" r="2" onmouseover="showOTT(evt, 5, '101,1,3,2', '1344,1,12,13', 1.33, 0.64, 24, 1.44, 0.58)" onmouseout="hideOTT(evt)" />
+<circle cx="735" cy="306" r="2"
+ onmouseover="showBTT(evt, 5, 1.64, 0.00, 0.49, 0.00, 24, 2, 0, 2, 2)"
+ onmouseout="hideBTT(evt)" />
+<circle cx="552" cy="294" r="2"
+ onmouseover="showBTT(evt, 5, 1.48, 0.00, 0.51, 0.00, 25, 2, 0, 2, 2)"
+ onmouseout="hideBTT(evt)" />
+<circle cx="275" cy="72" r="2"
+ onmouseover="showBTT(evt, 5, 1.24, 0.00, 0.88, 0.00, 2, 2, 0, 2, 2)"
+ onmouseout="hideBTT(evt)" />
+<circle cx="505" cy="296" r="2" onmouseover="showOTT(evt, 5, '1334,12,0,0', '1340,12,0,0', 1.44, 0.51, 25, 1.44, 0.58)" onmouseout="hideOTT(evt)" />
+<circle cx="551" cy="294" r="2" onmouseover="showOTT(evt, 5, '117,1,3,2', '1341,12,0,0', 1.48, 0.51, 25, 1.44, 0.58)" onmouseout="hideOTT(evt)" />
+<circle cx="276" cy="132" r="2" onmouseover="showOTT(evt, 5, '101,3,0,0', '1334,2,12,13', 1.24, 0.78, 25, 1.44, 0.58)" onmouseout="hideOTT(evt)" />
+<circle cx="460" cy="175" r="2"
+ onmouseover="showBTT(evt, 5, 1.40, 0.00, 0.71, 0.00, 2, 2, 0, 2, 2)"
+ onmouseout="hideBTT(evt)" />
+<circle cx="143" cy="89" r="2"
+ onmouseover="showBTT(evt, 5, 1.13, 0.00, 0.85, 0.00, 4, 2, 0, 2, 2)"
+ onmouseout="hideBTT(evt)" />
+<circle cx="506" cy="296" r="2"
+ onmouseover="showBTT(evt, 5, 1.44, 0.00, 0.51, 0.00, 35, 2, 0, 2, 2)"
+ onmouseout="hideBTT(evt)" />
+<circle cx="-138" cy="-7" r="2" onmouseover="showOTT(evt, 5, '1340,9,0,0', '1344,1,12,13', 0.88, 1.01, 25, 1.44, 0.58)" onmouseout="hideOTT(evt)" />
+<circle cx="349" cy="219" r="2" onmouseover="showOTT(evt, 5, '117,3,0,0', '13,2,0,0', 1.30, 0.63, 23, 1.44, 0.58)" onmouseout="hideOTT(evt)" />
+<circle cx="0" cy="166" r="2" onmouseover="showOTT(evt, 5, '101,1,3,2', '1340,9,0,0', 1.00, 0.72, 24, 1.44, 0.58)" onmouseout="hideOTT(evt)" />
+<circle cx="735" cy="258" r="2"
+ onmouseover="showBTT(evt, 5, 1.64, 0.00, 0.57, 0.00, 4, 2, 0, 2, 2)"
1
0
15 Apr '10
details: http://www.bx.psu.edu/hg/galaxy/rev/4906f2302c85
changeset: 3569:4906f2302c85
user: Nate Coraor <nate(a)bx.psu.edu>
date: Fri Mar 26 14:14:40 2010 -0400
description:
require numpy before bx-python where numpy is dependant
diffstat:
lib/galaxy/visualization/tracks/data/array_tree.py | 4 +++-
1 files changed, 3 insertions(+), 1 deletions(-)
diffs (14 lines):
diff -r 5bbd895570d4 -r 4906f2302c85 lib/galaxy/visualization/tracks/data/array_tree.py
--- a/lib/galaxy/visualization/tracks/data/array_tree.py Fri Mar 26 12:37:20 2010 -0400
+++ b/lib/galaxy/visualization/tracks/data/array_tree.py Fri Mar 26 14:14:40 2010 -0400
@@ -2,7 +2,9 @@
Array tree data provider for the Galaxy track browser.
"""
-import pkg_resources; pkg_resources.require( "bx-python" )
+import pkg_resources
+pkg_resources.require( "numpy" )
+pkg_resources.require( "bx-python" )
from bx.arrays.array_tree import FileArrayTreeDict
from math import floor, ceil, log, pow
1
0
15 Apr '10
details: http://www.bx.psu.edu/hg/galaxy/rev/5bbd895570d4
changeset: 3568:5bbd895570d4
user: Kelly Vincent <kpvincent(a)bx.psu.edu>
date: Fri Mar 26 12:37:20 2010 -0400
description:
Missed the actual tool files for new join in last commit...
diffstat:
tools/new_operations/column_join.py | 175 +++++++++++++++++++++++++++++++++++
tools/new_operations/column_join.xml | 150 ++++++++++++++++++++++++++++++
2 files changed, 325 insertions(+), 0 deletions(-)
diffs (333 lines):
diff -r a9e25e05ae8d -r 5bbd895570d4 tools/new_operations/column_join.py
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/tools/new_operations/column_join.py Fri Mar 26 12:37:20 2010 -0400
@@ -0,0 +1,175 @@
+#!/usr/bin/env python
+
+"""
+This tool takes a tab-delimited text file as input and creates filters on columns based on certain properties. The tool will skip over invalid lines within the file, informing the user about the number of lines skipped.
+
+usage: %prog output input1 input2 column1[,column2[,column3[,...]]] hinge1[,hinge2[,hinge3[,...]]] [other_input1 [other_input2 [other_input3 ...]]]
+ output: the output pileup
+ input1: the pileup file to start with
+ input2: the second pileup file to join
+ hinge: the columns to be used for matching
+ columns: the columns that should appear in the output
+ other_inputs: the other input files to join
+
+"""
+
+import os, re, sys, tempfile
+
+def stop_err( msg ):
+ sys.stderr.write( msg )
+ sys.exit()
+
+def ref_compare( ref1, ref2 ):
+ """
+ Compares items like 'chr10' and 'chrM' or 'scaffold2' and scaffold10' so that
+ first part handled as text but last part as number
+ """
+ pat = re.compile( '(?P<text>\D*)(?P<number>\d+)?' )
+ r1 = pat.match( ref1 )
+ r2 = pat.match( ref2 )
+ if not r2:
+ return 1
+ elif not r1:
+ return -1
+ text1, num1 = r1.groupdict()[ 'text' ].strip(), r1.groupdict()[ 'number' ]
+ text2, num2 = r2.groupdict()[ 'text' ].strip(), r2.groupdict()[ 'number' ]
+ if text2 == '' and ( num2 == '' or num2 is None ):
+ return 1
+ elif text1 == '' and ( num1 == '' or num1 is None ):
+ return -1
+ if text1 > text2:
+ return 1
+ elif text1 == text2:
+ if not ( num1 is None or num2 is None ):
+ num1 = int( num1 )
+ num2 = int( num2 )
+ if num1 > num2:
+ return 1
+ elif num1 == num2:
+ return 0
+ elif num1 < num2:
+ return -1
+ elif text1 < text2:
+ return -1
+
+def ref_pos_sort( infile, outfile ):
+ """Given input file name, sorts logically (text vs. numeric) into provided output file name."""
+ ref_locs = {}
+ bad_lines = []
+ fin = open( infile, 'rb' )
+ line = fin.readline()
+ while line.strip():
+ if True:
+ try:
+ ref_seq, ref_loc = line.split( '\t' )[:2]
+ try:
+ ref_locs[ ref_seq ][ long( ref_loc ) ] = fin.tell() - len( line.strip() ) - 1
+ except KeyError:
+ ref_locs[ ref_seq ] = { long( ref_loc ): fin.tell() - len( line.strip() ) - 1 }
+ except ValueError:
+ bad_lines.append( line )
+ except ValueError:
+ bad_line.append( line )
+ line = fin.readline()
+ fin.close()
+ refs = ref_locs.keys()
+ refs.sort( ref_compare )
+ fin = open( infile, 'rb' )
+ fout = open( outfile, 'wb' )
+ for ref in refs:
+ locs = ref_locs[ ref ].keys()
+ locs.sort()
+ for loc in locs:
+ fin.seek( ref_locs[ ref ][ loc ] )
+ fout.write( fin.readline() )
+ fout.close()
+ fin.close()
+
+def min_chr_pos( chr_pos ):
+ """Given line and hinge, identifies the 'smallest' one, from left to right"""
+ if len( chr_pos ) == 0 and ''.join( chr_pos ):
+ return ''
+ min_loc = len( chr_pos )
+ min_ref_pos = []
+ loc = 0
+ for c_pos in chr_pos:
+ if c_pos.strip():
+ ref, pos = c_pos.split( '\t' )[:2]
+ pos = int( pos )
+ if not min_ref_pos:
+ min_ref_pos = [ ref, pos ]
+ min_loc = loc
+ else:
+ ref_comp = ref_compare( ref, min_ref_pos[0] )
+ if ref_comp < 0:
+ min_ref_pos = [ ref, pos ]
+ min_loc = loc
+ elif ref_comp == 0 and pos < min_ref_pos[1]:
+ min_ref_pos[1] = pos
+ min_loc = loc
+ loc += 1
+ return '%s\t%s' % tuple( min_ref_pos ), min_loc
+
+def __main__():
+ output = sys.argv[1]
+ input1 = sys.argv[2]
+ input2 = sys.argv[3]
+ hinge = int( sys.argv[4] )
+ cols = [ int( c ) for c in sys.argv[5].split( ',' ) ]
+ inputs = sys.argv[6:]
+ assert len( cols ) > 2, 'You need to select at least one column in addition to the first two'
+ # make sure all files are sorted in same way, ascending
+ tmp_input_files = []
+ input_files = [ input1, input2 ]
+ input_files.extend( inputs )
+ for in_file in input_files:
+ tmp_file = tempfile.NamedTemporaryFile()
+ tmp_file_name = tmp_file.name
+ tmp_file.close()
+ ref_pos_sort( in_file, tmp_file_name )
+ tmp_file = open( tmp_file_name, 'rb' )
+ tmp_input_files.append( tmp_file )
+ # cycle through files, getting smallest line of all files one at a time
+ # also have to keep track of vertical position of extra columns
+ fout = file( output, 'w' )
+ old_current_chr_pos = ''
+ first_line = True
+ current_lines = [ f.readline() for f in tmp_input_files ]
+ last_lines = ''.join( current_lines ).strip()
+ last_loc = -1
+ while last_lines:
+ # get the "minimum" hinge, which should come first, and the file location in list
+ current_chr_pos, loc = min_chr_pos( [ '\t'.join( line.split( '\t' )[ :hinge ] ) for line in current_lines ] )
+ # first output empty columns for vertical alignment (account for "missing" files)
+ if current_chr_pos != old_current_chr_pos:
+ last_loc = -1
+ if loc - last_loc > 1:
+ current_data = [ '' for col in range( ( loc - last_loc - 1 ) * len( cols[ hinge: ] ) ) ]
+ else:
+ current_data = []
+ # now output actual data
+ split_line = current_lines[ loc ].strip().split( '\t' )
+ if ''.join( split_line ):
+ for col in cols:
+ if col > hinge:
+ current_data.append( split_line[ col - 1 ] )
+ current_lines[ loc ] = tmp_input_files[ loc ].readline()
+ if current_chr_pos == old_current_chr_pos:
+ fout.write( '\t%s' % '\t'.join( current_data ) )
+ else:
+ if not first_line:
+ fout.write( '\n' )
+ fout.write( '%s\t%s' % ( current_chr_pos, '\t'.join( current_data ) ) )
+ first_line = False
+ old_current_chr_pos = current_chr_pos
+ if last_lines == ''.join( current_lines ).strip():
+ break
+ last_lines = ''.join( current_lines ).strip()
+ last_loc = loc
+ fout.write( '\n' )
+ for f in tmp_input_files:
+ os.unlink( f.name )
+ fout.close()
+# sys.stderr.write('******************\n'+file(fout.name, 'r').read()+'\n******************\n')
+
+if __name__ == "__main__" : __main__()
diff -r a9e25e05ae8d -r 5bbd895570d4 tools/new_operations/column_join.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/tools/new_operations/column_join.xml Fri Mar 26 12:37:20 2010 -0400
@@ -0,0 +1,150 @@
+<tool id="column_join" name="Column Join" version="1.0.0">
+ <description></description>
+ <command interpreter="python">
+ column_join.py
+ $output
+ $input1
+ $input2
+ $hinge
+ $columns
+ #for $f in $file_chooser:
+ ${f.input}
+ #end for
+ </command>
+ <inputs>
+ <param name="input1" type="data" format="tabular" label="Choose the first file for the join" />
+ <param name="columns" type="data_column" data_ref="input1" multiple="true" numerical="false" label="Include these column" help="Multi-select list - hold the appropriate key while clicking to select multiple columns" />
+ <param name="hinge" type="data_column" data_ref="input1" multiple="false" numerical="false" label="Use this column and columns to left the 'hinge' (matching data for each join)" help="All columns to left of selected column (plus selected column) will be used. Select 2 for pileup" />
+ <param name="input2" type="data" format="tabular" label="Choose the second file for the join" />
+ <repeat name="file_chooser" title="Additional Input">
+ <param name="input" label="Additional input file" type="data" format="tabular" />
+ </repeat>
+ </inputs>
+ <outputs>
+ <data name="output" format="pileup" />
+ </outputs>
+ <tests>
+ <test>
+ <param name="input1" value="column_join_in1.pileup" ftype="pileup" />
+ <param name="columns" value="1,2,3,4,5,7" />
+ <param name="hinge" value="1,2" />
+ <param name="input2" value="column_join_in2.pileup" ftype="pileup" />
+ <param name="input" value="column_join_in3.pileup" ftype="pileup" />
+ <output name="output" file="column_join_out1.pileup" ftype="pileup" />
+ </test>
+ <test>
+ <param name="input1" value="column_join_in4.pileup" ftype="pileup" />
+ <param name="columns" value="1,2,3,4" />
+ <param name="hinge" value="1,2" />
+ <param name="input2" value="column_join_in5.pileup" ftype="pileup" />
+ <param name="input" value="column_join_in6.pileup" ftype="pileup" />
+ <output name="output" file="column_join_out2.pileup" ftype="pileup" />
+ </test>
+ <test>
+ <param name="input1" value="column_join_in7.pileup" ftype="pileup" />
+ <param name="columns" value="1,2,3,4,5" />
+ <param name="hinge" value="1,2" />
+ <param name="input2" value="column_join_in8.pileup" ftype="pileup" />
+ <param name="input" value="column_join_in9.pileup" ftype="pileup" />
+ <output name="output" file="column_join_out3.pileup" ftype="pileup" />
+ </test>
+ </tests>
+ <help>
+**What it does**
+
+This tool allows you to join several files with the same column structure into one file, removing certain columns if necessary. The user needs to select a 'hinge', which is the number of left-most columns to match on. They also need to select the columns to include in the join, which should include the hinge columns, too.
+
+-----
+
+**Example**
+
+Given the following files::
+
+ FILE 1
+ chr2 1 T 6 .C..., I$$III
+ chr2 2 G 6 ..N.., III@II
+ chr2 3 C 7 ..C..., I$IIIII
+ chr2 4 G 7 .G...., I#IIIII
+ chr2 5 G 7 ...N.., IIII#BI
+ chr2 6 A 7 ..T..., I$IDIII
+ chr1 1 C 1 ^:. I
+ chr1 2 G 2 .^:. $I
+ chr1 3 A 2 .. I%
+ chr1 4 C 2 .. I$
+ chr1 5 T 3 ..^:. I#I
+ chr1 6 G 3 ..^:, I#I
+
+ FILE 2
+ chr1 3 T 1 ^:. I
+ chr1 4 G 2 .^:. $I
+ chr1 5 T 2 .. I%
+ chr1 6 C 3 ..^:. III
+ chr1 7 G 3 ..^:. I#I
+ chr1 8 T 4 ...^:, I#II
+ chr2 77 C 6 .G..., I$$III
+ chr2 78 G 6 ..N.., III@II
+ chr2 79 T 7 ..N..., I$IIIII
+ chr2 80 C 7 .G...., I#IIIII
+ chr2 81 G 7 ...A.., IIII#BI
+ chr2 82 A 8 ...G..., I$IDIIII
+ chr2 83 T 8 .A.....N IIIIIIII
+ chr2 84 A 9 ......T. I$IIIIIII
+
+ FILE 3
+ chr1 1 A 1 . I
+ chr1 2 T 2 G. I$
+ chr1 3 C 2 ., I@
+ chr1 4 C 3 ..N III
+ chr1 42 C 5 ...N^:. III@I
+ chr1 43 C 5 .N..^:. IIIII
+ chr1 44 T 5 .A.., IA@II
+ chr1 45 A 6 .N...^:. IIIII$
+ chr1 46 G 6 .GN..^:. I@IIII
+ chr1 47 A 7 ....^:.., IIIII$I
+ chr2 73 T 5 .N.., II$II
+ chr2 74 A 5 ...., IIIII
+ chr2 75 T 5 ...., IIIII
+ chr2 76 T 5 ...., IIIII
+ chr2 77 C 5 ...., IIIBI
+ chr2 78 T 5 ...., IDIII
+
+To join on columns 3 and 4 combining on columns 1 and 2, columns 1-4 should be selected for the 'Include these columns' option, and column 2 selected for the 'hinge'. With these settings, the following would be output::
+
+ chr1 1 C 1 A 1
+ chr1 2 G 2 T 2
+ chr1 3 A 2 T 1 C 2
+ chr1 4 C 2 G 2 C 3
+ chr1 5 T 3 T 2
+ chr1 6 G 3 C 3
+ chr1 7 G 3
+ chr1 8 T 4
+ chr1 42 C 5
+ chr1 43 C 5
+ chr1 44 T 5
+ chr1 45 A 6
+ chr1 46 G 6
+ chr1 47 A 7
+ chr2 1 T 6
+ chr2 2 G 6
+ chr2 3 C 7
+ chr2 4 G 7
+ chr2 5 G 7
+ chr2 6 A 7
+ chr2 73 T 5
+ chr2 74 A 5
+ chr2 75 T 5
+ chr2 76 T 5
+ chr2 77 C 6 C 5
+ chr2 78 G 6 T 5
+ chr2 79 T 7
+ chr2 80 C 7
+ chr2 81 G 7
+ chr2 82 A 8
+ chr2 83 T 8
+ chr2 84 A 9
+
+
+ </help>
+</tool>
+
+
1
0
details: http://www.bx.psu.edu/hg/galaxy/rev/a9e25e05ae8d
changeset: 3567:a9e25e05ae8d
user: fubar: ross Lazarus at gmail period com
date: Fri Mar 26 12:11:01 2010 -0400
description:
merge to 3566:3ac95cd927d7
diffstat:
datatypes_conf.xml.sample | 2 +
lib/galaxy/datatypes/registry.py | 3 +
lib/galaxy/datatypes/tabular.py | 93 ++
lib/galaxy/datatypes/test/10col.pileup | 30 +
lib/galaxy/datatypes/test/6col.pileup | 30 +
test-data/1.pileup | 1000 ++++++++++++++++++++++++++++++++
test-data/column_join_in1.pileup | 30 +
test-data/column_join_in2.pileup | 30 +
test-data/column_join_in3.pileup | 30 +
test-data/column_join_in4.pileup | 25 +
test-data/column_join_in5.pileup | 25 +
test-data/column_join_in6.pileup | 25 +
test-data/column_join_in7.pileup | 32 +
test-data/column_join_in8.pileup | 23 +
test-data/column_join_in9.pileup | 25 +
test-data/column_join_out1.pileup | 60 +
test-data/column_join_out2.pileup | 65 ++
test-data/column_join_out3.pileup | 70 ++
test/functional/test_get_data.py | 17 +
tool_conf.xml.sample | 1 +
20 files changed, 1616 insertions(+), 0 deletions(-)
diffs (1743 lines):
diff -r 5cc5e94345b8 -r a9e25e05ae8d datatypes_conf.xml.sample
--- a/datatypes_conf.xml.sample Fri Mar 26 12:02:22 2010 -0400
+++ b/datatypes_conf.xml.sample Fri Mar 26 12:11:01 2010 -0400
@@ -61,6 +61,7 @@
<converter file="maf_to_interval_converter.xml" target_datatype="interval"/>
</datatype>
<datatype extension="pdf" type="galaxy.datatypes.images:Image" mimetype="application/pdf"/>
+ <datatype extension="pileup" type="galaxy.datatypes.tabular:Pileup" display_in_upload="true" />
<datatype extension="png" type="galaxy.datatypes.images:Image" mimetype="image/png"/>
<datatype extension="qual" type="galaxy.datatypes.qualityscore:QualityScore" />
<datatype extension="qualsolexa" type="galaxy.datatypes.qualityscore:QualityScoreSolexa" display_in_upload="true"/>
@@ -239,6 +240,7 @@
<sniffer type="galaxy.datatypes.interval:CustomTrack"/>
<sniffer type="galaxy.datatypes.interval:Gff"/>
<sniffer type="galaxy.datatypes.interval:Gff3"/>
+ <sniffer type="galaxy.datatypes.tabular:Pileup"/>
<sniffer type="galaxy.datatypes.interval:Interval"/>
<sniffer type="galaxy.datatypes.tabular:Sam"/>
</sniffers>
diff -r 5cc5e94345b8 -r a9e25e05ae8d lib/galaxy/datatypes/registry.py
--- a/lib/galaxy/datatypes/registry.py Fri Mar 26 12:02:22 2010 -0400
+++ b/lib/galaxy/datatypes/registry.py Fri Mar 26 12:11:01 2010 -0400
@@ -155,6 +155,7 @@
'laj' : images.Laj(),
'lav' : sequence.Lav(),
'maf' : sequence.Maf(),
+ 'pileup' : tabular.Pileup(),
'qualsolid' : qualityscore.QualityScoreSOLiD(),
'qualsolexa' : qualityscore.QualityScoreSolexa(),
'qual454' : qualityscore.QualityScore454(),
@@ -185,6 +186,7 @@
'laj' : 'text/plain',
'lav' : 'text/plain',
'maf' : 'text/plain',
+ 'pileup' : 'text/plain',
'qualsolid' : 'text/plain',
'qualsolexa' : 'text/plain',
'qual454' : 'text/plain',
@@ -218,6 +220,7 @@
interval.CustomTrack(),
interval.Gff(),
interval.Gff3(),
+ tabular.Pileup(),
interval.Interval(),
tabular.Sam()
]
diff -r 5cc5e94345b8 -r a9e25e05ae8d lib/galaxy/datatypes/tabular.py
--- a/lib/galaxy/datatypes/tabular.py Fri Mar 26 12:02:22 2010 -0400
+++ b/lib/galaxy/datatypes/tabular.py Fri Mar 26 12:11:01 2010 -0400
@@ -327,3 +327,96 @@
except:
pass
return False
+
+class Pileup( Tabular ):
+ """Tab delimited data in pileup (6- or 10-column) format"""
+ file_ext = "pileup"
+
+ """Add metadata elements"""
+ MetadataElement( name="chromCol", default=1, desc="Chrom column", param=metadata.ColumnParameter )
+ MetadataElement( name="startCol", default=2, desc="Start column", param=metadata.ColumnParameter )
+ MetadataElement( name="baseCol", default=3, desc="Reference base column", param=metadata.ColumnParameter )
+
+ def init_meta( self, dataset, copy_from=None ):
+ Tabular.init_meta( self, dataset, copy_from=copy_from )
+
+ def set_peek( self, dataset, line_count=None, is_multi_byte=False ):
+ """Set the peek and blurb text"""
+ if not dataset.dataset.purged:
+ dataset.peek = data.get_file_peek( dataset.file_name, is_multi_byte=is_multi_byte )
+ if line_count is None:
+ # See if line_count is stored in the metadata
+ if dataset.metadata.data_lines:
+ dataset.blurb = "%s genomic coordinates" % util.commaify( str( dataset.metadata.data_lines ) )
+ else:
+ # Number of lines is not known ( this should not happen ), and auto-detect is
+ # needed to set metadata
+ dataset.blurb = "? genomic coordinates"
+ else:
+ dataset.blurb = "%s genomic coordinates" % util.commaify( str( line_count ) )
+ else:
+ dataset.peek = 'file does not exist'
+ dataset.blurb = 'file purged from disk'
+
+ def make_html_table( self, dataset, skipchars=[] ):
+ """Create HTML table, used for displaying peek"""
+ out = ['<table cellspacing="0" cellpadding="3">']
+ comments = []
+ try:
+ # Generate column header
+ out.append('<tr>')
+ for i in range( 1, dataset.metadata.columns+1 ):
+ if i == dataset.metadata.chromCol:
+ out.append( '<th>%s.Chrom</th>' % i )
+ elif i == dataset.metadata.startCol:
+ out.append( '<th>%s.Start</th>' % i )
+ elif i == dataset.metadata.baseCol:
+ out.append( '<th>%s.Base</th>' % i )
+ else:
+ out.append( '<th>%s</th>' % i )
+ out.append('</tr>')
+ out.append( self.make_html_peek_rows( dataset, skipchars=skipchars ) )
+ out.append( '</table>' )
+ out = "".join( out )
+ except Exception, exc:
+ out = "Can't create peek %s" % str( exc )
+ return out
+
+ def repair_methods( self, dataset ):
+ """Return options for removing errors along with a description"""
+ return [ ("lines", "Remove erroneous lines") ]
+
+ def sniff( self, filename ):
+ """
+ Checks for 'pileup-ness'
+
+ There are two main types of pileup: 6-column and 10-column. For both,
+ the first three and last two columns are the same. We only check the
+ first three to allow for some personalization of the format.
+
+ >>> fname = get_test_fname( 'interval.interval' )
+ >>> Pileup().sniff( fname )
+ False
+ >>> fname = get_test_fname( '6col.pileup' )
+ >>> Pileup().sniff( fname )
+ True
+ >>> fname = get_test_fname( '10col.pileup' )
+ >>> Pileup().sniff( fname )
+ True
+ """
+ headers = get_headers( filename, '\t' )
+ try:
+ for hdr in headers:
+ if hdr and not hdr[0].startswith( '#' ):
+ if len( hdr ) < 3:
+ return False
+ try:
+ # chrom start in column 1 (with 0-based columns)
+ # and reference base is in column 2
+ check = int( hdr[1] )
+ assert hdr[2] in [ 'A', 'C', 'G', 'T', 'N', 'a', 'c', 'g', 't', 'n' ]
+ except:
+ return False
+ return True
+ except:
+ return False
diff -r 5cc5e94345b8 -r a9e25e05ae8d lib/galaxy/datatypes/test/10col.pileup
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/lib/galaxy/datatypes/test/10col.pileup Fri Mar 26 12:11:01 2010 -0400
@@ -0,0 +1,30 @@
+chrM 1 G G 25 0 25 1 ^:. I
+chrM 2 T T 25 0 25 1 . I
+chrM 3 T T 25 0 25 1 . I
+chrM 4 A A 36 0 25 3 .^:.^:. II+
+chrM 5 A A 36 0 25 3 ... III
+chrM 6 T T 36 0 25 3 ... III
+chrM 7 G G 42 0 25 5 ...^:.^:. IIIII
+chrM 8 T T 45 0 25 6 .....^:. IIIIII
+chrM 9 A A 51 0 25 8 ......^:.^:. IIIIIIII
+chrM 10 G G 54 0 25 9 ........^:. IIIIIIIII
+chrM 11 C C 57 0 25 10 .........^:. IIIIIIIIII
+chrM 12 T T 60 0 25 11 ..........^:. IIIIIIIIIII
+chrM 13 T T 78 0 25 17 ...........^:.^:.^:.^:.^:.^:. IIIIIIIIIIIIIIIII
+chrM 14 A A 56 0 25 18 .......G.........^:. BIIIIIII+IIIIIIIII
+chrM 15 A A 87 0 25 20 ..................^:.^:. DIIIIIII(IIIIIIIIIII
+chrM 16 T T 87 0 25 20 .................... IIIIIIIIIIIIIIIIIIII
+chrM 17 A A 87 0 25 20 .................... 9IIIIIIIIIIIIIIIIIII
+chrM 18 A A 87 0 25 20 .................... @IIIIIIIIIIIIIIIIIII
+chrM 19 T T 55 0 25 20 ..................GG IIIIIIIIIIIIIIIIII'A
+chrM 20 A A 54 0 25 20 ..................C. IIIIIIIIIIIIIII2II#$
+chrM 21 T T 87 0 25 20 .................... IIIIIIIIIIIIIIIIIIII
+chrM 22 A A 87 0 25 20 .................... IIIIIIIIIIIIIIAIIIII
+chrM 23 A A 87 0 25 20 .................... 9IIIIIIIIII0IIIIIIII
+chrM 24 A A 87 0 25 20 ........N........... IIIIIIII"IIIIICIIIII
+chrM 25 G G 57 0 25 21 ...A................^:. A@.$IIIIIIIFIIIIIIIII
+chrM 26 C C 57 0 25 21 .......A............. IIHIDII&IIIIIIIIIIIII
+chrM 27 A A 99 0 25 24 .....................^:.^:.^:. IE8IFIII9IIIIIIIIIIIIIII
+chrM 28 A A 99 0 25 24 ........................ 1FIIIIIIIIIIIIIIIIDEIIII
+chrM 29 G G 55 0 25 24 ..................NN.... ;IIIIII+HII=IIIIII""IIII
+chrM 30 G G 68 0 25 25 ...C....................^:. ;I?&IAI0IIIIIIIIIIIIIIIII
diff -r 5cc5e94345b8 -r a9e25e05ae8d lib/galaxy/datatypes/test/6col.pileup
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/lib/galaxy/datatypes/test/6col.pileup Fri Mar 26 12:11:01 2010 -0400
@@ -0,0 +1,30 @@
+chrM 42 C 1 ^:. I
+chrM 43 C 2 .^:. II
+chrM 44 T 2 .. II
+chrM 45 A 3 ..^:. III
+chrM 46 G 4 ...^:. IIII
+chrM 47 A 5 ....^:, IIIII
+chrM 48 T 5 ...., IIIII
+chrM 49 G 5 ...., IIIII
+chrM 50 A 5 ...., IIIII
+chrM 51 G 5 ...., IIIII
+chrM 52 T 5 ...., IIIII
+chrM 53 A 5 ...., IIIII
+chrM 54 T 5 ...., IIIII
+chrM 55 T 5 ...., IIIII
+chrM 56 C 5 ...., IIIII
+chrM 57 T 5 ...., IIIII
+chrM 58 T 5 ...., IIIII
+chrM 59 A 5 ...., IIIII
+chrM 60 C 5 ...., IIIII
+chrM 61 T 5 ...., IIIII
+chrM 62 C 5 ...., IIIII
+chrM 63 C 5 ...., IIIII
+chrM 64 A 5 ...., IIIII
+chrM 65 T 5 ...., IIIII
+chrM 66 A 5 ...., IIIII
+chrM 67 A 5 ...., IIIII
+chrM 68 A 5 ...., IIICI
+chrM 69 C 5 ...., IIIII
+chrM 70 A 5 ...., IIIII
+chrM 71 C 5 ...., IIIII
diff -r 5cc5e94345b8 -r a9e25e05ae8d test-data/1.pileup
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/1.pileup Fri Mar 26 12:11:01 2010 -0400
@@ -0,0 +1,1000 @@
+chrM 42 C 1 ^:. I
+chrM 43 C 2 .^:. II
+chrM 44 T 2 .. II
+chrM 45 A 3 ..^:. III
+chrM 46 G 4 ...^:. IIII
+chrM 47 A 5 ....^:, IIIII
+chrM 48 T 5 ...., IIIII
+chrM 49 G 5 ...., IIIII
+chrM 50 A 5 ...., IIIII
+chrM 51 G 5 ...., IIIII
+chrM 52 T 5 ...., IIIII
+chrM 53 A 5 ...., IIIII
+chrM 54 T 5 ...., IIIII
+chrM 55 T 5 ...., IIIII
+chrM 56 C 5 ...., IIIII
+chrM 57 T 5 ...., IIIII
+chrM 58 T 5 ...., IIIII
+chrM 59 A 5 ...., IIIII
+chrM 60 C 5 ...., IIIII
+chrM 61 T 5 ...., IIIII
+chrM 62 C 5 ...., IIIII
+chrM 63 C 5 ...., IIIII
+chrM 64 A 5 ...., IIIII
+chrM 65 T 5 ...., IIIII
+chrM 66 A 5 ...., IIIII
+chrM 67 A 5 ...., IIIII
+chrM 68 A 5 ...., IIICI
+chrM 69 C 5 ...., IIIII
+chrM 70 A 5 ...., IIIII
+chrM 71 C 5 ...., IIIII
+chrM 72 A 5 ...., IAIII
+chrM 73 T 5 ...., IIIII
+chrM 74 A 5 ...., IIIII
+chrM 75 G 5 ...., %IIII
+chrM 76 G 5 T..., *IIII
+chrM 77 C 5 .$..., GIIII
+chrM 78 T 4 .$.., IIII
+chrM 79 T 3 .., III
+chrM 80 G 3 .$., I1I
+chrM 81 G 2 .$, II
+chrM 82 T 1 ,$ I
+chrM 83 C 2 ^:.^:. II
+chrM 84 C 2 .. II
+chrM 85 T 2 .. II
+chrM 86 A 2 .. II
+chrM 87 G 2 .. II
+chrM 88 C 2 .. II
+chrM 89 C 2 .. II
+chrM 90 T 2 .. II
+chrM 91 T 2 .. II
+chrM 92 T 2 .. II
+chrM 93 T 2 .. II
+chrM 94 T 2 .. II
+chrM 95 A 2 .. II
+chrM 96 T 2 .. II
+chrM 97 T 2 .. II
+chrM 98 A 2 .. II
+chrM 99 G 2 .. II
+chrM 100 T 2 .. II
+chrM 101 T 2 .. II
+chrM 102 A 2 .. II
+chrM 103 T 2 .. II
+chrM 104 T 2 .. II
+chrM 105 A 2 .. IE
+chrM 106 A 2 .. II
+chrM 107 T 2 .. II
+chrM 108 A 2 .. II
+chrM 109 G 2 .. II
+chrM 110 A 2 .. II
+chrM 111 A 2 .. I2
+chrM 112 T 2 .. II
+chrM 113 T 2 .. II
+chrM 114 A 2 .. H7
+chrM 115 C 2 .. II
+chrM 116 A 2 .. II
+chrM 117 C 2 .. II
+chrM 118 A 2 .$.$ F8
+chrM 156 T 1 ^:, &
+chrM 157 C 1 , I
+chrM 158 A 2 g^:g I>
+chrM 159 C 2 ,, /F
+chrM 160 G 2 ,, II
+chrM 161 T 2 ,, I>
+chrM 162 C 2 ,, .-
+chrM 163 T 2 ,, I8
+chrM 164 C 2 ,, 4F
+chrM 165 T 2 ,, II
+chrM 166 A 2 ,, II
+chrM 167 C 2 ,, ;6
+chrM 168 G 2 ,, II
+chrM 169 A 2 ,, II
+chrM 170 T 2 ,, II
+chrM 171 T 2 ,, IB
+chrM 172 A 2 ,, II
+chrM 173 A 2 ,, II
+chrM 174 A 2 ,, II
+chrM 175 A 2 ,, II
+chrM 176 G 2 ,, II
+chrM 177 G 2 ,, II
+chrM 178 A 2 ,, II
+chrM 179 G 2 ,, II
+chrM 180 C 2 ,, II
+chrM 181 A 3 ,,^:, III
+chrM 182 G 3 ,,, III
+chrM 183 G 3 ,,, III
+chrM 184 T 3 ,,, III
+chrM 185 A 3 ,,, III
+chrM 186 T 3 ,,, III
+chrM 187 C 3 ,,, III
+chrM 188 A 3 ,,, III
+chrM 189 A 3 ,,, III
+chrM 190 G 3 ,,, III
+chrM 191 C 3 ,$,, III
+chrM 192 A 2 ,, II
+chrM 193 C 2 ,$, II
+chrM 194 A 1 , I
+chrM 195 C 1 , I
+chrM 196 T 1 , F
+chrM 197 A 1 , I
+chrM 198 G 1 , I
+chrM 199 A 1 , I
+chrM 200 A 1 , I
+chrM 201 A 2 ,^:. I-
+chrM 202 G 2 ,. II
+chrM 203 T 2 ,. II
+chrM 204 A 2 ,. II
+chrM 205 G 2 ,. I6
+chrM 206 C 2 ,. II
+chrM 207 T 2 ,. I,
+chrM 208 C 2 ,. II
+chrM 209 A 2 ,. II
+chrM 210 T 2 ,. II
+chrM 211 A 2 ,. II
+chrM 212 A 2 ,. IE
+chrM 213 C 2 ,. IC
+chrM 214 A 2 ,. I;
+chrM 215 C 2 ,. II
+chrM 216 C 2 ,$. II
+chrM 217 T 1 . I
+chrM 218 T 1 . I
+chrM 219 G 1 T I
+chrM 220 C 1 . I
+chrM 221 T 1 . I
+chrM 222 C 1 . E
+chrM 223 A 1 . 4
+chrM 224 G 1 T 9
+chrM 225 C 1 . :
+chrM 226 C 1 . ?
+chrM 227 A 1 . .
+chrM 228 C 1 . C
+chrM 229 A 3 .^:,^:, %II
+chrM 230 C 3 .,, 8II
+chrM 231 C 3 .,, 9II
+chrM 232 C 3 .,, III
+chrM 233 C 3 .,, AI'
+chrM 234 C 3 .,, DI+
+chrM 235 A 3 .,, &I@
+chrM 236 C 3 .$,a +I$
+chrM 237 G 2 ,, II
+chrM 238 G 2 ,, II
+chrM 239 G 2 ,, II
+chrM 240 A 2 ,, II
+chrM 241 C 2 ,, I+
+chrM 242 A 2 ,, II
+chrM 243 C 2 ,, II
+chrM 244 A 3 ,,^:, II;
+chrM 245 G 3 ,,, II*
+chrM 246 C 3 ,,n II"
+chrM 247 A 3 ,,, III
+chrM 248 G 4 ,,,^:. IIII
+chrM 249 T 4 ,,,. II)I
+chrM 250 G 4 ,,,. II2I
+chrM 251 A 4 ,,,. II(I
+chrM 252 T 4 ,,,. II*I
+chrM 253 A 4 ,,,. II7I
+chrM 254 A 4 ,,,. II1I
+chrM 255 A 4 ,,,. II?I
+chrM 256 A 4 ,,,. II9I
+chrM 257 A 4 ,,,. II?I
+chrM 258 T 4 ,,,. II$I
+chrM 259 T 5 ,,,.^:. II&II
+chrM 260 A 5 ,,,.. II,II
+chrM 261 A 5 ,,,.. II/II
+chrM 262 G 5 ,,,.. II5II
+chrM 263 C 5 ,,a.. II%II
+chrM 264 T 5 ,$,$,.. II%II
+chrM 265 A 3 ,.. )II
+chrM 266 T 3 ,.. +II
+chrM 267 G 4 ,..^:. *III
+chrM 268 A 4 ,... EIII
+chrM 269 A 4 ,... =III
+chrM 270 C 4 a... ;III
+chrM 271 G 4 ,... ;III
+chrM 272 A 4 ,... 8@II
+chrM 273 A 4 ,... 1III
+chrM 274 A 4 ,... ICII
+chrM 275 G 4 ,... IIII
+chrM 276 T 4 ,... IIII
+chrM 277 T 4 ,... IIII
+chrM 278 C 4 ,... IIII
+chrM 279 G 4 ,$... IIII
+chrM 280 A 3 ... III
+chrM 281 C 3 ... GII
+chrM 282 T 3 ... III
+chrM 283 A 3 .$.. IFI
+chrM 284 A 3 ..^:, IAI
+chrM 285 G 3 .., ;II
+chrM 286 T 4 ..,^:. IIII
+chrM 287 C 4 ..,. II4I
+chrM 288 A 4 ..,. @III
+chrM 289 T 4 ..,. IIII
+chrM 290 A 4 ..,. @:II
+chrM 291 T 4 ..,. IIAI
+chrM 292 T 4 ..,. IIII
+chrM 293 A 4 ..,. 8;II
+chrM 294 A 4 .$.,. I<II
+chrM 295 A 3 .,. 4II
+chrM 296 T 3 .,. III
+chrM 297 A 3 .,. BII
+chrM 298 A 3 .,. CII
+chrM 299 G 3 .,. III
+chrM 300 G 3 .,. ;II
+chrM 301 G 3 .,. III
+chrM 302 T 3 .$,. III
+chrM 303 T 2 ,. II
+chrM 304 G 2 ,. II
+chrM 305 G 2 ,. II
+chrM 306 T 2 ,. II
+chrM 307 A 2 ,. II
+chrM 308 A 2 ,. II
+chrM 309 A 2 ,. II
+chrM 310 T 2 ,. II
+chrM 311 T 2 ,. II
+chrM 312 T 3 ,.^:. III
+chrM 313 C 3 ,.. III
+chrM 314 G 3 ,.. III
+chrM 315 T 3 ,.. III
+chrM 316 G 3 ,.. III
+chrM 317 C 3 ,.. III
+chrM 318 C 3 ,.. III
+chrM 319 A 3 ,$.. III
+chrM 320 G 2 .. II
+chrM 321 C 2 .$. II
+chrM 322 C 1 . I
+chrM 323 A 1 . I
+chrM 324 C 1 . I
+chrM 325 C 1 . I
+chrM 326 G 1 . I
+chrM 327 C 1 . I
+chrM 328 G 1 . I
+chrM 329 G 1 . I
+chrM 330 T 1 . I
+chrM 331 C 1 . I
+chrM 332 A 1 . I
+chrM 333 T 1 . I
+chrM 334 A 1 . I
+chrM 335 C 1 . I
+chrM 336 G 1 . I
+chrM 337 A 1 . I
+chrM 338 T 1 . I
+chrM 339 T 1 . I
+chrM 340 A 1 . I
+chrM 341 A 1 . D
+chrM 342 C 1 . I
+chrM 343 C 1 . I
+chrM 344 C 1 . I
+chrM 345 A 1 . I
+chrM 346 A 1 . ;
+chrM 347 A 1 .$ 7
+chrM 360 C 1 ^:. I
+chrM 361 G 1 . I
+chrM 362 G 1 . I
+chrM 363 C 1 . I
+chrM 364 G 1 . I
+chrM 365 T 1 . I
+chrM 366 A 1 . I
+chrM 367 A 1 . I
+chrM 368 A 1 . I
+chrM 369 G 1 . I
+chrM 370 C 1 . I
+chrM 371 G 1 . I
+chrM 372 T 1 . I
+chrM 373 G 1 . I
+chrM 374 T 1 . I
+chrM 375 C 1 . I
+chrM 376 A 1 . I
+chrM 377 A 1 . I
+chrM 378 A 1 . I
+chrM 379 G 1 . I
+chrM 380 A 1 . I
+chrM 381 C 1 T I
+chrM 382 T 1 . I
+chrM 383 A 1 . I
+chrM 384 A 1 . I
+chrM 385 T 1 . I
+chrM 386 A 1 G I
+chrM 387 C 1 . I
+chrM 388 C 1 . I
+chrM 389 A 2 .^:. II
+chrM 390 A 3 ..^:. III
+chrM 391 A 3 ... >II
+chrM 392 A 3 ... III
+chrM 393 T 3 ... III
+chrM 394 A 3 ... III
+chrM 395 A 3 .$.. III
+chrM 396 A 2 .. II
+chrM 397 G 2 .. II
+chrM 398 T 2 .. EI
+chrM 399 T 2 .. II
+chrM 400 A 3 ..^:. III
+chrM 401 A 3 ... III
+chrM 402 A 3 ... III
+chrM 403 A 3 ... III
+chrM 404 C 3 ... III
+chrM 405 C 3 ... III
+chrM 406 C 3 ... EII
+chrM 407 A 3 ... III
+chrM 408 G 3 ... III
+chrM 409 T 3 ... 0II
+chrM 410 T 3 ... III
+chrM 411 A 4 ...^:, IIII
+chrM 412 A 4 ..., FIII
+chrM 413 G 4 ..., IIIH
+chrM 414 C 4 ...a III2
+chrM 415 C 4 TTTt III7
+chrM 416 G 5 ...,^:, II?7:
+chrM 417 T 5 ...,, ;IIE@
+chrM 418 A 5 ...,, IIIII
+chrM 419 A 5 ...,, IIIII
+chrM 420 A 5 ...,, FIIII
+chrM 421 A 5 ...,, IIIII
+chrM 422 A 5 ...,, >IIII
+chrM 423 G 6 ...,,^:, HII/I,
+chrM 424 C 6 .$..a,, ;II-I:
+chrM 425 T 5 .$.,,, IIIIF
+chrM 426 A 5 .,,,^:, III@I
+chrM 427 C 5 .,,,, III$I
+chrM 428 A 5 .,,,, IIIII
+chrM 429 A 5 .,,,, IIII.
+chrM 430 C 5 .,,,a I%I5'
+chrM 431 C 5 .,,,, I(I5<
+chrM 432 A 5 .,,,, IIIII
+chrM 433 A 5 .,,,, 0IIII
+chrM 434 A 5 .,,,, =IIII
+chrM 435 G 5 .$,,,, EIIII
+chrM 436 T 4 ,,,, III5
+chrM 437 A 4 ,,,, IIII
+chrM 438 A 4 ,,,, IIII
+chrM 439 A 4 ,,,, IIII
+chrM 440 A 4 ,,,, IIIF
+chrM 441 T 6 ,,,,^:.^:. III;II
+chrM 442 A 6 ,,,,.. IIIIII
+chrM 443 G 6 ,,,,.. IIIIII
+chrM 444 A 6 ,,,,.. IIIIII
+chrM 445 C 6 ,,,,.. IIIIII
+chrM 446 T 6 ,$,,,.. IIIIII
+chrM 447 A 5 ,,,.. IIIII
+chrM 448 C 5 ,,,.. IIIII
+chrM 449 G 6 ,,,..^:, IIIII6
+chrM 450 A 6 ,,,.., IIIIII
+chrM 451 A 6 ,$,,.., IIIIII
+chrM 452 A 5 ,,.., IIIII
+chrM 453 G 5 ,,.., IIIII
+chrM 454 T 6 ,,..,^:, IIIIII
+chrM 455 G 6 ,,..,, IIIIII
+chrM 456 A 6 ,,..,, IIIIII
+chrM 457 C 6 ,,..,, IIIII=
+chrM 458 T 6 ,$,..,, IIIIII
+chrM 459 T 5 ,..,, IIIII
+chrM 460 T 5 ,..,, IIIII
+chrM 461 A 5 ,$..,, IIIII
+chrM 462 A 4 ..,, IIII
+chrM 463 T 4 ..,, IIIC
+chrM 464 A 4 ..,, IIII
+chrM 465 C 4 ..,, IIII
+chrM 466 C 4 ..,, IIII
+chrM 467 T 4 ..,, II>?
+chrM 468 C 4 ..,, IIII
+chrM 469 T 4 ..,, IIIG
+chrM 470 G 4 ..,, %III
+chrM 471 A 4 ..,, 4;II
+chrM 472 C 4 ..,, II3I
+chrM 473 T 4 ..,, IIII
+chrM 474 A 4 ..,, ;III
+chrM 475 C 4 ..,, IIII
+chrM 476 A 4 .$.$,, 32II
+chrM 477 C 2 ,, II
+chrM 478 G 2 ,, II
+chrM 479 A 2 ,, II
+chrM 480 T 3 ,,^:. III
+chrM 481 A 3 ,,. III
+chrM 482 G 3 ,,. III
+chrM 483 C 4 ,,.^:, IIIE
+chrM 484 T 4 ,$,., III9
+chrM 485 A 3 ,., III
+chrM 486 A 3 ,., III
+chrM 487 G 3 ,., III
+chrM 488 A 3 ,., III
+chrM 489 C 3 ,$., III
+chrM 490 C 2 ., II
+chrM 491 C 2 ., II
+chrM 492 A 2 ., II
+chrM 493 A 2 ., II
+chrM 494 A 2 ., II
+chrM 495 C 2 ., II
+chrM 496 T 2 ., I2
+chrM 497 G 2 ., II
+chrM 498 G 2 ., II
+chrM 499 G 2 ., II
+chrM 500 A 2 ., II
+chrM 501 T 2 ., II
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diff -r 5cc5e94345b8 -r a9e25e05ae8d test-data/column_join_in1.pileup
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/column_join_in1.pileup Fri Mar 26 12:11:01 2010 -0400
@@ -0,0 +1,30 @@
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+chrM 26 C G 58 0 25 22 ...N....A............. IIHIDII&IIIIII@IIIIII
+chrM 27 T A 99 0 25 23 ....................^:.^:.^:. IE8IFIII9IIIIIIIIIIIIII
+chrM 28 A C 99 0 25 24 ..G..................... 1FIIIIIIIIIIIIIIIIDEIIII
+chrM 29 G C 58 0 25 25 ........C.........NN.... ;IIIIII+HII=III$III""IIII
+chrM 30 T T 65 0 25 25 ...C....................^:. ;I?&IAI0IIIIIIIIIIIIIIIII
diff -r 5cc5e94345b8 -r a9e25e05ae8d test-data/column_join_in2.pileup
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/column_join_in2.pileup Fri Mar 26 12:11:01 2010 -0400
@@ -0,0 +1,30 @@
+chrM 1 T G 25 0 25 1 ^:. I
+chrM 2 C A 25 0 25 1 . I
+chrM 3 C A 25 0 25 2 .. I+
+chrM 4 G A 36 0 25 3 .^:.^:. II+
+chrM 5 A T 36 0 25 3 ... IDI
+chrM 6 A G 36 0 25 4 ..T. IIBI
+chrM 7 C G 42 0 25 5 ...^:.^:. ID@II
+chrM 8 T T 45 0 25 6 .....^:. III$BI
+chrM 9 C A 51 0 25 8 ......^:.^:. $#III+III
+chrM 10 G G 54 0 25 9 ........^:. III$III#I
+chrM 11 T C 57 0 25 10 .........^:. IIIDBIIIII
+chrM 12 A T 60 0 25 11 ..........^:. IIIIIIIII$I
+chrM 13 A T 78 0 25 18 ..A.........^:.^:.^:.^:.^:.^:. III#$IIIIII+IIDIIB
+chrM 14 G A 56 0 25 19 ........T.........^:. BIIIIIII+IIII$IBIII
+chrM 15 G A 87 0 25 20 ..................^:.^:. DIIIIIII(IIIIIIIIIII
+chr1 1 T T 87 0 25 20 .............T...... IIIIIIIIIIII$DIIIIII
+chr1 2 A T 87 0 25 20 ......G............. 9IIIIIIIIIIIIICBIIII
+chr1 3 A G 87 0 25 20 ....A............... @IIIIIIIII#IIII#IIII
+chr1 4 A T 55 0 25 20 ..................GG IIIII@II$IIIIIIIII'A
+chr1 5 C A 54 0 25 20 .......A..........C. IIIIIIIIIDIIIII2II#$
+chr1 6 G T 87 0 25 20 .............A...... IIIIIIIBIIIIII#IIIII
+chr1 7 A C 87 0 25 20 ..........C......... IIIII+IIIIIIIIAIIIII
+chr1 8 G A 87 0 25 20 ....G.........T..... 9IIIIIIIIII0IIIIIIII
+chr1 9 A T 87 0 25 20 ........N........... IIII$III"IIIIICIIIII
+chr1 10 G A 57 0 25 21 ...A................^:. A@.$IIIIIIIFIIIIIIIII
+chr1 11 C A 57 0 25 22 ....G...A............. IIHIDII&IIIIII#III$II
+chr1 12 T A 99 0 25 24 .....................^:.^:.^:. IE8IFIII9IIIIIIIIIIIIIII
+chr1 13 A C 99 0 25 25 ...N..................... 1FIIIIIIIIIIIIIIIIDEII$II
+chr1 14 G C 55 0 25 25 ....G..............NN.... ;IIIBIII+HII=IIIIII""IIII
+chr1 15 T G 68 0 25 28 ...C.......N............^:. ;I?&IAI0IIIIIII@II#$II@II
diff -r 5cc5e94345b8 -r a9e25e05ae8d test-data/column_join_in3.pileup
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/column_join_in3.pileup Fri Mar 26 12:11:01 2010 -0400
@@ -0,0 +1,30 @@
+chr1 1 G G 25 0 25 1 ^:. I
+chr1 2 T T 25 0 25 1 . I
+chr1 3 T T 27 0 25 1 . I
+chr1 4 A A 36 0 25 2 .^:. I+
+chr1 5 A A 36 0 25 3 ... III
+chr1 6 T T 36 0 25 4 .N.. II#I
+chr1 7 G G 42 0 25 5 ...^:.^:. IIIII
+chr1 8 T T 45 0 25 6 .....^:. IIIIII
+chr1 9 A A 51 0 25 7 .....^:.^:. IBIIIII
+chr1 10 G G 54 0 25 9 ........^:. IIIIIIIII
+chr1 11 C C 57 0 25 10 .........^:. IIIIIIII"I
+chr1 12 T T 60 0 25 11 ..........^:. IIIIIIDIIII
+chr1 13 T T 78 0 25 17 ...........^:.^:.^:.^:.^:.^:. IIII"$IIIIIIIIIII
+chr1 14 A A 56 0 25 18 .......G.........^:. BIIIIIII+IIIIIIIII
+chr1 15 A A 87 0 25 20 ....N.............^:.^:. DIII$III(IIIIIIIIIII
+chr4 1 T T 90 0 25 20 ..........N......... IIIIIIIII$IIIIIIIIII
+chr4 2 A A 87 0 25 20 .......C............ 9IIIIIIIII"IIIIIIIII
+chr4 3 A A 34 0 25 20 ......G............. @IIIIIIIIIIII#IIIIII
+chr4 4 T T 55 0 25 21 ...........N.......GG IIIII@IIIIIIIIIIIII'A
+chr4 5 A A 54 0 25 21 ...N...............C. IIII"IIIIIIIIIII2II#$
+chr4 6 T T 87 0 25 21 ................N.... IIIIIIII$IIIIIIIIIIII
+chr4 7 A A 80 0 25 21 .....G............... III$IIIIIIIIIIIAIIIII
+chr4 8 A A 87 0 25 22 ..N................... 9IIIIIIIIII0IIIII"$III
+chr4 9 A A 87 0 25 22 .GG.......N........... IIII$IIIII"IIIIICIIIII
+chr4 10 G G 57 0 25 23 .....A................^:. A@.$IIIIIIIIIFIIIIIIIII
+chr4 11 C C 57 0 25 25 .......A.....GN.......... IIHIDII&III#IIIIIIIIIIIII
+chr4 12 A A 99 0 25 26 .......................^:.^:.^:. IE8IFIII9IIIIIII$IIIIIIIII
+chr4 13 A A 99 0 25 27 ........N.................. 1FIIIIII$IIIIIIIIIIIIDEIIII
+chr4 14 G G 55 0 25 28 ..N...................NN.... ;III$I#IIII+HII=IIIIII""IIII
+chr4 15 G G 68 0 25 30 ...C....N..G.................^:. ;I?&IAI0IIIIIII$#I$@IIIIIIIIII
diff -r 5cc5e94345b8 -r a9e25e05ae8d test-data/column_join_in4.pileup
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/column_join_in4.pileup Fri Mar 26 12:11:01 2010 -0400
@@ -0,0 +1,25 @@
+chr2 1 T 6 .C..., I$$III
+chr2 2 G 6 ..N.., III@II
+chr2 3 C 7 ..C..., I$IIIII
+chr2 4 G 7 .G...., I#IIIII
+chr2 5 G 7 ...N.., IIII#BI
+chr2 6 A 7 ..T..., I$IDIII
+chr2 7 T 8 ...C..., IIIBD$II
+chr2 8 A 8 ..A...., IBI#IIII
+chr2 9 C 9 .GA..N.., I$IBIII#I
+chr2 10 T 9 ........, I$II#IIII
+chr2 11 C 10 .>>..T..., IIII@I$I$I
+chr2 12 G 10 .N..G...., III$IIIIII
+chr2 13 A 11 ....A..T.., IIIIII#I@II
+chr1 1 C 1 ^:. I
+chr1 2 G 2 .^:. $I
+chr1 3 A 2 .. I%
+chr1 4 C 2 .. I$
+chr1 5 T 3 ..^:. I#I
+chr1 6 G 3 ..^:, I#I
+chr1 7 C 4 .N., IIII
+chr1 8 A 4 ..., I$II
+chr1 9 T 5 ..C., I#IDI
+chr1 10 G 5 N..., IBII@
+chr1 11 A 5 .C.., I$II#
+chr1 12 C 5 ..N., I$III
diff -r 5cc5e94345b8 -r a9e25e05ae8d test-data/column_join_in5.pileup
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/column_join_in5.pileup Fri Mar 26 12:11:01 2010 -0400
@@ -0,0 +1,25 @@
+chr1 42 T 1 ^:. I
+chr1 43 G 2 .^:. $I
+chr1 44 T 2 .. I%
+chr1 45 C 3 ..^:. III
+chr1 46 G 3 ..^:. I#I
+chr1 47 T 4 ...^:, I#II
+chr1 48 A 4 .N., IIII
+chr1 49 C 5 ...., IIIII
+chr1 50 A 5 ..G., IIIDI
+chr1 51 A 5 A..., IBIII
+chr1 52 A 5 ...., IIII#
+chr1 53 G 5 ..N., I$III
+chr2 77 C 6 .G..., I$$III
+chr2 78 G 6 ..N.., III@II
+chr2 79 T 7 ..N..., I$IIIII
+chr2 80 C 7 .G...., I#IIIII
+chr2 81 G 7 ...A.., IIII#BI
+chr2 82 A 8 ...G..., I$IDIIII
+chr2 83 A 8 ...T..., IIIBD$II
+chr2 84 T 8 ..A...., IBI#IIII
+chr2 85 G 8 .GA...., IIBIII#I
+chr2 86 C 9 ........, I$II#IIII
+chr2 87 G 9 ....T..., IIIII$I$I
+chr2 88 G 10 .N..G...., III$IIIIII
+chr2 89 G 10 ...A..T.., IIIII#I@II
diff -r 5cc5e94345b8 -r a9e25e05ae8d test-data/column_join_in6.pileup
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/column_join_in6.pileup Fri Mar 26 12:11:01 2010 -0400
@@ -0,0 +1,25 @@
+chr1 42 C 1 ^:. I
+chr1 43 C 2 .^:. II
+chr1 44 T 2 .. II
+chr1 45 A 3 ..^:. III
+chr1 46 G 4 ...^:. IIII
+chr1 47 A 5 ....^:, IIIII
+chr1 48 T 5 ...N, I#III
+chr1 49 G 5 ...., IIIII
+chr1 50 A 5 .G.., IIIII
+chr1 51 G 5 ...., IIIII
+chr2 52 T 5 .N.., II$II
+chr2 53 A 5 ...., IIIII
+chr2 54 T 5 ...., IIIII
+chr2 55 T 5 ...., IIIII
+chr2 56 C 5 ...., IIIBI
+chr2 57 T 5 ...., IDIII
+chr2 58 T 6 .N..., IIIIII
+chr2 59 A 6 ....., IIII$I
+chr3 60 C 6 ...G., I#IIII
+chr3 61 T 6 ..N.., IIIIII
+chr3 62 C 6 ...A., IIIIII
+chr3 63 C 7 .N...., IIIIIII
+chr3 64 A 7 ...G.., IIIII$I
+chr3 65 T 7 ...AA., IIIII@@
+chr3 66 A 7 ....N., IIIIIII
diff -r 5cc5e94345b8 -r a9e25e05ae8d test-data/column_join_in7.pileup
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/column_join_in7.pileup Fri Mar 26 12:11:01 2010 -0400
@@ -0,0 +1,32 @@
+chr2 1 T 6 .C..., I$$III
+chr2 2 G 6 ..N.., III@II
+chr2 3 C 7 ..C..., I$IIIII
+chr2 4 G 7 .G...., I#IIIII
+chr2 5 G 7 ...N.., IIII#BI
+chr2 6 A 7 ..T..., I$IDIII
+chr2 7 T 8 ...C..., IIIBD$II
+chr2 8 A 8 ..A...., IBI#IIII
+chr2 9 C 9 .GA..N.., I$IBIII#I
+chr2 10 T 9 ........, I$II#IIII
+chr2 11 C 10 .>>..T..., IIII@I$I$I
+chr2 12 G 10 .N..G...., III$IIIIII
+chr2 13 A 11 ....A..T.., IIIIII#I@II
+chr2 14 G 11 ..N....... IICIBII@AII
+chr2 15 C 11 A.....NG.. IIIIIDIIIII
+chr2 16 T 11 ...C.....G I$IIIB@IIIC
+chr2 17 C 12 G......TN.. IIAII@IIII$I
+chr2 18 A 12 N......G..A IIIBIII$IIII
+chr2 19 A 13 .......NN... IIIIIIBIII$$@
+chr2 20 C 13 ..GT.......N IIIIABIIC$III
+chr1 1 C 1 ^:. I
+chr1 2 G 2 .^:. $I
+chr1 3 A 2 .. I%
+chr1 4 C 2 .. I$
+chr1 5 T 3 ..^:. I#I
+chr1 6 G 3 ..^:, I#I
+chr1 7 C 4 .N., IIII
+chr1 8 A 4 ..., I$II
+chr1 9 T 5 ..C., I#IDI
+chr1 10 G 5 N..., IBII@
+chr1 11 A 5 .C.., I$II#
+chr1 12 C 5 ..N., I$III
diff -r 5cc5e94345b8 -r a9e25e05ae8d test-data/column_join_in8.pileup
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/column_join_in8.pileup Fri Mar 26 12:11:01 2010 -0400
@@ -0,0 +1,23 @@
+chr1 42 T 1 ^:. I
+chr1 43 G 2 .^:. $I
+chr1 44 T 2 .. I%
+chr1 45 C 3 ..^:. III
+chr1 46 G 3 ..^:. I#I
+chr1 47 T 4 ...^:, I#II
+chr1 48 A 4 .N., IIII
+chr1 49 C 5 ...., IIIII
+chr1 50 A 5 ..G., IIIDI
+chr1 51 A 5 A..., IBIII
+chr1 52 A 5 ...., IIII#
+chr1 53 G 5 ..N., I$III
+chr2 77 C 6 .G..., I$$III
+chr2 78 G 6 ..N.., III@II
+chr2 79 T 7 ..N..., I$IIIII
+chr2 80 C 7 .G...., I#IIIII
+chr2 81 G 7 ...A.., IIII#BI
+chr2 82 A 8 ...G..., I$IDIIII
+chr2 83 A 8 ...T..., IIIBD$II
+chr2 84 T 8 ..A...., IBI#IIII
+chr2 85 G 8 .GA...., IIBIII#I
+chr2 86 C 9 ........, I$II#IIII
+chr2 87 G 9 ....T..., IIIII$I$I
diff -r 5cc5e94345b8 -r a9e25e05ae8d test-data/column_join_in9.pileup
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/column_join_in9.pileup Fri Mar 26 12:11:01 2010 -0400
@@ -0,0 +1,25 @@
+chr1 43 C 2 .^:. II
+chr3 65 T 7 ...AA., IIIII@@
+chr1 44 T 2 .. II
+chr2 54 T 5 ...., IIIII
+chr1 45 A 3 ..^:. III
+chr1 47 A 5 ....^:, IIIII
+chr1 50 A 5 .G.., IIIII
+chr1 51 G 5 ...., IIIII
+chr2 52 T 5 .N.., II$II
+chr2 53 A 5 ...., IIIII
+chr3 60 C 6 ...G., I#IIII
+chr3 61 T 6 ..N.., IIIIII
+chr1 49 G 5 ...., IIIII
+chr2 55 T 5 ...., IIIII
+chr2 56 C 5 ...., IIIBI
+chr2 58 T 6 .N..., IIIIII
+chr2 59 A 6 ....., IIII$I
+chr3 62 C 6 ...A., IIIIII
+chr1 42 C 1 ^:. I
+chr3 63 C 7 .N...., IIIIIII
+chr1 48 T 5 ...N, I#III
+chr1 46 G 4 ...^:. IIII
+chr3 64 A 7 ...G.., IIIII$I
+chr3 66 A 7 ....N., IIIIIII
+chr2 57 T 5 ...., IDIII
diff -r 5cc5e94345b8 -r a9e25e05ae8d test-data/column_join_out1.pileup
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/column_join_out1.pileup Fri Mar 26 12:11:01 2010 -0400
@@ -0,0 +1,60 @@
+chr1 1 T T 87 25 G G 25 25
+chr1 2 A T 87 25 T T 25 25
+chr1 3 A G 87 25 T T 27 25
+chr1 4 A T 55 25 A A 36 25
+chr1 5 C A 54 25 A A 36 25
+chr1 6 G T 87 25 T T 36 25
+chr1 7 A C 87 25 G G 42 25
+chr1 8 G A 87 25 T T 45 25
+chr1 9 A T 87 25 A A 51 25
+chr1 10 G A 57 25 G G 54 25
+chr1 11 C A 57 25 C C 57 25
+chr1 12 T A 99 25 T T 60 25
+chr1 13 A C 99 25 T T 78 25
+chr1 14 G C 55 25 A A 56 25
+chr1 15 T G 68 25 A A 87 25
+chr4 1 T T 90 25
+chr4 2 A A 87 25
+chr4 3 A A 34 25
+chr4 4 T T 55 25
+chr4 5 A A 54 25
+chr4 6 T T 87 25
+chr4 7 A A 80 25
+chr4 8 A A 87 25
+chr4 9 A A 87 25
+chr4 10 G G 57 25
+chr4 11 C C 57 25
+chr4 12 A A 99 25
+chr4 13 A A 99 25
+chr4 14 G G 55 25
+chr4 15 G G 68 25
+chrM 1 A G 25 25 T G 25 25
+chrM 2 C T 25 25 C A 25 25
+chrM 3 T G 27 25 C A 25 25
+chrM 4 G C 36 25 G A 36 25
+chrM 5 T A 38 25 A T 36 25
+chrM 6 T A 39 25 A G 36 25
+chrM 7 G C 43 25 C G 42 25
+chrM 8 A C 46 25 T T 45 25
+chrM 9 T G 53 25 C A 51 25
+chrM 10 T G 56 25 G G 54 25
+chrM 11 C G 57 25 T C 57 25
+chrM 12 T C 61 25 A T 60 25
+chrM 13 T G 79 25 A T 78 25
+chrM 14 A C 58 25 G A 56 25
+chrM 15 G A 87 25 G A 87 25
+chrM 16 G C 88 25
+chrM 17 A C 88 25
+chrM 18 G A 89 25
+chrM 19 G T 58 25
+chrM 20 T C 55 25
+chrM 21 C T 87 25
+chrM 22 C A 87 25
+chrM 23 A G 87 25
+chrM 24 A T 89 25
+chrM 25 G A 57 25
+chrM 26 C G 58 25
+chrM 27 T A 99 25
+chrM 28 A C 99 25
+chrM 29 G C 58 25
+chrM 30 T T 65 25
diff -r 5cc5e94345b8 -r a9e25e05ae8d test-data/column_join_out2.pileup
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/column_join_out2.pileup Fri Mar 26 12:11:01 2010 -0400
@@ -0,0 +1,65 @@
+chr1 1 C 1
+chr1 2 G 2
+chr1 3 A 2
+chr1 4 C 2
+chr1 5 T 3
+chr1 6 G 3
+chr1 7 C 4
+chr1 8 A 4
+chr1 9 T 5
+chr1 10 G 5
+chr1 11 A 5
+chr1 12 C 5
+chr1 42 T 1 C 1
+chr1 43 G 2 C 2
+chr1 44 T 2 T 2
+chr1 45 C 3 A 3
+chr1 46 G 3 G 4
+chr1 47 T 4 A 5
+chr1 48 A 4 T 5
+chr1 49 C 5 G 5
+chr1 50 A 5 A 5
+chr1 51 A 5 G 5
+chr1 52 A 5
+chr1 53 G 5
+chr2 1 T 6
+chr2 2 G 6
+chr2 3 C 7
+chr2 4 G 7
+chr2 5 G 7
+chr2 6 A 7
+chr2 7 T 8
+chr2 8 A 8
+chr2 9 C 9
+chr2 10 T 9
+chr2 11 C 10
+chr2 12 G 10
+chr2 13 A 11
+chr2 52 T 5
+chr2 53 A 5
+chr2 54 T 5
+chr2 55 T 5
+chr2 56 C 5
+chr2 57 T 5
+chr2 58 T 6
+chr2 59 A 6
+chr2 77 C 6
+chr2 78 G 6
+chr2 79 T 7
+chr2 80 C 7
+chr2 81 G 7
+chr2 82 A 8
+chr2 83 A 8
+chr2 84 T 8
+chr2 85 G 8
+chr2 86 C 9
+chr2 87 G 9
+chr2 88 G 10
+chr2 89 G 10
+chr3 60 C 6
+chr3 61 T 6
+chr3 62 C 6
+chr3 63 C 7
+chr3 64 A 7
+chr3 65 T 7
+chr3 66 A 7
diff -r 5cc5e94345b8 -r a9e25e05ae8d test-data/column_join_out3.pileup
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/column_join_out3.pileup Fri Mar 26 12:11:01 2010 -0400
@@ -0,0 +1,70 @@
+chr1 1 C 1 ^:.
+chr1 2 G 2 .^:.
+chr1 3 A 2 ..
+chr1 4 C 2 ..
+chr1 5 T 3 ..^:.
+chr1 6 G 3 ..^:,
+chr1 7 C 4 .N.,
+chr1 8 A 4 ...,
+chr1 9 T 5 ..C.,
+chr1 10 G 5 N...,
+chr1 11 A 5 .C..,
+chr1 12 C 5 ..N.,
+chr1 42 T 1 ^:. C 1 ^:.
+chr1 43 G 2 .^:. C 2 .^:.
+chr1 44 T 2 .. T 2 ..
+chr1 45 C 3 ..^:. A 3 ..^:.
+chr1 46 G 3 ..^:. G 4 ...^:.
+chr1 47 T 4 ...^:, A 5 ....^:,
+chr1 48 A 4 .N., T 5 ...N,
+chr1 49 C 5 ...., G 5 ....,
+chr1 50 A 5 ..G., A 5 .G..,
+chr1 51 A 5 A..., G 5 ....,
+chr1 52 A 5 ....,
+chr1 53 G 5 ..N.,
+chr2 1 T 6 .C...,
+chr2 2 G 6 ..N..,
+chr2 3 C 7 ..C...,
+chr2 4 G 7 .G....,
+chr2 5 G 7 ...N..,
+chr2 6 A 7 ..T...,
+chr2 7 T 8 ...C...,
+chr2 8 A 8 ..A....,
+chr2 9 C 9 .GA..N..,
+chr2 10 T 9 ........,
+chr2 11 C 10 .>>..T...,
+chr2 12 G 10 .N..G....,
+chr2 13 A 11 ....A..T..,
+chr2 14 G 11 ..N.......
+chr2 15 C 11 A.....NG..
+chr2 16 T 11 ...C.....G
+chr2 17 C 12 G......TN..
+chr2 18 A 12 N......G..A
+chr2 19 A 13 .......NN...
+chr2 20 C 13 ..GT.......N
+chr2 52 T 5 .N..,
+chr2 53 A 5 ....,
+chr2 54 T 5 ....,
+chr2 55 T 5 ....,
+chr2 56 C 5 ....,
+chr2 57 T 5 ....,
+chr2 58 T 6 .N...,
+chr2 59 A 6 .....,
+chr2 77 C 6 .G...,
+chr2 78 G 6 ..N..,
+chr2 79 T 7 ..N...,
+chr2 80 C 7 .G....,
+chr2 81 G 7 ...A..,
+chr2 82 A 8 ...G...,
+chr2 83 A 8 ...T...,
+chr2 84 T 8 ..A....,
+chr2 85 G 8 .GA....,
+chr2 86 C 9 ........,
+chr2 87 G 9 ....T...,
+chr3 60 C 6 ...G.,
+chr3 61 T 6 ..N..,
+chr3 62 C 6 ...A.,
+chr3 63 C 7 .N....,
+chr3 64 A 7 ...G..,
+chr3 65 T 7 ...AA.,
+chr3 66 A 7 ....N.,
diff -r 5cc5e94345b8 -r a9e25e05ae8d test/functional/test_get_data.py
--- a/test/functional/test_get_data.py Fri Mar 26 12:02:22 2010 -0400
+++ b/test/functional/test_get_data.py Fri Mar 26 12:11:01 2010 -0400
@@ -575,5 +575,22 @@
self.check_history_for_string( 'Pasted Entry' )
self.check_history_for_string( 'hello world' )
self.delete_history( id=self.security.encode_id( history.id ) )
+ def test_0165_upload_file( self ):
+ """Test uploading 1.pileup, NOT setting the file format"""
+ self.check_history_for_string( 'Your history is empty' )
+ history = sa_session.query( galaxy.model.History ) \
+ .filter( and_( galaxy.model.History.table.c.deleted==False,
+ galaxy.model.History.table.c.user_id==admin_user.id ) ) \
+ .order_by( desc( galaxy.model.History.table.c.create_time ) ) \
+ .first()
+ self.upload_file( '1.pileup' )
+ hda = sa_session.query( galaxy.model.HistoryDatasetAssociation ) \
+ .order_by( desc( galaxy.model.HistoryDatasetAssociation.table.c.create_time ) ) \
+ .first()
+ assert hda is not None, "Problem retrieving hda from database"
+ self.verify_dataset_correctness( '1.pileup', hid=str( hda.hid ) )
+ self.check_history_for_string( '1.pileup format: <span class="pileup">pileup</span>, database: \? Info: uploaded file' )
+ self.check_metadata_for_string( 'value="1.pileup" value="\?" Change data type selected value="pileup" selected="yes"' )
+ self.delete_history( id=self.security.encode_id( history.id ) )
def test_9999_clean_up( self ):
self.logout()
diff -r 5cc5e94345b8 -r a9e25e05ae8d tool_conf.xml.sample
--- a/tool_conf.xml.sample Fri Mar 26 12:02:22 2010 -0400
+++ b/tool_conf.xml.sample Fri Mar 26 12:11:01 2010 -0400
@@ -61,6 +61,7 @@
<tool file="filters/compare.xml"/>
<tool file="new_operations/subtract_query.xml"/>
<tool file="stats/grouping.xml" />
+ <tool file="new_operations/column_join.xml" />
</section>
<section name="Convert Formats" id="convert">
<tool file="filters/axt_to_concat_fasta.xml" />
1
0
15 Apr '10
details: http://www.bx.psu.edu/hg/galaxy/rev/5cc5e94345b8
changeset: 3566:5cc5e94345b8
user: fubar: ross Lazarus at gmail period com
date: Fri Mar 26 12:02:22 2010 -0400
description:
Add a tool_runner entry for hapmap - similar to the existing biomart one
Updated WGA/SNP entries in tool_conf.xml.sample
diffstat:
.hgignore | 4 +++
lib/galaxy/web/controllers/tool_runner.py | 6 +++++
tool_conf.xml.sample | 35 +++++++++++++++++++-----------
3 files changed, 32 insertions(+), 13 deletions(-)
diffs (93 lines):
diff -r 5f927f52191c -r 5cc5e94345b8 .hgignore
--- a/.hgignore Fri Mar 26 09:51:03 2010 -0400
+++ b/.hgignore Fri Mar 26 12:02:22 2010 -0400
@@ -1,5 +1,6 @@
syntax: glob
+.hg*
# Downloaded and locally built eggs
eggs
scripts/scramble/build
@@ -10,6 +11,8 @@
database/beaker_sessions
database/compiled_templates
database/files
+database/pbs
+database/tmp
database/*.sqlite
# Python bytecode
@@ -20,6 +23,7 @@
reports_wsgi.ini
datatypes_conf.xml
tool_conf.xml
+static/welcome.html.*
tool-data/*.loc
# Test output
diff -r 5f927f52191c -r 5cc5e94345b8 lib/galaxy/web/controllers/tool_runner.py
--- a/lib/galaxy/web/controllers/tool_runner.py Fri Mar 26 09:51:03 2010 -0400
+++ b/lib/galaxy/web/controllers/tool_runner.py Fri Mar 26 12:02:22 2010 -0400
@@ -25,6 +25,12 @@
"""Catches the tool id and redirects as needed"""
return self.index(trans, tool_id=tool_id, **kwd)
+ #test to get hapmap to work, ideally, we could pass tool_id to hapmap biomart and receive it back
+ @web.expose
+ def hapmapmart(self, trans, tool_id='hapmapmart', **kwd):
+ """Catches the tool id and redirects as needed"""
+ return self.index(trans, tool_id=tool_id, **kwd)
+
@web.expose
def default(self, trans, tool_id=None, **kwd):
"""Catches the tool id and redirects as needed"""
diff -r 5f927f52191c -r 5cc5e94345b8 tool_conf.xml.sample
--- a/tool_conf.xml.sample Fri Mar 26 09:51:03 2010 -0400
+++ b/tool_conf.xml.sample Fri Mar 26 12:02:22 2010 -0400
@@ -235,24 +235,33 @@
<tool file="genetrack/genetrack_indexer.xml" />
<tool file="genetrack/genetrack_peak_prediction.xml" />
</section>
- <section name="Rg Data" id="rgData1">
- <tool file="rgenetics/rgenetics_import.xml"/>
- <tool file="rgenetics/rgLpedPbed.xml"/>
+ <section name="SNP/WGA: Data; Filters" id="rgdat">
+ <label text="Data: Import and upload" id="rgimport" />
+ <tool file="data_source/upload.xml"/>
+ <tool file="data_source/access_libraries.xml" />
+ <tool file="data_source/hapmapmart.xml" />
+ <label text="Data: Filter and Clean" id="rgfilter" />
<tool file="rgenetics/rgClean.xml"/>
+ <tool file="rgenetics/rgPedSub.xml"/>
+ <tool file="rgenetics/rgLDIndep.xml"/>
+ <label text="Simulate" id="rgsim" />
+ <tool file="rgenetics/rgfakePhe.xml"/>
+ <tool file="rgenetics/rgfakePed.xml"/>
+ </section>
+ <section name="SNP/WGA: QC; LD; Plots" id="rgqcplot">
+ <label text="QC; Eigenstrat" id="rgvisual" />
<tool file="rgenetics/rgQC.xml"/>
+ <tool file="rgenetics/rgEigPCA.xml"/>
+ <label text="LD; Manhattan/QQ; GRR" id="rgld" />
+ <tool file="rgenetics/rgHaploView.xml"/>
+ <tool file="rgenetics/rgManQQ.xml"/>
+ <tool file="rgenetics/rgGRR.xml"/>
</section>
- <section name="Rg Simulate" id="rgSim1">
- <tool file="rgenetics/rgfakePhe.xml"/>
- </section>
- <section name="Rg Visualise" id="rgVis1">
- <tool file="rgenetics/rgQC.xml"/>
- <tool file="rgenetics/rgEigPCA2.xml"/>
- <tool file="rgenetics/rgQQ.xml"/>
- </section>
- <section name="Rg Model Data" id="rgModel1">
- <tool file="rgenetics/rgGLM.xml"/>
+ <section name="SNP/WGA: Statistical Models" id="rgmodel">
<tool file="rgenetics/rgCaCo.xml"/>
<tool file="rgenetics/rgTDT.xml"/>
+ <tool file="rgenetics/rgGLM.xml"/>
+ <tool file="rgenetics/rgManQQ.xml"/>
</section>
<!--
TODO: uncomment the following EMBOSS section whenever
1
0
15 Apr '10
details: http://www.bx.psu.edu/hg/galaxy/rev/3ac95cd927d7
changeset: 3565:3ac95cd927d7
user: Kelly Vincent <kpvincent(a)bx.psu.edu>
date: Fri Mar 26 12:00:55 2010 -0400
description:
Added new tabular/pileup join tool and associated test files. Also added pileup datatype.
diffstat:
datatypes_conf.xml.sample | 2 +
lib/galaxy/datatypes/registry.py | 3 +
lib/galaxy/datatypes/tabular.py | 93 ++
lib/galaxy/datatypes/test/10col.pileup | 30 +
lib/galaxy/datatypes/test/6col.pileup | 30 +
test-data/1.pileup | 1000 ++++++++++++++++++++++++++++++++
test-data/column_join_in1.pileup | 30 +
test-data/column_join_in2.pileup | 30 +
test-data/column_join_in3.pileup | 30 +
test-data/column_join_in4.pileup | 25 +
test-data/column_join_in5.pileup | 25 +
test-data/column_join_in6.pileup | 25 +
test-data/column_join_in7.pileup | 32 +
test-data/column_join_in8.pileup | 23 +
test-data/column_join_in9.pileup | 25 +
test-data/column_join_out1.pileup | 60 +
test-data/column_join_out2.pileup | 65 ++
test-data/column_join_out3.pileup | 70 ++
test/functional/test_get_data.py | 17 +
tool_conf.xml.sample | 1 +
20 files changed, 1616 insertions(+), 0 deletions(-)
diffs (1743 lines):
diff -r 5f927f52191c -r 3ac95cd927d7 datatypes_conf.xml.sample
--- a/datatypes_conf.xml.sample Fri Mar 26 09:51:03 2010 -0400
+++ b/datatypes_conf.xml.sample Fri Mar 26 12:00:55 2010 -0400
@@ -61,6 +61,7 @@
<converter file="maf_to_interval_converter.xml" target_datatype="interval"/>
</datatype>
<datatype extension="pdf" type="galaxy.datatypes.images:Image" mimetype="application/pdf"/>
+ <datatype extension="pileup" type="galaxy.datatypes.tabular:Pileup" display_in_upload="true" />
<datatype extension="png" type="galaxy.datatypes.images:Image" mimetype="image/png"/>
<datatype extension="qual" type="galaxy.datatypes.qualityscore:QualityScore" />
<datatype extension="qualsolexa" type="galaxy.datatypes.qualityscore:QualityScoreSolexa" display_in_upload="true"/>
@@ -239,6 +240,7 @@
<sniffer type="galaxy.datatypes.interval:CustomTrack"/>
<sniffer type="galaxy.datatypes.interval:Gff"/>
<sniffer type="galaxy.datatypes.interval:Gff3"/>
+ <sniffer type="galaxy.datatypes.tabular:Pileup"/>
<sniffer type="galaxy.datatypes.interval:Interval"/>
<sniffer type="galaxy.datatypes.tabular:Sam"/>
</sniffers>
diff -r 5f927f52191c -r 3ac95cd927d7 lib/galaxy/datatypes/registry.py
--- a/lib/galaxy/datatypes/registry.py Fri Mar 26 09:51:03 2010 -0400
+++ b/lib/galaxy/datatypes/registry.py Fri Mar 26 12:00:55 2010 -0400
@@ -155,6 +155,7 @@
'laj' : images.Laj(),
'lav' : sequence.Lav(),
'maf' : sequence.Maf(),
+ 'pileup' : tabular.Pileup(),
'qualsolid' : qualityscore.QualityScoreSOLiD(),
'qualsolexa' : qualityscore.QualityScoreSolexa(),
'qual454' : qualityscore.QualityScore454(),
@@ -185,6 +186,7 @@
'laj' : 'text/plain',
'lav' : 'text/plain',
'maf' : 'text/plain',
+ 'pileup' : 'text/plain',
'qualsolid' : 'text/plain',
'qualsolexa' : 'text/plain',
'qual454' : 'text/plain',
@@ -218,6 +220,7 @@
interval.CustomTrack(),
interval.Gff(),
interval.Gff3(),
+ tabular.Pileup(),
interval.Interval(),
tabular.Sam()
]
diff -r 5f927f52191c -r 3ac95cd927d7 lib/galaxy/datatypes/tabular.py
--- a/lib/galaxy/datatypes/tabular.py Fri Mar 26 09:51:03 2010 -0400
+++ b/lib/galaxy/datatypes/tabular.py Fri Mar 26 12:00:55 2010 -0400
@@ -327,3 +327,96 @@
except:
pass
return False
+
+class Pileup( Tabular ):
+ """Tab delimited data in pileup (6- or 10-column) format"""
+ file_ext = "pileup"
+
+ """Add metadata elements"""
+ MetadataElement( name="chromCol", default=1, desc="Chrom column", param=metadata.ColumnParameter )
+ MetadataElement( name="startCol", default=2, desc="Start column", param=metadata.ColumnParameter )
+ MetadataElement( name="baseCol", default=3, desc="Reference base column", param=metadata.ColumnParameter )
+
+ def init_meta( self, dataset, copy_from=None ):
+ Tabular.init_meta( self, dataset, copy_from=copy_from )
+
+ def set_peek( self, dataset, line_count=None, is_multi_byte=False ):
+ """Set the peek and blurb text"""
+ if not dataset.dataset.purged:
+ dataset.peek = data.get_file_peek( dataset.file_name, is_multi_byte=is_multi_byte )
+ if line_count is None:
+ # See if line_count is stored in the metadata
+ if dataset.metadata.data_lines:
+ dataset.blurb = "%s genomic coordinates" % util.commaify( str( dataset.metadata.data_lines ) )
+ else:
+ # Number of lines is not known ( this should not happen ), and auto-detect is
+ # needed to set metadata
+ dataset.blurb = "? genomic coordinates"
+ else:
+ dataset.blurb = "%s genomic coordinates" % util.commaify( str( line_count ) )
+ else:
+ dataset.peek = 'file does not exist'
+ dataset.blurb = 'file purged from disk'
+
+ def make_html_table( self, dataset, skipchars=[] ):
+ """Create HTML table, used for displaying peek"""
+ out = ['<table cellspacing="0" cellpadding="3">']
+ comments = []
+ try:
+ # Generate column header
+ out.append('<tr>')
+ for i in range( 1, dataset.metadata.columns+1 ):
+ if i == dataset.metadata.chromCol:
+ out.append( '<th>%s.Chrom</th>' % i )
+ elif i == dataset.metadata.startCol:
+ out.append( '<th>%s.Start</th>' % i )
+ elif i == dataset.metadata.baseCol:
+ out.append( '<th>%s.Base</th>' % i )
+ else:
+ out.append( '<th>%s</th>' % i )
+ out.append('</tr>')
+ out.append( self.make_html_peek_rows( dataset, skipchars=skipchars ) )
+ out.append( '</table>' )
+ out = "".join( out )
+ except Exception, exc:
+ out = "Can't create peek %s" % str( exc )
+ return out
+
+ def repair_methods( self, dataset ):
+ """Return options for removing errors along with a description"""
+ return [ ("lines", "Remove erroneous lines") ]
+
+ def sniff( self, filename ):
+ """
+ Checks for 'pileup-ness'
+
+ There are two main types of pileup: 6-column and 10-column. For both,
+ the first three and last two columns are the same. We only check the
+ first three to allow for some personalization of the format.
+
+ >>> fname = get_test_fname( 'interval.interval' )
+ >>> Pileup().sniff( fname )
+ False
+ >>> fname = get_test_fname( '6col.pileup' )
+ >>> Pileup().sniff( fname )
+ True
+ >>> fname = get_test_fname( '10col.pileup' )
+ >>> Pileup().sniff( fname )
+ True
+ """
+ headers = get_headers( filename, '\t' )
+ try:
+ for hdr in headers:
+ if hdr and not hdr[0].startswith( '#' ):
+ if len( hdr ) < 3:
+ return False
+ try:
+ # chrom start in column 1 (with 0-based columns)
+ # and reference base is in column 2
+ check = int( hdr[1] )
+ assert hdr[2] in [ 'A', 'C', 'G', 'T', 'N', 'a', 'c', 'g', 't', 'n' ]
+ except:
+ return False
+ return True
+ except:
+ return False
diff -r 5f927f52191c -r 3ac95cd927d7 lib/galaxy/datatypes/test/10col.pileup
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/lib/galaxy/datatypes/test/10col.pileup Fri Mar 26 12:00:55 2010 -0400
@@ -0,0 +1,30 @@
+chrM 1 G G 25 0 25 1 ^:. I
+chrM 2 T T 25 0 25 1 . I
+chrM 3 T T 25 0 25 1 . I
+chrM 4 A A 36 0 25 3 .^:.^:. II+
+chrM 5 A A 36 0 25 3 ... III
+chrM 6 T T 36 0 25 3 ... III
+chrM 7 G G 42 0 25 5 ...^:.^:. IIIII
+chrM 8 T T 45 0 25 6 .....^:. IIIIII
+chrM 9 A A 51 0 25 8 ......^:.^:. IIIIIIII
+chrM 10 G G 54 0 25 9 ........^:. IIIIIIIII
+chrM 11 C C 57 0 25 10 .........^:. IIIIIIIIII
+chrM 12 T T 60 0 25 11 ..........^:. IIIIIIIIIII
+chrM 13 T T 78 0 25 17 ...........^:.^:.^:.^:.^:.^:. IIIIIIIIIIIIIIIII
+chrM 14 A A 56 0 25 18 .......G.........^:. BIIIIIII+IIIIIIIII
+chrM 15 A A 87 0 25 20 ..................^:.^:. DIIIIIII(IIIIIIIIIII
+chrM 16 T T 87 0 25 20 .................... IIIIIIIIIIIIIIIIIIII
+chrM 17 A A 87 0 25 20 .................... 9IIIIIIIIIIIIIIIIIII
+chrM 18 A A 87 0 25 20 .................... @IIIIIIIIIIIIIIIIIII
+chrM 19 T T 55 0 25 20 ..................GG IIIIIIIIIIIIIIIIII'A
+chrM 20 A A 54 0 25 20 ..................C. IIIIIIIIIIIIIII2II#$
+chrM 21 T T 87 0 25 20 .................... IIIIIIIIIIIIIIIIIIII
+chrM 22 A A 87 0 25 20 .................... IIIIIIIIIIIIIIAIIIII
+chrM 23 A A 87 0 25 20 .................... 9IIIIIIIIII0IIIIIIII
+chrM 24 A A 87 0 25 20 ........N........... IIIIIIII"IIIIICIIIII
+chrM 25 G G 57 0 25 21 ...A................^:. A@.$IIIIIIIFIIIIIIIII
+chrM 26 C C 57 0 25 21 .......A............. IIHIDII&IIIIIIIIIIIII
+chrM 27 A A 99 0 25 24 .....................^:.^:.^:. IE8IFIII9IIIIIIIIIIIIIII
+chrM 28 A A 99 0 25 24 ........................ 1FIIIIIIIIIIIIIIIIDEIIII
+chrM 29 G G 55 0 25 24 ..................NN.... ;IIIIII+HII=IIIIII""IIII
+chrM 30 G G 68 0 25 25 ...C....................^:. ;I?&IAI0IIIIIIIIIIIIIIIII
diff -r 5f927f52191c -r 3ac95cd927d7 lib/galaxy/datatypes/test/6col.pileup
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/lib/galaxy/datatypes/test/6col.pileup Fri Mar 26 12:00:55 2010 -0400
@@ -0,0 +1,30 @@
+chrM 42 C 1 ^:. I
+chrM 43 C 2 .^:. II
+chrM 44 T 2 .. II
+chrM 45 A 3 ..^:. III
+chrM 46 G 4 ...^:. IIII
+chrM 47 A 5 ....^:, IIIII
+chrM 48 T 5 ...., IIIII
+chrM 49 G 5 ...., IIIII
+chrM 50 A 5 ...., IIIII
+chrM 51 G 5 ...., IIIII
+chrM 52 T 5 ...., IIIII
+chrM 53 A 5 ...., IIIII
+chrM 54 T 5 ...., IIIII
+chrM 55 T 5 ...., IIIII
+chrM 56 C 5 ...., IIIII
+chrM 57 T 5 ...., IIIII
+chrM 58 T 5 ...., IIIII
+chrM 59 A 5 ...., IIIII
+chrM 60 C 5 ...., IIIII
+chrM 61 T 5 ...., IIIII
+chrM 62 C 5 ...., IIIII
+chrM 63 C 5 ...., IIIII
+chrM 64 A 5 ...., IIIII
+chrM 65 T 5 ...., IIIII
+chrM 66 A 5 ...., IIIII
+chrM 67 A 5 ...., IIIII
+chrM 68 A 5 ...., IIICI
+chrM 69 C 5 ...., IIIII
+chrM 70 A 5 ...., IIIII
+chrM 71 C 5 ...., IIIII
diff -r 5f927f52191c -r 3ac95cd927d7 test-data/1.pileup
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/1.pileup Fri Mar 26 12:00:55 2010 -0400
@@ -0,0 +1,1000 @@
+chrM 42 C 1 ^:. I
+chrM 43 C 2 .^:. II
+chrM 44 T 2 .. II
+chrM 45 A 3 ..^:. III
+chrM 46 G 4 ...^:. IIII
+chrM 47 A 5 ....^:, IIIII
+chrM 48 T 5 ...., IIIII
+chrM 49 G 5 ...., IIIII
+chrM 50 A 5 ...., IIIII
+chrM 51 G 5 ...., IIIII
+chrM 52 T 5 ...., IIIII
+chrM 53 A 5 ...., IIIII
+chrM 54 T 5 ...., IIIII
+chrM 55 T 5 ...., IIIII
+chrM 56 C 5 ...., IIIII
+chrM 57 T 5 ...., IIIII
+chrM 58 T 5 ...., IIIII
+chrM 59 A 5 ...., IIIII
+chrM 60 C 5 ...., IIIII
+chrM 61 T 5 ...., IIIII
+chrM 62 C 5 ...., IIIII
+chrM 63 C 5 ...., IIIII
+chrM 64 A 5 ...., IIIII
+chrM 65 T 5 ...., IIIII
+chrM 66 A 5 ...., IIIII
+chrM 67 A 5 ...., IIIII
+chrM 68 A 5 ...., IIICI
+chrM 69 C 5 ...., IIIII
+chrM 70 A 5 ...., IIIII
+chrM 71 C 5 ...., IIIII
+chrM 72 A 5 ...., IAIII
+chrM 73 T 5 ...., IIIII
+chrM 74 A 5 ...., IIIII
+chrM 75 G 5 ...., %IIII
+chrM 76 G 5 T..., *IIII
+chrM 77 C 5 .$..., GIIII
+chrM 78 T 4 .$.., IIII
+chrM 79 T 3 .., III
+chrM 80 G 3 .$., I1I
+chrM 81 G 2 .$, II
+chrM 82 T 1 ,$ I
+chrM 83 C 2 ^:.^:. II
+chrM 84 C 2 .. II
+chrM 85 T 2 .. II
+chrM 86 A 2 .. II
+chrM 87 G 2 .. II
+chrM 88 C 2 .. II
+chrM 89 C 2 .. II
+chrM 90 T 2 .. II
+chrM 91 T 2 .. II
+chrM 92 T 2 .. II
+chrM 93 T 2 .. II
+chrM 94 T 2 .. II
+chrM 95 A 2 .. II
+chrM 96 T 2 .. II
+chrM 97 T 2 .. II
+chrM 98 A 2 .. II
+chrM 99 G 2 .. II
+chrM 100 T 2 .. II
+chrM 101 T 2 .. II
+chrM 102 A 2 .. II
+chrM 103 T 2 .. II
+chrM 104 T 2 .. II
+chrM 105 A 2 .. IE
+chrM 106 A 2 .. II
+chrM 107 T 2 .. II
+chrM 108 A 2 .. II
+chrM 109 G 2 .. II
+chrM 110 A 2 .. II
+chrM 111 A 2 .. I2
+chrM 112 T 2 .. II
+chrM 113 T 2 .. II
+chrM 114 A 2 .. H7
+chrM 115 C 2 .. II
+chrM 116 A 2 .. II
+chrM 117 C 2 .. II
+chrM 118 A 2 .$.$ F8
+chrM 156 T 1 ^:, &
+chrM 157 C 1 , I
+chrM 158 A 2 g^:g I>
+chrM 159 C 2 ,, /F
+chrM 160 G 2 ,, II
+chrM 161 T 2 ,, I>
+chrM 162 C 2 ,, .-
+chrM 163 T 2 ,, I8
+chrM 164 C 2 ,, 4F
+chrM 165 T 2 ,, II
+chrM 166 A 2 ,, II
+chrM 167 C 2 ,, ;6
+chrM 168 G 2 ,, II
+chrM 169 A 2 ,, II
+chrM 170 T 2 ,, II
+chrM 171 T 2 ,, IB
+chrM 172 A 2 ,, II
+chrM 173 A 2 ,, II
+chrM 174 A 2 ,, II
+chrM 175 A 2 ,, II
+chrM 176 G 2 ,, II
+chrM 177 G 2 ,, II
+chrM 178 A 2 ,, II
+chrM 179 G 2 ,, II
+chrM 180 C 2 ,, II
+chrM 181 A 3 ,,^:, III
+chrM 182 G 3 ,,, III
+chrM 183 G 3 ,,, III
+chrM 184 T 3 ,,, III
+chrM 185 A 3 ,,, III
+chrM 186 T 3 ,,, III
+chrM 187 C 3 ,,, III
+chrM 188 A 3 ,,, III
+chrM 189 A 3 ,,, III
+chrM 190 G 3 ,,, III
+chrM 191 C 3 ,$,, III
+chrM 192 A 2 ,, II
+chrM 193 C 2 ,$, II
+chrM 194 A 1 , I
+chrM 195 C 1 , I
+chrM 196 T 1 , F
+chrM 197 A 1 , I
+chrM 198 G 1 , I
+chrM 199 A 1 , I
+chrM 200 A 1 , I
+chrM 201 A 2 ,^:. I-
+chrM 202 G 2 ,. II
+chrM 203 T 2 ,. II
+chrM 204 A 2 ,. II
+chrM 205 G 2 ,. I6
+chrM 206 C 2 ,. II
+chrM 207 T 2 ,. I,
+chrM 208 C 2 ,. II
+chrM 209 A 2 ,. II
+chrM 210 T 2 ,. II
+chrM 211 A 2 ,. II
+chrM 212 A 2 ,. IE
+chrM 213 C 2 ,. IC
+chrM 214 A 2 ,. I;
+chrM 215 C 2 ,. II
+chrM 216 C 2 ,$. II
+chrM 217 T 1 . I
+chrM 218 T 1 . I
+chrM 219 G 1 T I
+chrM 220 C 1 . I
+chrM 221 T 1 . I
+chrM 222 C 1 . E
+chrM 223 A 1 . 4
+chrM 224 G 1 T 9
+chrM 225 C 1 . :
+chrM 226 C 1 . ?
+chrM 227 A 1 . .
+chrM 228 C 1 . C
+chrM 229 A 3 .^:,^:, %II
+chrM 230 C 3 .,, 8II
+chrM 231 C 3 .,, 9II
+chrM 232 C 3 .,, III
+chrM 233 C 3 .,, AI'
+chrM 234 C 3 .,, DI+
+chrM 235 A 3 .,, &I@
+chrM 236 C 3 .$,a +I$
+chrM 237 G 2 ,, II
+chrM 238 G 2 ,, II
+chrM 239 G 2 ,, II
+chrM 240 A 2 ,, II
+chrM 241 C 2 ,, I+
+chrM 242 A 2 ,, II
+chrM 243 C 2 ,, II
+chrM 244 A 3 ,,^:, II;
+chrM 245 G 3 ,,, II*
+chrM 246 C 3 ,,n II"
+chrM 247 A 3 ,,, III
+chrM 248 G 4 ,,,^:. IIII
+chrM 249 T 4 ,,,. II)I
+chrM 250 G 4 ,,,. II2I
+chrM 251 A 4 ,,,. II(I
+chrM 252 T 4 ,,,. II*I
+chrM 253 A 4 ,,,. II7I
+chrM 254 A 4 ,,,. II1I
+chrM 255 A 4 ,,,. II?I
+chrM 256 A 4 ,,,. II9I
+chrM 257 A 4 ,,,. II?I
+chrM 258 T 4 ,,,. II$I
+chrM 259 T 5 ,,,.^:. II&II
+chrM 260 A 5 ,,,.. II,II
+chrM 261 A 5 ,,,.. II/II
+chrM 262 G 5 ,,,.. II5II
+chrM 263 C 5 ,,a.. II%II
+chrM 264 T 5 ,$,$,.. II%II
+chrM 265 A 3 ,.. )II
+chrM 266 T 3 ,.. +II
+chrM 267 G 4 ,..^:. *III
+chrM 268 A 4 ,... EIII
+chrM 269 A 4 ,... =III
+chrM 270 C 4 a... ;III
+chrM 271 G 4 ,... ;III
+chrM 272 A 4 ,... 8@II
+chrM 273 A 4 ,... 1III
+chrM 274 A 4 ,... ICII
+chrM 275 G 4 ,... IIII
+chrM 276 T 4 ,... IIII
+chrM 277 T 4 ,... IIII
+chrM 278 C 4 ,... IIII
+chrM 279 G 4 ,$... IIII
+chrM 280 A 3 ... III
+chrM 281 C 3 ... GII
+chrM 282 T 3 ... III
+chrM 283 A 3 .$.. IFI
+chrM 284 A 3 ..^:, IAI
+chrM 285 G 3 .., ;II
+chrM 286 T 4 ..,^:. IIII
+chrM 287 C 4 ..,. II4I
+chrM 288 A 4 ..,. @III
+chrM 289 T 4 ..,. IIII
+chrM 290 A 4 ..,. @:II
+chrM 291 T 4 ..,. IIAI
+chrM 292 T 4 ..,. IIII
+chrM 293 A 4 ..,. 8;II
+chrM 294 A 4 .$.,. I<II
+chrM 295 A 3 .,. 4II
+chrM 296 T 3 .,. III
+chrM 297 A 3 .,. BII
+chrM 298 A 3 .,. CII
+chrM 299 G 3 .,. III
+chrM 300 G 3 .,. ;II
+chrM 301 G 3 .,. III
+chrM 302 T 3 .$,. III
+chrM 303 T 2 ,. II
+chrM 304 G 2 ,. II
+chrM 305 G 2 ,. II
+chrM 306 T 2 ,. II
+chrM 307 A 2 ,. II
+chrM 308 A 2 ,. II
+chrM 309 A 2 ,. II
+chrM 310 T 2 ,. II
+chrM 311 T 2 ,. II
+chrM 312 T 3 ,.^:. III
+chrM 313 C 3 ,.. III
+chrM 314 G 3 ,.. III
+chrM 315 T 3 ,.. III
+chrM 316 G 3 ,.. III
+chrM 317 C 3 ,.. III
+chrM 318 C 3 ,.. III
+chrM 319 A 3 ,$.. III
+chrM 320 G 2 .. II
+chrM 321 C 2 .$. II
+chrM 322 C 1 . I
+chrM 323 A 1 . I
+chrM 324 C 1 . I
+chrM 325 C 1 . I
+chrM 326 G 1 . I
+chrM 327 C 1 . I
+chrM 328 G 1 . I
+chrM 329 G 1 . I
+chrM 330 T 1 . I
+chrM 331 C 1 . I
+chrM 332 A 1 . I
+chrM 333 T 1 . I
+chrM 334 A 1 . I
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+chrM 1000 A 3 ... III
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+chrM 1002 A 2 .. II
+chrM 1003 A 2 .. II
+chrM 1004 G 2 .. II
+chrM 1005 T 2 .. II
+chrM 1006 C 2 .. II
+chrM 1007 G 2 .. CI
+chrM 1008 T 2 .. II
+chrM 1009 A 2 .$. II
+chrM 1010 A 1 . I
+chrM 1011 C 1 . I
+chrM 1012 A 1 . I
+chrM 1013 A 1 . I
+chrM 1014 G 1 . I
+chrM 1015 G 1 . I
+chrM 1016 T 1 . I
+chrM 1017 A 1 . I
+chrM 1018 A 1 . I
+chrM 1019 G 1 . I
+chrM 1020 T 1 . I
+chrM 1021 A 1 . I
+chrM 1022 T 1 . I
+chrM 1023 A 1 . I
+chrM 1024 C 1 . I
+chrM 1025 C 1 . I
+chrM 1026 G 1 . I
+chrM 1027 G 1 . I
+chrM 1028 A 1 . I
+chrM 1029 A 1 . I
+chrM 1030 G 1 . I
+chrM 1031 G 2 .^:. II
+chrM 1032 T 2 .. EI
+chrM 1033 G 2 .. II
+chrM 1034 T 2 .$. II
+chrM 1035 A 2 .^:. II
+chrM 1036 C 2 .. II
+chrM 1037 T 2 .. II
+chrM 1038 T 2 .. II
+chrM 1039 G 2 .. II
+chrM 1040 G 2 .. II
+chrM 1041 A 2 .. II
+chrM 1042 T 2 .. II
+chrM 1043 A 3 ..^:, III
+chrM 1044 A 3 .., III
+chrM 1045 C 3 .., II7
+chrM 1046 C 3 .., II-
+chrM 1047 A 3 .., III
+chrM 1048 A 3 .., III
+chrM 1049 A 3 .., III
+chrM 1050 G 3 .., III
+chrM 1051 T 3 .., III
+chrM 1052 G 3 .., III
+chrM 1053 T 3 .., GII
+chrM 1054 A 3 .., III
+chrM 1055 G 3 .., :II
+chrM 1056 C 3 ..a HI%
+chrM 1057 T 3 .., III
+chrM 1058 T 3 .., III
+chrM 1059 A 3 .., BII
+chrM 1060 A 3 .., GII
+chrM 1061 A 3 .., HII
+chrM 1062 C 3 .., III
+chrM 1063 A 3 .., DII
+chrM 1064 A 3 .., BII
+chrM 1065 A 3 .., 1II
+chrM 1066 G 3 .$., &II
+chrM 1067 C 2 ., II
+chrM 1068 A 2 ., II
+chrM 1069 T 2 ., II
+chrM 1070 C 2 .$, II
+chrM 1071 C 1 , I
+chrM 1072 A 1 , I
+chrM 1073 G 1 , I
+chrM 1074 C 1 , I
+chrM 1075 T 1 , I
+chrM 1076 T 1 , I
+chrM 1077 A 1 , I
+chrM 1078 C 1 ,$ I
+chrM 1090 T 1 ^:, I
+chrM 1091 T 1 , I
+chrM 1092 C 1 n "
+chrM 1093 A 1 , I
+chrM 1094 C 1 , I
+chrM 1095 T 1 , 7
+chrM 1096 C 1 a B
+chrM 1097 A 1 , I
+chrM 1098 A 1 , I
+chrM 1099 A 1 , I
+chrM 1100 A 1 , I
+chrM 1101 T 1 , I
+chrM 1102 G 2 ,^:, (I
+chrM 1103 A 2 ,, II
+chrM 1104 A 2 ,, I+
+chrM 1105 C 2 ,, .I
+chrM 1106 A 2 ,, 8I
diff -r 5f927f52191c -r 3ac95cd927d7 test-data/column_join_in1.pileup
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/column_join_in1.pileup Fri Mar 26 12:00:55 2010 -0400
@@ -0,0 +1,30 @@
+chrM 1 A G 25 0 25 1 ^:. I
+chrM 2 C T 25 0 25 2 .N I$
+chrM 3 T G 27 0 25 2 .. II
+chrM 4 G C 36 0 25 3 .^:.^:. II+
+chrM 5 T A 38 0 25 3 ... III
+chrM 6 T A 39 0 25 4 .N.. I$II
+chrM 7 G C 43 0 25 5 ...^:.^:. IIIII
+chrM 8 A C 46 0 25 6 .....^:. IIIIII
+chrM 9 T G 53 0 25 8 ..G...^:.^:. IIIII$II
+chrM 10 T G 56 0 25 9 ........^:. IIIIIIIII
+chrM 11 C G 57 0 25 10 .........^:. IIIIIIIIII
+chrM 12 T C 61 0 25 11 ..........^:. IIIIIIIIIII
+chrM 13 T G 79 0 25 15 .........^:.^:.^:.^:.^:.^:. IIIIIIIIIIII#II
+chrM 14 A C 58 0 25 18 .......G.........^:. BIIIIIII+IIIIIIIII
+chrM 15 G A 87 0 25 19 ..N...............^:.^:. DIIIIII$(IIIIIIIIIII
+chrM 16 G C 88 0 25 20 .........N.......... IIIIIIIIIIIIIIIIIIII
+chrM 17 A C 88 0 25 20 .........G.......... 9IIIIIIIIIIIIIIIIIII
+chrM 18 G A 89 0 25 20 ...A................ @IIIIIIIIIIIIIIIIIII
+chrM 19 G T 58 0 25 20 ....T.............GG IIIIIIIIIIIIIIIIII'A
+chrM 20 T C 55 0 25 20 .........C........C. IIIIIIIIIIIIIII2II#$
+chrM 21 C T 87 0 25 20 ..........G......... IIIIIIIIIIIIIIIIIIII
+chrM 22 C A 87 0 25 20 ..........N......... IIIIIIIIIIIIIIAIIIII
+chrM 23 A G 87 0 25 20 .....T.............. 9IIIIIIIIII0IIIIIIII
+chrM 24 A T 89 0 25 20 .....N..N........... III$IIII"IIIIICII#II
+chrM 25 G A 57 0 25 21 ...A................^:. A@.$IIIIIIIFIIIIIIIII
+chrM 26 C G 58 0 25 22 ...N....A............. IIHIDII&IIIIII@IIIIII
+chrM 27 T A 99 0 25 23 ....................^:.^:.^:. IE8IFIII9IIIIIIIIIIIIII
+chrM 28 A C 99 0 25 24 ..G..................... 1FIIIIIIIIIIIIIIIIDEIIII
+chrM 29 G C 58 0 25 25 ........C.........NN.... ;IIIIII+HII=III$III""IIII
+chrM 30 T T 65 0 25 25 ...C....................^:. ;I?&IAI0IIIIIIIIIIIIIIIII
diff -r 5f927f52191c -r 3ac95cd927d7 test-data/column_join_in2.pileup
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/column_join_in2.pileup Fri Mar 26 12:00:55 2010 -0400
@@ -0,0 +1,30 @@
+chrM 1 T G 25 0 25 1 ^:. I
+chrM 2 C A 25 0 25 1 . I
+chrM 3 C A 25 0 25 2 .. I+
+chrM 4 G A 36 0 25 3 .^:.^:. II+
+chrM 5 A T 36 0 25 3 ... IDI
+chrM 6 A G 36 0 25 4 ..T. IIBI
+chrM 7 C G 42 0 25 5 ...^:.^:. ID@II
+chrM 8 T T 45 0 25 6 .....^:. III$BI
+chrM 9 C A 51 0 25 8 ......^:.^:. $#III+III
+chrM 10 G G 54 0 25 9 ........^:. III$III#I
+chrM 11 T C 57 0 25 10 .........^:. IIIDBIIIII
+chrM 12 A T 60 0 25 11 ..........^:. IIIIIIIII$I
+chrM 13 A T 78 0 25 18 ..A.........^:.^:.^:.^:.^:.^:. III#$IIIIII+IIDIIB
+chrM 14 G A 56 0 25 19 ........T.........^:. BIIIIIII+IIII$IBIII
+chrM 15 G A 87 0 25 20 ..................^:.^:. DIIIIIII(IIIIIIIIIII
+chr1 1 T T 87 0 25 20 .............T...... IIIIIIIIIIII$DIIIIII
+chr1 2 A T 87 0 25 20 ......G............. 9IIIIIIIIIIIIICBIIII
+chr1 3 A G 87 0 25 20 ....A............... @IIIIIIIII#IIII#IIII
+chr1 4 A T 55 0 25 20 ..................GG IIIII@II$IIIIIIIII'A
+chr1 5 C A 54 0 25 20 .......A..........C. IIIIIIIIIDIIIII2II#$
+chr1 6 G T 87 0 25 20 .............A...... IIIIIIIBIIIIII#IIIII
+chr1 7 A C 87 0 25 20 ..........C......... IIIII+IIIIIIIIAIIIII
+chr1 8 G A 87 0 25 20 ....G.........T..... 9IIIIIIIIII0IIIIIIII
+chr1 9 A T 87 0 25 20 ........N........... IIII$III"IIIIICIIIII
+chr1 10 G A 57 0 25 21 ...A................^:. A@.$IIIIIIIFIIIIIIIII
+chr1 11 C A 57 0 25 22 ....G...A............. IIHIDII&IIIIII#III$II
+chr1 12 T A 99 0 25 24 .....................^:.^:.^:. IE8IFIII9IIIIIIIIIIIIIII
+chr1 13 A C 99 0 25 25 ...N..................... 1FIIIIIIIIIIIIIIIIDEII$II
+chr1 14 G C 55 0 25 25 ....G..............NN.... ;IIIBIII+HII=IIIIII""IIII
+chr1 15 T G 68 0 25 28 ...C.......N............^:. ;I?&IAI0IIIIIII@II#$II@II
diff -r 5f927f52191c -r 3ac95cd927d7 test-data/column_join_in3.pileup
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/column_join_in3.pileup Fri Mar 26 12:00:55 2010 -0400
@@ -0,0 +1,30 @@
+chr1 1 G G 25 0 25 1 ^:. I
+chr1 2 T T 25 0 25 1 . I
+chr1 3 T T 27 0 25 1 . I
+chr1 4 A A 36 0 25 2 .^:. I+
+chr1 5 A A 36 0 25 3 ... III
+chr1 6 T T 36 0 25 4 .N.. II#I
+chr1 7 G G 42 0 25 5 ...^:.^:. IIIII
+chr1 8 T T 45 0 25 6 .....^:. IIIIII
+chr1 9 A A 51 0 25 7 .....^:.^:. IBIIIII
+chr1 10 G G 54 0 25 9 ........^:. IIIIIIIII
+chr1 11 C C 57 0 25 10 .........^:. IIIIIIII"I
+chr1 12 T T 60 0 25 11 ..........^:. IIIIIIDIIII
+chr1 13 T T 78 0 25 17 ...........^:.^:.^:.^:.^:.^:. IIII"$IIIIIIIIIII
+chr1 14 A A 56 0 25 18 .......G.........^:. BIIIIIII+IIIIIIIII
+chr1 15 A A 87 0 25 20 ....N.............^:.^:. DIII$III(IIIIIIIIIII
+chr4 1 T T 90 0 25 20 ..........N......... IIIIIIIII$IIIIIIIIII
+chr4 2 A A 87 0 25 20 .......C............ 9IIIIIIIII"IIIIIIIII
+chr4 3 A A 34 0 25 20 ......G............. @IIIIIIIIIIII#IIIIII
+chr4 4 T T 55 0 25 21 ...........N.......GG IIIII@IIIIIIIIIIIII'A
+chr4 5 A A 54 0 25 21 ...N...............C. IIII"IIIIIIIIIII2II#$
+chr4 6 T T 87 0 25 21 ................N.... IIIIIIII$IIIIIIIIIIII
+chr4 7 A A 80 0 25 21 .....G............... III$IIIIIIIIIIIAIIIII
+chr4 8 A A 87 0 25 22 ..N................... 9IIIIIIIIII0IIIII"$III
+chr4 9 A A 87 0 25 22 .GG.......N........... IIII$IIIII"IIIIICIIIII
+chr4 10 G G 57 0 25 23 .....A................^:. A@.$IIIIIIIIIFIIIIIIIII
+chr4 11 C C 57 0 25 25 .......A.....GN.......... IIHIDII&III#IIIIIIIIIIIII
+chr4 12 A A 99 0 25 26 .......................^:.^:.^:. IE8IFIII9IIIIIII$IIIIIIIII
+chr4 13 A A 99 0 25 27 ........N.................. 1FIIIIII$IIIIIIIIIIIIDEIIII
+chr4 14 G G 55 0 25 28 ..N...................NN.... ;III$I#IIII+HII=IIIIII""IIII
+chr4 15 G G 68 0 25 30 ...C....N..G.................^:. ;I?&IAI0IIIIIII$#I$@IIIIIIIIII
diff -r 5f927f52191c -r 3ac95cd927d7 test-data/column_join_in4.pileup
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/column_join_in4.pileup Fri Mar 26 12:00:55 2010 -0400
@@ -0,0 +1,25 @@
+chr2 1 T 6 .C..., I$$III
+chr2 2 G 6 ..N.., III@II
+chr2 3 C 7 ..C..., I$IIIII
+chr2 4 G 7 .G...., I#IIIII
+chr2 5 G 7 ...N.., IIII#BI
+chr2 6 A 7 ..T..., I$IDIII
+chr2 7 T 8 ...C..., IIIBD$II
+chr2 8 A 8 ..A...., IBI#IIII
+chr2 9 C 9 .GA..N.., I$IBIII#I
+chr2 10 T 9 ........, I$II#IIII
+chr2 11 C 10 .>>..T..., IIII@I$I$I
+chr2 12 G 10 .N..G...., III$IIIIII
+chr2 13 A 11 ....A..T.., IIIIII#I@II
+chr1 1 C 1 ^:. I
+chr1 2 G 2 .^:. $I
+chr1 3 A 2 .. I%
+chr1 4 C 2 .. I$
+chr1 5 T 3 ..^:. I#I
+chr1 6 G 3 ..^:, I#I
+chr1 7 C 4 .N., IIII
+chr1 8 A 4 ..., I$II
+chr1 9 T 5 ..C., I#IDI
+chr1 10 G 5 N..., IBII@
+chr1 11 A 5 .C.., I$II#
+chr1 12 C 5 ..N., I$III
diff -r 5f927f52191c -r 3ac95cd927d7 test-data/column_join_in5.pileup
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/column_join_in5.pileup Fri Mar 26 12:00:55 2010 -0400
@@ -0,0 +1,25 @@
+chr1 42 T 1 ^:. I
+chr1 43 G 2 .^:. $I
+chr1 44 T 2 .. I%
+chr1 45 C 3 ..^:. III
+chr1 46 G 3 ..^:. I#I
+chr1 47 T 4 ...^:, I#II
+chr1 48 A 4 .N., IIII
+chr1 49 C 5 ...., IIIII
+chr1 50 A 5 ..G., IIIDI
+chr1 51 A 5 A..., IBIII
+chr1 52 A 5 ...., IIII#
+chr1 53 G 5 ..N., I$III
+chr2 77 C 6 .G..., I$$III
+chr2 78 G 6 ..N.., III@II
+chr2 79 T 7 ..N..., I$IIIII
+chr2 80 C 7 .G...., I#IIIII
+chr2 81 G 7 ...A.., IIII#BI
+chr2 82 A 8 ...G..., I$IDIIII
+chr2 83 A 8 ...T..., IIIBD$II
+chr2 84 T 8 ..A...., IBI#IIII
+chr2 85 G 8 .GA...., IIBIII#I
+chr2 86 C 9 ........, I$II#IIII
+chr2 87 G 9 ....T..., IIIII$I$I
+chr2 88 G 10 .N..G...., III$IIIIII
+chr2 89 G 10 ...A..T.., IIIII#I@II
diff -r 5f927f52191c -r 3ac95cd927d7 test-data/column_join_in6.pileup
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/column_join_in6.pileup Fri Mar 26 12:00:55 2010 -0400
@@ -0,0 +1,25 @@
+chr1 42 C 1 ^:. I
+chr1 43 C 2 .^:. II
+chr1 44 T 2 .. II
+chr1 45 A 3 ..^:. III
+chr1 46 G 4 ...^:. IIII
+chr1 47 A 5 ....^:, IIIII
+chr1 48 T 5 ...N, I#III
+chr1 49 G 5 ...., IIIII
+chr1 50 A 5 .G.., IIIII
+chr1 51 G 5 ...., IIIII
+chr2 52 T 5 .N.., II$II
+chr2 53 A 5 ...., IIIII
+chr2 54 T 5 ...., IIIII
+chr2 55 T 5 ...., IIIII
+chr2 56 C 5 ...., IIIBI
+chr2 57 T 5 ...., IDIII
+chr2 58 T 6 .N..., IIIIII
+chr2 59 A 6 ....., IIII$I
+chr3 60 C 6 ...G., I#IIII
+chr3 61 T 6 ..N.., IIIIII
+chr3 62 C 6 ...A., IIIIII
+chr3 63 C 7 .N...., IIIIIII
+chr3 64 A 7 ...G.., IIIII$I
+chr3 65 T 7 ...AA., IIIII@@
+chr3 66 A 7 ....N., IIIIIII
diff -r 5f927f52191c -r 3ac95cd927d7 test-data/column_join_in7.pileup
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/column_join_in7.pileup Fri Mar 26 12:00:55 2010 -0400
@@ -0,0 +1,32 @@
+chr2 1 T 6 .C..., I$$III
+chr2 2 G 6 ..N.., III@II
+chr2 3 C 7 ..C..., I$IIIII
+chr2 4 G 7 .G...., I#IIIII
+chr2 5 G 7 ...N.., IIII#BI
+chr2 6 A 7 ..T..., I$IDIII
+chr2 7 T 8 ...C..., IIIBD$II
+chr2 8 A 8 ..A...., IBI#IIII
+chr2 9 C 9 .GA..N.., I$IBIII#I
+chr2 10 T 9 ........, I$II#IIII
+chr2 11 C 10 .>>..T..., IIII@I$I$I
+chr2 12 G 10 .N..G...., III$IIIIII
+chr2 13 A 11 ....A..T.., IIIIII#I@II
+chr2 14 G 11 ..N....... IICIBII@AII
+chr2 15 C 11 A.....NG.. IIIIIDIIIII
+chr2 16 T 11 ...C.....G I$IIIB@IIIC
+chr2 17 C 12 G......TN.. IIAII@IIII$I
+chr2 18 A 12 N......G..A IIIBIII$IIII
+chr2 19 A 13 .......NN... IIIIIIBIII$$@
+chr2 20 C 13 ..GT.......N IIIIABIIC$III
+chr1 1 C 1 ^:. I
+chr1 2 G 2 .^:. $I
+chr1 3 A 2 .. I%
+chr1 4 C 2 .. I$
+chr1 5 T 3 ..^:. I#I
+chr1 6 G 3 ..^:, I#I
+chr1 7 C 4 .N., IIII
+chr1 8 A 4 ..., I$II
+chr1 9 T 5 ..C., I#IDI
+chr1 10 G 5 N..., IBII@
+chr1 11 A 5 .C.., I$II#
+chr1 12 C 5 ..N., I$III
diff -r 5f927f52191c -r 3ac95cd927d7 test-data/column_join_in8.pileup
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/column_join_in8.pileup Fri Mar 26 12:00:55 2010 -0400
@@ -0,0 +1,23 @@
+chr1 42 T 1 ^:. I
+chr1 43 G 2 .^:. $I
+chr1 44 T 2 .. I%
+chr1 45 C 3 ..^:. III
+chr1 46 G 3 ..^:. I#I
+chr1 47 T 4 ...^:, I#II
+chr1 48 A 4 .N., IIII
+chr1 49 C 5 ...., IIIII
+chr1 50 A 5 ..G., IIIDI
+chr1 51 A 5 A..., IBIII
+chr1 52 A 5 ...., IIII#
+chr1 53 G 5 ..N., I$III
+chr2 77 C 6 .G..., I$$III
+chr2 78 G 6 ..N.., III@II
+chr2 79 T 7 ..N..., I$IIIII
+chr2 80 C 7 .G...., I#IIIII
+chr2 81 G 7 ...A.., IIII#BI
+chr2 82 A 8 ...G..., I$IDIIII
+chr2 83 A 8 ...T..., IIIBD$II
+chr2 84 T 8 ..A...., IBI#IIII
+chr2 85 G 8 .GA...., IIBIII#I
+chr2 86 C 9 ........, I$II#IIII
+chr2 87 G 9 ....T..., IIIII$I$I
diff -r 5f927f52191c -r 3ac95cd927d7 test-data/column_join_in9.pileup
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/column_join_in9.pileup Fri Mar 26 12:00:55 2010 -0400
@@ -0,0 +1,25 @@
+chr1 43 C 2 .^:. II
+chr3 65 T 7 ...AA., IIIII@@
+chr1 44 T 2 .. II
+chr2 54 T 5 ...., IIIII
+chr1 45 A 3 ..^:. III
+chr1 47 A 5 ....^:, IIIII
+chr1 50 A 5 .G.., IIIII
+chr1 51 G 5 ...., IIIII
+chr2 52 T 5 .N.., II$II
+chr2 53 A 5 ...., IIIII
+chr3 60 C 6 ...G., I#IIII
+chr3 61 T 6 ..N.., IIIIII
+chr1 49 G 5 ...., IIIII
+chr2 55 T 5 ...., IIIII
+chr2 56 C 5 ...., IIIBI
+chr2 58 T 6 .N..., IIIIII
+chr2 59 A 6 ....., IIII$I
+chr3 62 C 6 ...A., IIIIII
+chr1 42 C 1 ^:. I
+chr3 63 C 7 .N...., IIIIIII
+chr1 48 T 5 ...N, I#III
+chr1 46 G 4 ...^:. IIII
+chr3 64 A 7 ...G.., IIIII$I
+chr3 66 A 7 ....N., IIIIIII
+chr2 57 T 5 ...., IDIII
diff -r 5f927f52191c -r 3ac95cd927d7 test-data/column_join_out1.pileup
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/column_join_out1.pileup Fri Mar 26 12:00:55 2010 -0400
@@ -0,0 +1,60 @@
+chr1 1 T T 87 25 G G 25 25
+chr1 2 A T 87 25 T T 25 25
+chr1 3 A G 87 25 T T 27 25
+chr1 4 A T 55 25 A A 36 25
+chr1 5 C A 54 25 A A 36 25
+chr1 6 G T 87 25 T T 36 25
+chr1 7 A C 87 25 G G 42 25
+chr1 8 G A 87 25 T T 45 25
+chr1 9 A T 87 25 A A 51 25
+chr1 10 G A 57 25 G G 54 25
+chr1 11 C A 57 25 C C 57 25
+chr1 12 T A 99 25 T T 60 25
+chr1 13 A C 99 25 T T 78 25
+chr1 14 G C 55 25 A A 56 25
+chr1 15 T G 68 25 A A 87 25
+chr4 1 T T 90 25
+chr4 2 A A 87 25
+chr4 3 A A 34 25
+chr4 4 T T 55 25
+chr4 5 A A 54 25
+chr4 6 T T 87 25
+chr4 7 A A 80 25
+chr4 8 A A 87 25
+chr4 9 A A 87 25
+chr4 10 G G 57 25
+chr4 11 C C 57 25
+chr4 12 A A 99 25
+chr4 13 A A 99 25
+chr4 14 G G 55 25
+chr4 15 G G 68 25
+chrM 1 A G 25 25 T G 25 25
+chrM 2 C T 25 25 C A 25 25
+chrM 3 T G 27 25 C A 25 25
+chrM 4 G C 36 25 G A 36 25
+chrM 5 T A 38 25 A T 36 25
+chrM 6 T A 39 25 A G 36 25
+chrM 7 G C 43 25 C G 42 25
+chrM 8 A C 46 25 T T 45 25
+chrM 9 T G 53 25 C A 51 25
+chrM 10 T G 56 25 G G 54 25
+chrM 11 C G 57 25 T C 57 25
+chrM 12 T C 61 25 A T 60 25
+chrM 13 T G 79 25 A T 78 25
+chrM 14 A C 58 25 G A 56 25
+chrM 15 G A 87 25 G A 87 25
+chrM 16 G C 88 25
+chrM 17 A C 88 25
+chrM 18 G A 89 25
+chrM 19 G T 58 25
+chrM 20 T C 55 25
+chrM 21 C T 87 25
+chrM 22 C A 87 25
+chrM 23 A G 87 25
+chrM 24 A T 89 25
+chrM 25 G A 57 25
+chrM 26 C G 58 25
+chrM 27 T A 99 25
+chrM 28 A C 99 25
+chrM 29 G C 58 25
+chrM 30 T T 65 25
diff -r 5f927f52191c -r 3ac95cd927d7 test-data/column_join_out2.pileup
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/column_join_out2.pileup Fri Mar 26 12:00:55 2010 -0400
@@ -0,0 +1,65 @@
+chr1 1 C 1
+chr1 2 G 2
+chr1 3 A 2
+chr1 4 C 2
+chr1 5 T 3
+chr1 6 G 3
+chr1 7 C 4
+chr1 8 A 4
+chr1 9 T 5
+chr1 10 G 5
+chr1 11 A 5
+chr1 12 C 5
+chr1 42 T 1 C 1
+chr1 43 G 2 C 2
+chr1 44 T 2 T 2
+chr1 45 C 3 A 3
+chr1 46 G 3 G 4
+chr1 47 T 4 A 5
+chr1 48 A 4 T 5
+chr1 49 C 5 G 5
+chr1 50 A 5 A 5
+chr1 51 A 5 G 5
+chr1 52 A 5
+chr1 53 G 5
+chr2 1 T 6
+chr2 2 G 6
+chr2 3 C 7
+chr2 4 G 7
+chr2 5 G 7
+chr2 6 A 7
+chr2 7 T 8
+chr2 8 A 8
+chr2 9 C 9
+chr2 10 T 9
+chr2 11 C 10
+chr2 12 G 10
+chr2 13 A 11
+chr2 52 T 5
+chr2 53 A 5
+chr2 54 T 5
+chr2 55 T 5
+chr2 56 C 5
+chr2 57 T 5
+chr2 58 T 6
+chr2 59 A 6
+chr2 77 C 6
+chr2 78 G 6
+chr2 79 T 7
+chr2 80 C 7
+chr2 81 G 7
+chr2 82 A 8
+chr2 83 A 8
+chr2 84 T 8
+chr2 85 G 8
+chr2 86 C 9
+chr2 87 G 9
+chr2 88 G 10
+chr2 89 G 10
+chr3 60 C 6
+chr3 61 T 6
+chr3 62 C 6
+chr3 63 C 7
+chr3 64 A 7
+chr3 65 T 7
+chr3 66 A 7
diff -r 5f927f52191c -r 3ac95cd927d7 test-data/column_join_out3.pileup
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/column_join_out3.pileup Fri Mar 26 12:00:55 2010 -0400
@@ -0,0 +1,70 @@
+chr1 1 C 1 ^:.
+chr1 2 G 2 .^:.
+chr1 3 A 2 ..
+chr1 4 C 2 ..
+chr1 5 T 3 ..^:.
+chr1 6 G 3 ..^:,
+chr1 7 C 4 .N.,
+chr1 8 A 4 ...,
+chr1 9 T 5 ..C.,
+chr1 10 G 5 N...,
+chr1 11 A 5 .C..,
+chr1 12 C 5 ..N.,
+chr1 42 T 1 ^:. C 1 ^:.
+chr1 43 G 2 .^:. C 2 .^:.
+chr1 44 T 2 .. T 2 ..
+chr1 45 C 3 ..^:. A 3 ..^:.
+chr1 46 G 3 ..^:. G 4 ...^:.
+chr1 47 T 4 ...^:, A 5 ....^:,
+chr1 48 A 4 .N., T 5 ...N,
+chr1 49 C 5 ...., G 5 ....,
+chr1 50 A 5 ..G., A 5 .G..,
+chr1 51 A 5 A..., G 5 ....,
+chr1 52 A 5 ....,
+chr1 53 G 5 ..N.,
+chr2 1 T 6 .C...,
+chr2 2 G 6 ..N..,
+chr2 3 C 7 ..C...,
+chr2 4 G 7 .G....,
+chr2 5 G 7 ...N..,
+chr2 6 A 7 ..T...,
+chr2 7 T 8 ...C...,
+chr2 8 A 8 ..A....,
+chr2 9 C 9 .GA..N..,
+chr2 10 T 9 ........,
+chr2 11 C 10 .>>..T...,
+chr2 12 G 10 .N..G....,
+chr2 13 A 11 ....A..T..,
+chr2 14 G 11 ..N.......
+chr2 15 C 11 A.....NG..
+chr2 16 T 11 ...C.....G
+chr2 17 C 12 G......TN..
+chr2 18 A 12 N......G..A
+chr2 19 A 13 .......NN...
+chr2 20 C 13 ..GT.......N
+chr2 52 T 5 .N..,
+chr2 53 A 5 ....,
+chr2 54 T 5 ....,
+chr2 55 T 5 ....,
+chr2 56 C 5 ....,
+chr2 57 T 5 ....,
+chr2 58 T 6 .N...,
+chr2 59 A 6 .....,
+chr2 77 C 6 .G...,
+chr2 78 G 6 ..N..,
+chr2 79 T 7 ..N...,
+chr2 80 C 7 .G....,
+chr2 81 G 7 ...A..,
+chr2 82 A 8 ...G...,
+chr2 83 A 8 ...T...,
+chr2 84 T 8 ..A....,
+chr2 85 G 8 .GA....,
+chr2 86 C 9 ........,
+chr2 87 G 9 ....T...,
+chr3 60 C 6 ...G.,
+chr3 61 T 6 ..N..,
+chr3 62 C 6 ...A.,
+chr3 63 C 7 .N....,
+chr3 64 A 7 ...G..,
+chr3 65 T 7 ...AA.,
+chr3 66 A 7 ....N.,
diff -r 5f927f52191c -r 3ac95cd927d7 test/functional/test_get_data.py
--- a/test/functional/test_get_data.py Fri Mar 26 09:51:03 2010 -0400
+++ b/test/functional/test_get_data.py Fri Mar 26 12:00:55 2010 -0400
@@ -575,5 +575,22 @@
self.check_history_for_string( 'Pasted Entry' )
self.check_history_for_string( 'hello world' )
self.delete_history( id=self.security.encode_id( history.id ) )
+ def test_0165_upload_file( self ):
+ """Test uploading 1.pileup, NOT setting the file format"""
+ self.check_history_for_string( 'Your history is empty' )
+ history = sa_session.query( galaxy.model.History ) \
+ .filter( and_( galaxy.model.History.table.c.deleted==False,
+ galaxy.model.History.table.c.user_id==admin_user.id ) ) \
+ .order_by( desc( galaxy.model.History.table.c.create_time ) ) \
+ .first()
+ self.upload_file( '1.pileup' )
+ hda = sa_session.query( galaxy.model.HistoryDatasetAssociation ) \
+ .order_by( desc( galaxy.model.HistoryDatasetAssociation.table.c.create_time ) ) \
+ .first()
+ assert hda is not None, "Problem retrieving hda from database"
+ self.verify_dataset_correctness( '1.pileup', hid=str( hda.hid ) )
+ self.check_history_for_string( '1.pileup format: <span class="pileup">pileup</span>, database: \? Info: uploaded file' )
+ self.check_metadata_for_string( 'value="1.pileup" value="\?" Change data type selected value="pileup" selected="yes"' )
+ self.delete_history( id=self.security.encode_id( history.id ) )
def test_9999_clean_up( self ):
self.logout()
diff -r 5f927f52191c -r 3ac95cd927d7 tool_conf.xml.sample
--- a/tool_conf.xml.sample Fri Mar 26 09:51:03 2010 -0400
+++ b/tool_conf.xml.sample Fri Mar 26 12:00:55 2010 -0400
@@ -61,6 +61,7 @@
<tool file="filters/compare.xml"/>
<tool file="new_operations/subtract_query.xml"/>
<tool file="stats/grouping.xml" />
+ <tool file="new_operations/column_join.xml" />
</section>
<section name="Convert Formats" id="convert">
<tool file="filters/axt_to_concat_fasta.xml" />
1
0
15 Apr '10
details: http://www.bx.psu.edu/hg/galaxy/rev/5f927f52191c
changeset: 3564:5f927f52191c
user: James Taylor <james(a)jamestaylor.org>
date: Fri Mar 26 09:51:03 2010 -0400
description:
Add template for structured history display
diffstat:
templates/history/display_structured.mako | 124 ++++++++++++++++++++++++++++++
1 files changed, 124 insertions(+), 0 deletions(-)
diffs (129 lines):
diff -r 9ed4a26508ea -r 5f927f52191c templates/history/display_structured.mako
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/templates/history/display_structured.mako Fri Mar 26 09:51:03 2010 -0400
@@ -0,0 +1,124 @@
+<%inherit file="/base.mako"/>
+<%namespace file="/root/history_common.mako" import="render_dataset" />
+
+<%def name="stylesheets()">
+ ${parent.stylesheets()}
+ ${h.css( "history" )}
+ <style type="text/css">
+ body {
+ background: white;
+ padding: 5px;
+ }
+
+ .clickable {
+ cursor: pointer;
+ }
+
+ .workflow {
+ border: solid gray 1px;
+ border-left-width: 5px;
+ }
+
+ .workflow > .header {
+ background: lightgray;
+ padding: 5px 10px;
+
+ font-weight: bold;
+ }
+
+ .workflow > .body {
+ border-top: solid gray 1px;
+ padding: 5px;
+ }
+
+ div.toolForm {
+ margin: 5px 0;
+ border-left-width: 5px;
+ }
+ div.toolFormBody {
+ padding: 5px 5px;
+ }
+ </style>
+</%def>
+
+<%def name="javascripts()">
+ ${parent.javascripts()}
+ <script type="text/javascript">
+ $(function(){
+
+ $(".workflow, .tool").each( function() {
+ var body = $(this).children( ".body" );
+ $(this).children( ".header" ).click( function() {
+ body.toggle();
+ }).addClass( "clickable" );
+ // body.hide();
+ });
+
+ $(".historyItem").each( function() {
+ var id = this.id;
+ var body = $(this).children( "div.historyItemBody" );
+ var peek = body.find( "pre.peek" )
+ $(this).children( ".historyItemTitleBar" ).find( ".historyItemTitle" ).wrap( "<a href='#'></a>" ).click( function() {
+ if ( body.is(":visible") ) {
+ // Hiding stuff here
+ if ( $.browser.mozilla ) { peek.css( "overflow", "hidden" ) }
+ body.slideUp( "fast" );
+ } else {
+ // Showing stuff here
+ body.slideDown( "fast", function() {
+ if ( $.browser.mozilla ) { peek.css( "overflow", "auto" ); }
+ });
+ }
+ return false;
+ });
+ body.hide();
+ });
+ });
+ </script>
+</%def>
+
+<%def name="render_item( entity, children )">
+<%
+entity_name = entity.__class__.__name__
+if entity_name == "HistoryDatasetAssociation":
+ render_item_hda( entity, children )
+elif entity_name == "Job":
+ render_item_job( entity, children )
+elif entity_name == "WorkflowInvocation":
+ render_item_wf( entity, children )
+%>
+</%def>
+
+<%def name="render_item_hda( hda, children )">
+ ${render_dataset( hda, hda.hid )}
+</%def>
+
+<%def name="render_item_job( job, children )">
+
+ <div class="tool toolForm">
+ <div class="header toolFormTitle">Tool: ${trans.app.toolbox.tools_by_id[job.tool_id].name}</div>
+ <div class="body toolFormBody">
+ %for e, c in children:
+ ${render_item( e, c )}
+ %endfor
+ </div>
+ </div>
+
+</%def>
+
+<%def name="render_item_wf( wf, children )">
+
+ <div class="workflow">
+ <div class="header">Workflow: ${wf.workflow.name}</div>
+ <div class="body">
+ %for e, c in children:
+ ${render_item( e, c )}
+ %endfor
+ </div>
+ </div>
+
+</%def>
+
+%for entity, children in items:
+ ${render_item( entity, children )}
+%endfor
\ No newline at end of file
1
0
15 Apr '10
details: http://www.bx.psu.edu/hg/galaxy/rev/9ed4a26508ea
changeset: 3563:9ed4a26508ea
user: fubar: ross Lazarus at gmail period com
date: Thu Mar 25 23:07:14 2010 -0400
description:
added sim_size as a way of comparing (eg) .png outputs
diffstat:
test/base/twilltestcase.py | 6 ++++++
1 files changed, 6 insertions(+), 0 deletions(-)
diffs (16 lines):
diff -r 0890f7bf9d49 -r 9ed4a26508ea test/base/twilltestcase.py
--- a/test/base/twilltestcase.py Thu Mar 25 15:21:57 2010 -0400
+++ b/test/base/twilltestcase.py Thu Mar 25 23:07:14 2010 -0400
@@ -749,6 +749,12 @@
self.files_re_match( local_name, temp_name, attributes=attributes )
elif compare == 're_match_multiline':
self.files_re_match_multiline( local_name, temp_name, attributes=attributes )
+ elif compare == 'sim_size':
+ delta = attributes.get('delta','100')
+ s1 = len(data)
+ s2 = os.path.getsize(local_name)
+ if abs(s1-s2) > int(delta):
+ raise Exception, 'Files %s=%db but %s=%db - compare (delta=%s) failed' % (temp_name,s1,local_name,s2,delta)
else:
raise Exception, 'Unimplemented Compare type: %s' % compare
except AssertionError, err:
1
0