[galaxy-commits] [hg] galaxy 3792: More tweaks to some snp/wga composite output t...
Nate Coraor
nate at bx.psu.edu
Tue May 25 08:52:53 EDT 2010
details: http://www.bx.psu.edu/hg/galaxy/rev/2d49a94c8d28
changeset: 3792:2d49a94c8d28
user: fubar: ross Lazarus at gmail period com
date: Thu May 20 12:38:35 2010 -0400
description:
More tweaks to some snp/wga composite output test comparisons - all png/pdf should be sim_size rather than lines_diff
Updated test outputs for snp/wga tools
Testing a new hgignore so welcome.html should not be overwritten
diffstat:
lib/galaxy/datatypes/converters/pbed_ldreduced_converter.py | 119 +
lib/galaxy/datatypes/converters/pbed_ldreduced_converter.xml | 18 +
lib/galaxy/datatypes/genetics.py | 51 +-
static/welcome.html | 6 +-
test-data/rgtestouts/rgEigPCA/Rplots.pdf | 46 +-
test-data/rgtestouts/rgEigPCA/rgEigPCAtest1.R | 2 +-
test-data/rgtestouts/rgEigPCA/rgEigPCAtest1.html | 31 +-
test-data/rgtestouts/rgEigPCA/rgEigPCAtest1_PCAPlot.pdf | 50 +-
test-data/rgtestouts/rgEigPCA/rgEigPCAtest1_eigensoftplot.pdf.pdf | 0
test-data/rgtestouts/rgEigPCA/rgEigPCAtest1_eigensoftplot.pdf.ps | 2 +-
test-data/rgtestouts/rgEigPCA/rgEigPCAtest1_eval.xls | 2 +-
test-data/rgtestouts/rgEigPCA/rgEigPCAtest1_log.txt | 6 +-
test-data/rgtestouts/rgEigPCA/rgEigPCAtest1_pca.xls | 80 +-
test-data/rgtestouts/rgEigPCA/rgEigPCAtest1_pca.xls.par | 6 +-
test-data/rgtestouts/rgGRR/Log_rgGRRtest1.txt | 18 +-
test-data/rgtestouts/rgGRR/rgGRRtest1.html | 37 +-
test-data/rgtestouts/rgGRR/rgGRRtest1.svg | 529 ++-
test-data/rgtestouts/rgGRR/rgGRRtest1_table.xls | 1562 +++++-----
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 | 16 +-
test-data/rgtestouts/rgHaploView/alljoin.pdf | 0
test-data/rgtestouts/rgHaploView/allnup.pdf | 0
test-data/rgtestouts/rgHaploView/rgHaploViewtest1.html | 16 +-
test-data/rgtestouts/rgHaploView/rgHaploViewtest1.ped.LD.PNG | 0
test-data/rgtestouts/rgHaploView/rgHaploViewtest1.ped.TAGS | 18 +-
test-data/rgtestouts/rgHaploView/rgHaploViewtest1.ped.TESTS | 14 +-
test-data/rgtestouts/rgQC/FQNormtinywga_s_het_cum.jpg | 0
test-data/rgtestouts/rgQC/FQNormtinywga_s_het_cum.pdf | 182 +-
test-data/rgtestouts/rgQC/Ranked_Subject_Missing_Genotype.xls | 36 +-
test-data/rgtestouts/rgQC/SubjectDetails_rgQCtest1.xls | 72 +-
test-data/rgtestouts/rgQC/ldp_tinywga.bed | 2 +-
test-data/rgtestouts/rgQC/ldp_tinywga.bim | 10 +-
test-data/rgtestouts/rgQC/ldp_tinywga.log | 18 +-
test-data/rgtestouts/rgQC/rgQCtest1.html | 208 +-
test-data/rgtestouts/rgQC/tinywga.het | 80 +-
test-data/rgtestouts/rgQC/tinywga.log | 6 +-
test-data/rgtestouts/rgQC/tinywga.prune.in | 10 +-
test-data/rgtestouts/rgQC/tinywga.prune.out | 10 +-
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 | 50 +-
test-data/rgtestouts/rgQC/tinywga_fracmiss_cum.jpg | 0
test-data/rgtestouts/rgQC/tinywga_fracmiss_cum.pdf | 52 +-
test-data/rgtestouts/rgQC/tinywga_s_het.jpg | 0
test-data/rgtestouts/rgQC/tinywga_s_het.pdf | 343 +-
test-data/rgtestouts/rgQC/tinywga_s_het_cum.jpg | 0
test-data/rgtestouts/rgQC/tinywga_s_het_cum.pdf | 182 +-
test/functional/test_toolbox.py | 2 +-
tools/rgenetics/rgEigPCA.xml | 2 +-
tools/rgenetics/rgGRR.xml | 2 +-
tools/rgenetics/rgLDIndep.xml | 4 +-
tools/rgenetics/rgQC.xml | 10 +-
tools/rgenetics/rgutils.py | 81 -
63 files changed, 2104 insertions(+), 1887 deletions(-)
diffs (truncated from 5382 to 3000 lines):
diff -r 7f95e51e06f7 -r 2d49a94c8d28 lib/galaxy/datatypes/converters/pbed_ldreduced_converter.py
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/lib/galaxy/datatypes/converters/pbed_ldreduced_converter.py Thu May 20 12:38:35 2010 -0400
@@ -0,0 +1,119 @@
+# converter for ldreduced rgenetics datatype
+# used for grr and eigenstrat - shellfish if we get around to it
+#
+
+import os,sys,tempfile,subprocess,time
+
+from galaxy import eggs
+
+prog="pbed_ldreduced_converter.py"
+
+galhtmlprefix = """<?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 %s 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">
+"""
+
+plinke = 'plink'
+
+
+def timenow():
+ """return current time as a string
+ """
+ return time.strftime('%d/%m/%Y %H:%M:%S', time.localtime(time.time()))
+
+
+def pruneLD(plinktasks=[],cd='./',vclbase = []):
+ """
+ """
+ fplog,plog = tempfile.mkstemp()
+ alog = []
+ alog.append('## Rgenetics: http://rgenetics.org Galaxy Tools rgQC.py Plink pruneLD runner\n')
+ for task in plinktasks: # each is a list
+ vcl = vclbase + task
+ sto = file(plog,'w')
+ x = subprocess.Popen(' '.join(vcl),shell=True,stdout=sto,stderr=sto,cwd=cd)
+ retval = x.wait()
+ sto.close()
+ try:
+ lplog = file(plog,'r').readlines()
+ lplog = [x for x in lplog if x.find('Pruning SNP') == -1]
+ alog += lplog
+ alog.append('\n')
+ os.unlink(plog) # no longer needed
+ except:
+ alog.append('### %s Strange - no std out from plink when running command line\n%s\n' % (timenow(),' '.join(vcl)))
+ return alog
+
+
+def makeLDreduced(basename,infpath=None,outfpath=None,plinke='plink',forcerebuild=False,returnFname=False,
+ winsize="60", winmove="40", r2thresh="0.1" ):
+ """ not there so make and leave in output dir for post job hook to copy back into input extra files path for next time
+ """
+ ldr = basename # we store ld reduced and thinned data
+ ldreduced = os.path.join(outfpath,ldr) # note where this is going
+ outbase = os.path.join(outfpath,basename)
+ inbase = os.path.join(infpath)
+ loglines = []
+ ldbedname = '%s.bed' % ldreduced
+ bedname = '%s.bed' % basename
+ ldbedfn = os.path.join(infpath,ldbedname)
+ bedfn = os.path.join(infpath,bedname)
+ bmap = os.path.join(infpath,'%s.bim' % basename)
+ plinktasks = []
+ vclbase = [plinke,'--noweb']
+ plinktasks += [['--bfile',inbase,'--indep-pairwise %s %s %s' % (winsize,winmove,r2thresh),'--out %s' % outbase],
+ ['--bfile',inbase,'--extract %s.prune.in --make-bed --out %s' % (outbase, outbase)]]
+ vclbase = [plinke,'--noweb']
+ loglines = pruneLD(plinktasks=plinktasks,cd=outfpath,vclbase = vclbase)
+
+def main():
+ """
+ need to work with rgenetics composite datatypes
+ so in and out are html files with data in extrafiles path
+ <command interpreter="python">
+ pbed_ldreduced_converter.py '$input1.extra_files_path/$input1.metadata.base_name' '$winsize' '$winmove' '$r2thresh'
+ '$output1' '$output1.files_path' 'plink'
+ </command>
+ """
+ nparm = 7
+ if len(sys.argv) < nparm:
+ sys.stderr.write('## %s called with %s - needs %d parameters \n' % (prog,sys.argv,nparm))
+ sys.exit(1)
+ inpedfilepath = sys.argv[1]
+ base_name = os.path.split(inpedfilepath)[-1]
+ winsize = sys.argv[2]
+ winmove = sys.argv[3]
+ r2thresh = sys.argv[4]
+ outhtmlname = sys.argv[5]
+ outfilepath = sys.argv[6]
+ try:
+ os.makedirs(outfilepath)
+ except:
+ pass
+ plink = sys.argv[7]
+ makeLDreduced(base_name,infpath=inpedfilepath,outfpath=outfilepath,plinke=plink,forcerebuild=False,returnFname=False,
+ winsize=winsize,winmove=winmove,r2thresh=r2thresh)
+ f = file(outhtmlname,'w')
+ f.write(galhtmlprefix % prog)
+ flist = os.listdir(outfilepath)
+ s1 = '## Rgenetics: http://rgenetics.org Galaxy Tools %s %s' % (prog,timenow()) # becomes info
+ s2 = 'Input %s, winsize=%s, winmove=%s, r2thresh=%s' % (base_name,winsize,winmove,r2thresh)
+ print '%s %s' % (s1,s2)
+ f.write('<div>%s\n%s\n<ol>' % (s1,s2))
+ for i, data in enumerate( flist ):
+ f.write('<li><a href="%s">%s</a></li>\n' % (os.path.split(data)[-1],os.path.split(data)[-1]))
+ f.write("</div></body></html>")
+ f.close()
+
+
+if __name__ == "__main__":
+ main()
+
diff -r 7f95e51e06f7 -r 2d49a94c8d28 lib/galaxy/datatypes/converters/pbed_ldreduced_converter.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/lib/galaxy/datatypes/converters/pbed_ldreduced_converter.xml Thu May 20 12:38:35 2010 -0400
@@ -0,0 +1,18 @@
+<tool id="pbed2ldindepconvert" name="Convert plink pbed to ld reduced format" version="0.01">
+ <!-- <description>__NOT_USED_CURRENTLY_FOR_CONVERTERS__</description> -->
+ <!-- Used on the metadata edit page. -->
+ <command interpreter="python">
+ pbed_ldreduced_converter.py '$input1.extra_files_path/$input1.metadata.base_name' '60' '55' '0.1' '$output1' '$output1.files_path' 'plink'
+ </command>
+ <inputs>
+ <page>
+ <param format="pbed" name="input1" type="data" label="Choose a compressed Plink binary format genotype file"/>
+ </page>
+ </inputs>
+ <outputs>
+ <data format="ldindep" name="output1" metadata_source="input1"/>
+ </outputs>
+ <help>
+ </help>
+</tool>
+
diff -r 7f95e51e06f7 -r 2d49a94c8d28 lib/galaxy/datatypes/genetics.py
--- a/lib/galaxy/datatypes/genetics.py Wed May 19 10:28:41 2010 -0400
+++ b/lib/galaxy/datatypes/genetics.py Thu May 20 12:38:35 2010 -0400
@@ -349,18 +349,6 @@
return True
-class ldIndep(Rgenetics):
- """
- LD (a good measure of redundancy of information) depleted Plink Binary compressed 2bit/geno
- """
- file_ext="ldreduced"
-
- def __init__( self, **kwd ):
- Rgenetics.__init__(self, **kwd)
- self.add_composite_file( '%s_INDEP.bim', substitute_name_with_metadata = 'base_name', is_binary = True )
- self.add_composite_file( '%s_INDEP.bed', substitute_name_with_metadata = 'base_name', is_binary = True )
- self.add_composite_file( '%s_INDEP.fam', substitute_name_with_metadata = 'base_name', is_binary = True )
-
class SNPMatrix(Rgenetics):
"""
@@ -396,8 +384,8 @@
def __init__( self, **kwd ):
Rgenetics.__init__(self, **kwd)
- self.add_composite_file( '%s.ped', description = 'Pedigree File', substitute_name_with_metadata = 'base_name', is_binary = True )
- self.add_composite_file( '%s.map', description = 'Map File', substitute_name_with_metadata = 'base_name', is_binary = True )
+ self.add_composite_file( '%s.ped', description = 'Pedigree File', substitute_name_with_metadata = 'base_name', is_binary = False )
+ self.add_composite_file( '%s.map', description = 'Map File', substitute_name_with_metadata = 'base_name', is_binary = False )
class Pphe(Rgenetics):
@@ -408,7 +396,7 @@
def __init__( self, **kwd ):
Rgenetics.__init__(self, **kwd)
- self.add_composite_file( '%s.pphe', description = 'Plink Phenotype File', substitute_name_with_metadata = 'base_name', is_binary = True )
+ self.add_composite_file( '%s.pphe', description = 'Plink Phenotype File', substitute_name_with_metadata = 'base_name', is_binary = False )
@@ -432,7 +420,8 @@
def __init__( self, **kwd ):
Rgenetics.__init__(self, **kwd)
- self.add_composite_file( '%s.phe', description = 'Phenotype File', substitute_name_with_metadata = 'base_name' )
+ self.add_composite_file( '%s.phe', description = 'Phenotype File', substitute_name_with_metadata = 'base_name',
+ is_binary = False )
@@ -445,7 +434,8 @@
def __init__( self, **kwd ):
Rgenetics.__init__(self, **kwd)
- self.add_composite_file( '%s.fped', description = 'FBAT format pedfile', substitute_name_with_metadata = 'base_name' )
+ self.add_composite_file( '%s.fped', description = 'FBAT format pedfile', substitute_name_with_metadata = 'base_name',
+ is_binary = False )
class Pbed(Rgenetics):
@@ -456,9 +446,24 @@
def __init__( self, **kwd ):
Rgenetics.__init__(self, **kwd)
- self.add_composite_file( '%s.bim', substitute_name_with_metadata = 'base_name', is_binary = True )
+ self.add_composite_file( '%s.bim', substitute_name_with_metadata = 'base_name', is_binary = False )
self.add_composite_file( '%s.bed', substitute_name_with_metadata = 'base_name', is_binary = True )
- self.add_composite_file( '%s.fam', substitute_name_with_metadata = 'base_name', is_binary = True )
+ self.add_composite_file( '%s.fam', substitute_name_with_metadata = 'base_name', is_binary = False )
+
+class ldIndep(Rgenetics):
+ """
+ LD (a good measure of redundancy of information) depleted Plink Binary compressed 2bit/geno
+ This is really a plink binary, but some tools work better with less redundancy so are constrained to
+ these files
+ """
+ file_ext="ldreduced"
+
+ def __init__( self, **kwd ):
+ Rgenetics.__init__(self, **kwd)
+ self.add_composite_file( '%s.bim', substitute_name_with_metadata = 'base_name', is_binary = False )
+ self.add_composite_file( '%s.bed', substitute_name_with_metadata = 'base_name', is_binary = True )
+ self.add_composite_file( '%s.fam', substitute_name_with_metadata = 'base_name', is_binary = False )
+
class Eigenstratgeno(Rgenetics):
"""
@@ -470,9 +475,9 @@
def __init__( self, **kwd ):
Rgenetics.__init__(self, **kwd)
- self.add_composite_file( '%s.eigenstratgeno', substitute_name_with_metadata = 'base_name', is_binary = True )
- self.add_composite_file( '%s.ind', substitute_name_with_metadata = 'base_name', is_binary = True )
- self.add_composite_file( '%s.map', substitute_name_with_metadata = 'base_name', is_binary = True )
+ self.add_composite_file( '%s.eigenstratgeno', substitute_name_with_metadata = 'base_name', is_binary = False )
+ self.add_composite_file( '%s.ind', substitute_name_with_metadata = 'base_name', is_binary = False )
+ self.add_composite_file( '%s.map', substitute_name_with_metadata = 'base_name', is_binary = False )
@@ -524,7 +529,7 @@
def __init__( self, **kwd ):
Html.__init__(self,**kwd)
self.add_composite_file( '%s.pheno', description = 'Phenodata tab text file',
- substitute_name_with_metadata = 'base_name', is_binary=True)
+ substitute_name_with_metadata = 'base_name', is_binary=False)
def generate_primary_file( self, dataset = None ):
"""
diff -r 7f95e51e06f7 -r 2d49a94c8d28 static/welcome.html
--- a/static/welcome.html Wed May 19 10:28:41 2010 -0400
+++ b/static/welcome.html Thu May 20 12:38:35 2010 -0400
@@ -8,12 +8,12 @@
<body>
<div class="document">
<div class="warningmessagelarge">
- <strong>Welcome to the <a href="http://rgenetics.org">Rgenetics</a> development site</strong>
+ <strong>Hello world! It's running...</strong>
<hr>
- This is a volatile and experimental resource - use the <a href="http://usegalaxy.org">main galaxy</a> for real research
+ To customize this page edit <code>static/welcome.html</code>
</div>
<br/>
- <img src="images/Armitagep_manhattan.png" alt="One click manhattan plot anyone?" style="display: block; margin-left: auto; margin-right: auto;" />
+ <img src="images/noodles.png" alt="WWFSMD?" style="display: block; margin-left: auto; margin-right: auto;" />
<hr/>
This project is supported in part by <a target="_blank" class="reference" href="http://www.nsf.gov">NSF</a>, <a target="_blank" class="reference" href="http://www.genome.gov">NHGRI</a>, and <a target="_blank" class="reference" href="http://www.huck.psu.edu">the Huck Institutes of the Life Sciences</a>.
</div>
diff -r 7f95e51e06f7 -r 2d49a94c8d28 test-data/rgtestouts/rgEigPCA/Rplots.pdf
--- a/test-data/rgtestouts/rgEigPCA/Rplots.pdf Wed May 19 10:28:41 2010 -0400
+++ b/test-data/rgtestouts/rgEigPCA/Rplots.pdf Thu May 20 12:38:35 2010 -0400
@@ -2,8 +2,8 @@
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diff -r 7f95e51e06f7 -r 2d49a94c8d28 test-data/rgtestouts/rgEigPCA/rgEigPCAtest1.R
--- a/test-data/rgtestouts/rgEigPCA/rgEigPCAtest1.R Wed May 19 10:28:41 2010 -0400
+++ b/test-data/rgtestouts/rgEigPCA/rgEigPCAtest1.R Thu May 20 12:38:35 2010 -0400
@@ -16,4 +16,4 @@
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 09/05/2010 21:23:43
+#R script autogenerated by rgenetics/rgutils.py on 19/05/2010 15:14:48
diff -r 7f95e51e06f7 -r 2d49a94c8d28 test-data/rgtestouts/rgEigPCA/rgEigPCAtest1.html
--- a/test-data/rgtestouts/rgEigPCA/rgEigPCAtest1.html Wed May 19 10:28:41 2010 -0400
+++ b/test-data/rgtestouts/rgEigPCA/rgEigPCAtest1.html Thu May 20 12:38:35 2010 -0400
@@ -9,27 +9,30 @@
</head>
<body>
<div class="document">
-<h4>Output from rgEigPCA.py run at 09/05/2010 21:23:43<br/>
+<h4>Output from rgEigPCA.py run at 19/05/2010 15:14:48<br/>
</h4>
-newfilepath=/share/shared/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>
+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.html">rgEigPCAtest1.html </a></li>
-<li><a href="rgEigPCAtest1_pca.xls.par">rgEigPCAtest1_pca.xls.par (338 B)</a></li>
+<div class="document">All Files:<ol><li><a href="Rplots.pdf">Rplots.pdf (813 B)</a></li>
+<li><a href="rgEigPCAtest1.R">rgEigPCAtest1.R (1.6 KB)</a></li>
+<li><a href="rgEigPCAtest1.html">rgEigPCAtest1.html </a></li>
<li><a href="rgEigPCAtest1.txt">rgEigPCAtest1.txt (3.3 KB)</a></li>
-<li><a href="rgEigPCAtest1_log.txt">rgEigPCAtest1_log.txt (6.1 KB)</a></li>
-<li><a href="rgEigPCAtest1_PCAPlot.pdf">rgEigPCAtest1_PCAPlot.pdf (10.4 KB)</a></li>
+<li><a href="rgEigPCAtest1_PCAPlot.pdf">rgEigPCAtest1_PCAPlot.pdf (7.9 KB)</a></li>
+<li><a href="rgEigPCAtest1_PCAPlot.pdf.png">rgEigPCAtest1_PCAPlot.pdf.png (27.1 KB)</a></li>
+<li><a href="rgEigPCAtest1_eigensoftplot.pdf.pdf">rgEigPCAtest1_eigensoftplot.pdf.pdf (2.1 KB)</a></li>
+<li><a href="rgEigPCAtest1_eigensoftplot.pdf.ps">rgEigPCAtest1_eigensoftplot.pdf.ps (13.6 KB)</a></li>
+<li><a href="rgEigPCAtest1_eigensoftplot.pdf.xtxt">rgEigPCAtest1_eigensoftplot.pdf.xtxt (257 B)</a></li>
<li><a href="rgEigPCAtest1_eval.xls">rgEigPCAtest1_eval.xls (507 B)</a></li>
-<li><a href="rgEigPCAtest1_pca.xls">rgEigPCAtest1_pca.xls (1.2 KB)</a></li>
-<li><a href="rgEigPCAtest1.R">rgEigPCAtest1.R (1.6 KB)</a></li>
-<li><a href="Rplots.pdf">Rplots.pdf (3.3 KB)</a></li>
+<li><a href="rgEigPCAtest1_log.txt">rgEigPCAtest1_log.txt (6.0 KB)</a></li>
+<li><a href="rgEigPCAtest1_pca.xls">rgEigPCAtest1_pca.xls (1.3 KB)</a></li>
<li><a href="rgEigPCAtest1_pca.xls.evec">rgEigPCAtest1_pca.xls.evec (3.3 KB)</a></li>
-<li><a href="rgEigPCAtest1_PCAPlot.pdf.png">rgEigPCAtest1_PCAPlot.pdf.png (27.1 KB)</a></li>
+<li><a href="rgEigPCAtest1_pca.xls.par">rgEigPCAtest1_pca.xls.par (311 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: /share/shared/galaxy/test-data/tinywga.ped
-snpname: /share/shared/galaxy/test-data/tinywga.map
-indivname: /share/shared/galaxy/test-data/tinywga.ped
+genotypename: /opt/galaxy/test-data/tinywga.bed
+snpname: /opt/galaxy/test-data/tinywga.bim
+indivname: /opt/galaxy/test-data/tinywga.fam
evecoutname: rgEigPCAtest1_pca.xls.evec
evaloutname: rgEigPCAtest1_eval.xls
altnormstyle: NO
@@ -153,5 +156,5 @@
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 /share/shared/galaxy/test-data/tinywga.ped -a /share/shared/galaxy/test-data/tinywga.map -b /share/shared/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
+smartpca.perl -i /opt/galaxy/test-data/tinywga.bed -a /opt/galaxy/test-data/tinywga.bim -b /opt/galaxy/test-data/tinywga.fam -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 7f95e51e06f7 -r 2d49a94c8d28 test-data/rgtestouts/rgEigPCA/rgEigPCAtest1_PCAPlot.pdf
--- a/test-data/rgtestouts/rgEigPCA/rgEigPCAtest1_PCAPlot.pdf Wed May 19 10:28:41 2010 -0400
+++ b/test-data/rgtestouts/rgEigPCA/rgEigPCAtest1_PCAPlot.pdf Thu May 20 12:38:35 2010 -0400
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diff -r 7f95e51e06f7 -r 2d49a94c8d28 test-data/rgtestouts/rgEigPCA/rgEigPCAtest1_eigensoftplot.pdf.pdf
Binary file test-data/rgtestouts/rgEigPCA/rgEigPCAtest1_eigensoftplot.pdf.pdf has changed
diff -r 7f95e51e06f7 -r 2d49a94c8d28 test-data/rgtestouts/rgEigPCA/rgEigPCAtest1_eigensoftplot.pdf.ps
--- a/test-data/rgtestouts/rgEigPCA/rgEigPCAtest1_eigensoftplot.pdf.ps Wed May 19 10:28:41 2010 -0400
+++ b/test-data/rgtestouts/rgEigPCA/rgEigPCAtest1_eigensoftplot.pdf.ps Thu May 20 12:38:35 2010 -0400
@@ -1,6 +1,6 @@
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diff -r 7f95e51e06f7 -r 2d49a94c8d28 test-data/rgtestouts/rgEigPCA/rgEigPCAtest1_eval.xls
--- a/test-data/rgtestouts/rgEigPCA/rgEigPCAtest1_eval.xls Wed May 19 10:28:41 2010 -0400
+++ b/test-data/rgtestouts/rgEigPCA/rgEigPCAtest1_eval.xls Thu May 20 12:38:35 2010 -0400
@@ -24,6 +24,7 @@
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diff -r 7f95e51e06f7 -r 2d49a94c8d28 test-data/rgtestouts/rgEigPCA/rgEigPCAtest1_log.txt
--- a/test-data/rgtestouts/rgEigPCA/rgEigPCAtest1_log.txt Wed May 19 10:28:41 2010 -0400
+++ b/test-data/rgtestouts/rgEigPCA/rgEigPCAtest1_log.txt Thu May 20 12:38:35 2010 -0400
@@ -1,9 +1,9 @@
parameter file: rgEigPCAtest1_pca.xls.par
### THE INPUT PARAMETERS
##PARAMETER NAME: VALUE
-genotypename: /share/shared/galaxy/test-data/tinywga.ped
-snpname: /share/shared/galaxy/test-data/tinywga.map
-indivname: /share/shared/galaxy/test-data/tinywga.ped
+genotypename: /opt/galaxy/test-data/tinywga.bed
+snpname: /opt/galaxy/test-data/tinywga.bim
+indivname: /opt/galaxy/test-data/tinywga.fam
evecoutname: rgEigPCAtest1_pca.xls.evec
evaloutname: rgEigPCAtest1_eval.xls
altnormstyle: NO
diff -r 7f95e51e06f7 -r 2d49a94c8d28 test-data/rgtestouts/rgEigPCA/rgEigPCAtest1_pca.xls
--- a/test-data/rgtestouts/rgEigPCA/rgEigPCAtest1_pca.xls Wed May 19 10:28:41 2010 -0400
+++ b/test-data/rgtestouts/rgEigPCA/rgEigPCAtest1_pca.xls Thu May 20 12:38:35 2010 -0400
@@ -3,43 +3,43 @@
7.7400
7.2550
4.2710
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+ 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
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+ -0.2453 -0.0165 -0.0856 0.0221
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+ 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 7f95e51e06f7 -r 2d49a94c8d28 test-data/rgtestouts/rgEigPCA/rgEigPCAtest1_pca.xls.par
--- a/test-data/rgtestouts/rgEigPCA/rgEigPCAtest1_pca.xls.par Wed May 19 10:28:41 2010 -0400
+++ b/test-data/rgtestouts/rgEigPCA/rgEigPCAtest1_pca.xls.par Thu May 20 12:38:35 2010 -0400
@@ -1,6 +1,6 @@
-genotypename: /share/shared/galaxy/test-data/tinywga.ped
-snpname: /share/shared/galaxy/test-data/tinywga.map
-indivname: /share/shared/galaxy/test-data/tinywga.ped
+genotypename: /opt/galaxy/test-data/tinywga.bed
+snpname: /opt/galaxy/test-data/tinywga.bim
+indivname: /opt/galaxy/test-data/tinywga.fam
evecoutname: rgEigPCAtest1_pca.xls.evec
evaloutname: rgEigPCAtest1_eval.xls
altnormstyle: NO
diff -r 7f95e51e06f7 -r 2d49a94c8d28 test-data/rgtestouts/rgGRR/Log_rgGRRtest1.txt
--- a/test-data/rgtestouts/rgGRR/Log_rgGRRtest1.txt Wed May 19 10:28:41 2010 -0400
+++ b/test-data/rgtestouts/rgGRR/Log_rgGRRtest1.txt Thu May 20 12:38:35 2010 -0400
@@ -1,14 +1,14 @@
-Reading genotypes for 40 subjects and 5 markers
+Reading genotypes for 40 subjects and 25 markers
Calculating 780 pairs...
Estimated time is 0.00 to 0.00 seconds ...
-T1: 0.00482821464539 T2: 0.0623338222504 T3: 0.000771522521973 TOT: 0.0691449642181 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)=1.73 sdev(mean)=0.20, mean(sdev)=0.38 sdev(sdev)=0.23
-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)=1.63 sdev(mean)=0.20, mean(sdev)=0.54 sdev(sdev)=0.22
-Relstate unrelated: mean(mean)=1.55 sdev(mean)=0.24, mean(sdev)=0.59 sdev(sdev)=0.24
-Relstate unknown: mean(mean)=nan sdev(mean)=0.00, mean(sdev)=nan sdev(sdev)=0.00
+T1: 0.00254368782043 T2: 0.018296957016 T3: 0.000444173812866 TOT: 0.022047996521 0 pairs with no (or not enough) comparable genotypes (0.0%)
+Relstate dupe (n=0): mean(mean)=nan sdev(mean)=0.00, mean(sdev)=nan sdev(sdev)=0.00
+Relstate parentchild (n=26): mean(mean)=1.68 sdev(mean)=0.19, mean(sdev)=0.39 sdev(sdev)=0.19
+Relstate sibpairs (n=0): mean(mean)=nan sdev(mean)=0.00, mean(sdev)=nan sdev(sdev)=0.00
+Relstate halfsibs (n=0): mean(mean)=nan sdev(mean)=0.00, mean(sdev)=nan sdev(sdev)=0.00
+Relstate parents (n=40): mean(mean)=1.46 sdev(mean)=0.25, mean(sdev)=0.55 sdev(sdev)=0.17
+Relstate unrelated (n=714): mean(mean)=1.44 sdev(mean)=0.21, mean(sdev)=0.58 sdev(sdev)=0.15
+Relstate unknown (n=0): 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 7f95e51e06f7 -r 2d49a94c8d28 test-data/rgtestouts/rgGRR/rgGRRtest1.html
--- a/test-data/rgtestouts/rgGRR/rgGRRtest1.html Wed May 19 10:28:41 2010 -0400
+++ b/test-data/rgtestouts/rgGRR/rgGRRtest1.html Thu May 20 12:38:35 2010 -0400
@@ -9,39 +9,26 @@
</head>
<body>
<div class="document">
-<h4><div>Output from rgGRR.py run at 09/05/2010 21:23:42<br>
+<h4><div>Output from rgGRR.py run at 19/05/2010 15:14:41<br>
</h4>
If you need to rerun this analysis, the command line was
-<pre>'/share/shared/galaxy/tools/rgenetics/rgGRR.py' '/share/shared/galaxy/test-data/tinywga' 'tinywga' '/share/shared/galaxy/test-data/rgtestouts/rgGRR/rgGRRtest1.html' '/share/shared/galaxy/test-data/rgtestouts/rgGRR' 'rgGRRtest1' '100' '6' 'true'</pre>
+<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>
-<li><a href="rgGRRtest1.html">rgGRRtest1.html</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 5 markers
-
+</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...
-
Estimated time is 0.00 to 0.00 seconds ...
-
-T1: 0.00482821464539 T2: 0.0623338222504 T3: 0.000771522521973 TOT: 0.0691449642181 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)=1.73 sdev(mean)=0.20, mean(sdev)=0.38 sdev(sdev)=0.23
-
-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)=1.63 sdev(mean)=0.20, mean(sdev)=0.54 sdev(sdev)=0.22
-
-Relstate unrelated: mean(mean)=1.55 sdev(mean)=0.24, mean(sdev)=0.59 sdev(sdev)=0.24
-
-Relstate unknown: mean(mean)=nan sdev(mean)=0.00, mean(sdev)=nan sdev(sdev)=0.00
-
+T1: 0.00254368782043 T2: 0.018296957016 T3: 0.000444173812866 TOT: 0.022047996521 0 pairs with no (or not enough) comparable genotypes (0.0%)
+Relstate dupe (n=0): mean(mean)=nan sdev(mean)=0.00, mean(sdev)=nan sdev(sdev)=0.00
+Relstate parentchild (n=26): mean(mean)=1.68 sdev(mean)=0.19, mean(sdev)=0.39 sdev(sdev)=0.19
+Relstate sibpairs (n=0): mean(mean)=nan sdev(mean)=0.00, mean(sdev)=nan sdev(sdev)=0.00
+Relstate halfsibs (n=0): mean(mean)=nan sdev(mean)=0.00, mean(sdev)=nan sdev(sdev)=0.00
+Relstate parents (n=40): mean(mean)=1.46 sdev(mean)=0.25, mean(sdev)=0.55 sdev(sdev)=0.17
+Relstate unrelated (n=714): mean(mean)=1.44 sdev(mean)=0.21, mean(sdev)=0.58 sdev(sdev)=0.15
+Relstate unknown (n=0): 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 7f95e51e06f7 -r 2d49a94c8d28 test-data/rgtestouts/rgGRR/rgGRRtest1.svg
--- a/test-data/rgtestouts/rgGRR/rgGRRtest1.svg Wed May 19 10:28:41 2010 -0400
+++ b/test-data/rgtestouts/rgGRR/rgGRRtest1.svg Thu May 20 12:38:35 2010 -0400
@@ -17,7 +17,7 @@
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);
@@ -28,7 +28,7 @@
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) {
@@ -36,7 +36,7 @@
}
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;
@@ -133,7 +133,7 @@
document.getElementById("otRmean").textContent = "relmean="+rmean;
document.getElementById("otRsdev").textContent = "relsdev="+rsdev;
document.getElementById("otHead").setAttribute('fill', fill);
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+
var tt = document.getElementById("otTip");
tt.setAttribute("transform", "translate("+x+","+y+")");
tt.setAttribute('visibility', 'visible');
@@ -147,7 +147,7 @@
document.getElementById("otTip").setAttributeNS(null, 'visibility', 'hidden');
}
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+ ]]>
</script>
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<g style="fill:none; stroke:#dddddd; stroke-width:1; stroke-dasharray:2,2; text-anchor:end; shape-rendering:crispEdges">
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<text x="15" y="215" style="fill:black; stroke:none" font-size="12" font-family="Arial" >Zscore 4 to 15</text>
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<text x="15" y="235" style="fill:black; stroke:none" font-size="12" font-family="Arial" >Zscore lt 4</text>
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<g id="checkboxes">
</g>
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@@ -232,7 +232,7 @@
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<text x="564" y="630" >1.5</text>
<text x="842" y="630" >1.75</text>
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</g>
<g transform="rotate(270)" style="fill:black; stroke:none" font-size="17" font-family="Arial">
@@ -247,103 +247,492 @@
<!-- Plot Title -->
<g style="fill:black; stroke:none" font-size="18" font-family="Arial">
- <text x="425" y="-30">rgGRRtest1 (40 subjects, 5 snp)</text>
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diff -r 7f95e51e06f7 -r 2d49a94c8d28 test-data/rgtestouts/rgGRR/rgGRRtest1_table.xls
--- a/test-data/rgtestouts/rgGRR/rgGRRtest1_table.xls Wed May 19 10:28:41 2010 -0400
+++ b/test-data/rgtestouts/rgGRR/rgGRRtest1_table.xls Thu May 20 12:38:35 2010 -0400
@@ -1,781 +1,781 @@
-fid1 iid1 fid2 iid2 mean sdev zmean zsdev geno relcode
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-101_1 101_3 1.400000 0.894427 0.105472 0.511563 5 5
-101_1 105_1 1.400000 0.894427 -0.219631 -0.070847 5 5
-101_1 105_2 1.400000 0.894427 0.821646 -0.397216 5 5
-101_1 105_3 1.400000 0.894427 0.821646 -0.397216 5 5
-101_1 112_1 1.400000 0.894427 -0.219631 1.712469 5 5
-101_1 112_2 1.400000 0.894427 -1.260908 1.532838 5 5
-101_1 112_3 1.400000 0.894427 -0.219631 -0.070847 5 5
-101_1 117_1 1.400000 0.894427 0.821646 -0.397216 5 5
-101_1 117_2 1.400000 0.894427 0.821646 -0.397216 5 5
-101_1 117_3 1.400000 0.894427 0.821646 -0.397216 5 5
-101_1 12_1 1.400000 0.894427 0.821646 -0.397216 5 5
-101_1 12_2 1.400000 0.894427 0.821646 -0.397216 5 5
-101_1 12_3 1.400000 0.894427 0.821646 -0.397216 5 5
-101_1 13_1 1.400000 0.894427 -0.219631 -0.070847 5 5
-101_1 13_2 1.400000 0.894427 -0.219631 1.712469 5 5
-101_1 13_3 1.400000 0.894427 0.821646 -0.397216 5 5
-101_1 1334_1 1.400000 0.894427 0.821646 -0.397216 5 5
-101_1 1334_10 1.400000 0.894427 -0.219631 -0.070847 5 5
-101_1 1334_11 1.400000 0.894427 -1.260908 1.532838 5 5
-101_1 1334_12 1.400000 0.894427 -1.260908 1.532838 5 5
-101_1 1334_13 1.400000 0.894427 -0.219631 -0.070847 5 5
-101_1 1334_2 1.400000 0.894427 -1.260908 1.532838 5 5
-101_1 1340_1 1.400000 0.894427 -0.219631 -0.070847 5 5
-101_1 1340_10 1.400000 0.894427 -0.219631 -0.070847 5 5
-101_1 1340_11 1.400000 0.894427 -0.219631 -0.070847 5 5
-101_1 1340_12 1.400000 0.894427 0.821646 -0.397216 5 5
-101_1 1340_2 1.400000 0.894427 -1.260908 -0.397216 5 5
-101_1 1340_9 1.400000 0.894427 -1.260908 1.532838 5 5
-101_1 1341_1 1.400000 0.894427 0.821646 -0.397216 5 5
-101_1 1341_11 1.400000 0.894427 -1.260908 1.532838 5 5
-101_1 1341_12 1.400000 0.894427 -0.219631 -0.070847 5 5
-101_1 1341_13 1.400000 0.894427 -0.219631 1.712469 5 5
-101_1 1341_14 1.400000 0.894427 -0.219631 1.712469 5 5
-101_1 1341_2 1.400000 0.894427 -0.219631 1.712469 5 5
-101_1 1344_1 1.400000 0.894427 -1.260908 1.532838 5 5
-101_1 1344_12 1.400000 0.894427 -1.260908 -0.397216 5 5
-101_1 1344_13 1.400000 0.894427 -1.260908 -0.397216 5 5
-101_1 1345_12 1.400000 0.894427 -0.219631 -0.070847 5 5
-101_2 101_3 1.400000 0.894427 -0.132290 0.048238 5 5
-101_2 105_1 1.400000 0.894427 -0.219631 -0.070847 5 5
-101_2 105_2 1.400000 0.894427 1.029902 -0.619941 5 5
-101_2 105_3 1.400000 0.894427 1.029902 -0.619941 5 5
-101_2 112_1 1.400000 0.894427 0.196880 1.267018 5 5
-101_2 112_2 1.400000 0.894427 -0.636142 1.267018 5 5
-101_2 112_3 1.400000 0.894427 0.196880 -0.195857 5 5
-101_2 117_1 1.400000 0.894427 1.029902 -0.619941 5 5
-101_2 117_2 1.400000 0.894427 1.029902 -0.619941 5 5
-101_2 117_3 1.400000 0.894427 1.029902 -0.619941 5 5
-101_2 12_1 1.400000 0.894427 1.029902 -0.619941 5 5
-101_2 12_2 1.400000 0.894427 1.029902 -0.619941 5 5
-101_2 12_3 1.400000 0.894427 1.029902 -0.619941 5 5
-101_2 13_1 1.400000 0.894427 0.196880 -0.195857 5 5
-101_2 13_2 1.400000 0.894427 -0.219631 1.712469 5 5
-101_2 13_3 1.400000 0.894427 1.029902 -0.619941 5 5
-101_2 1334_1 1.400000 0.894427 1.029902 -0.619941 5 5
-101_2 1334_10 1.400000 0.894427 0.196880 -0.195857 5 5
-101_2 1334_11 1.400000 0.894427 -0.636142 1.267018 5 5
-101_2 1334_12 1.400000 0.894427 -0.636142 1.267018 5 5
-101_2 1334_13 1.400000 0.894427 0.196880 -0.195857 5 5
-101_2 1334_2 1.400000 0.894427 -0.636142 1.267018 5 5
-101_2 1340_1 1.400000 0.894427 0.196880 -0.195857 5 5
-101_2 1340_10 1.400000 0.894427 0.196880 -0.195857 5 5
-101_2 1340_11 1.400000 0.894427 0.196880 -0.195857 5 5
-101_2 1340_12 1.400000 0.894427 1.029902 -0.619941 5 5
-101_2 1340_2 1.400000 0.894427 -0.636142 -0.195857 5 5
-101_2 1340_9 1.400000 0.894427 -0.636142 1.267018 5 5
-101_2 1341_1 1.400000 0.894427 1.029902 -0.619941 5 5
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-101_2 1341_12 1.400000 0.894427 0.196880 -0.195857 5 5
-101_2 1341_13 1.400000 0.894427 0.196880 1.267018 5 5
-101_2 1341_14 1.400000 0.894427 0.196880 1.267018 5 5
-101_2 1341_2 1.400000 0.894427 0.196880 1.267018 5 5
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-101_2 1344_13 1.400000 0.894427 -0.636142 -0.195857 5 5
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-101_3 105_2 1.400000 0.894427 -0.636142 -0.195857 5 5
-101_3 105_3 1.400000 0.894427 -0.636142 -0.195857 5 5
-101_3 112_1 1.400000 0.894427 -1.469163 1.023277 5 5
-101_3 112_2 1.400000 0.894427 -2.302185 1.712469 5 5
-101_3 112_3 1.400000 0.894427 0.196880 -0.195857 5 5
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-101_3 117_3 1.400000 0.894427 -0.636142 -0.195857 5 5
-101_3 12_1 1.400000 0.894427 1.029902 -0.619941 5 5
-101_3 12_2 1.400000 0.894427 1.029902 -0.619941 5 5
-101_3 12_3 1.400000 0.894427 -0.636142 -0.195857 5 5
-101_3 13_1 1.400000 0.894427 0.196880 -0.195857 5 5
-101_3 13_2 1.400000 0.894427 -1.260908 1.532838 5 5
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-101_3 1334_11 1.400000 0.894427 -2.302185 1.712469 5 5
-101_3 1334_12 1.400000 0.894427 -0.636142 1.267018 5 5
-101_3 1334_13 1.400000 0.894427 -1.469163 -0.619941 5 5
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-101_3 1340_1 1.400000 0.894427 -1.469163 -0.619941 5 5
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-101_3 1341_1 1.400000 0.894427 -0.636142 -0.195857 5 5
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-1334_13 1340_2 1.400000 0.894427 1.029902 -0.619941 5 5
-1334_13 1340_9 1.400000 0.894427 -0.636142 -0.195857 5 5
-1334_13 1341_1 1.400000 0.894427 1.029902 -0.619941 5 5
-1334_13 1341_11 1.400000 0.894427 -0.636142 -0.195857 5 5
-1334_13 1341_12 1.400000 0.894427 0.196880 -0.195857 5 5
-1334_13 1341_13 1.400000 0.894427 0.196880 -0.195857 5 5
-1334_13 1341_14 1.400000 0.894427 0.196880 -0.195857 5 5
-1334_13 1341_2 1.400000 0.894427 0.196880 -0.195857 5 5
-1334_13 1344_1 1.400000 0.894427 -0.636142 -0.195857 5 5
-1334_13 1344_12 1.400000 0.894427 1.029902 -0.619941 5 5
-1334_13 1344_13 1.400000 0.894427 1.029902 -0.619941 5 5
-1334_13 1345_12 1.400000 0.894427 0.196880 -0.195857 5 5
-1334_2 1340_1 1.400000 0.894427 -0.636142 -0.195857 5 5
-1334_2 1340_10 1.400000 0.894427 -0.636142 -0.195857 5 5
-1334_2 1340_11 1.400000 0.894427 -0.636142 -0.195857 5 5
-1334_2 1340_12 1.400000 0.894427 0.196880 -0.195857 5 5
-1334_2 1340_2 1.400000 0.894427 -1.469163 1.023277 5 5
-1334_2 1340_9 1.400000 0.894427 1.862924 -2.506901 5 5
-1334_2 1341_1 1.400000 0.894427 0.196880 -0.195857 5 5
-1334_2 1341_11 1.400000 0.894427 0.196880 1.267018 5 5
-1334_2 1341_12 1.400000 0.894427 1.029902 -0.619941 5 5
-1334_2 1341_13 1.400000 0.894427 1.029902 -0.619941 5 5
-1334_2 1341_14 1.400000 0.894427 1.029902 -0.619941 5 5
-1334_2 1341_2 1.400000 0.894427 1.029902 -0.619941 5 5
-1334_2 1344_1 1.400000 0.894427 -3.135207 2.115187 5 5
-1334_2 1344_12 1.400000 0.894427 -1.469163 1.023277 5 5
-1334_2 1344_13 1.400000 0.894427 -1.469163 1.023277 5 5
-1334_2 1345_12 1.400000 0.894427 1.029902 -0.619941 5 5
-1340_1 1340_10 1.400000 0.894427 1.351962 -1.627597 5 5
-1340_1 1340_11 1.400000 0.894427 -0.132290 0.048238 5 5
-1340_1 1340_12 1.400000 0.894427 0.875635 -0.416708 5 5
-1340_1 1340_2 1.400000 0.894427 -1.140216 0.048238 5 5
-1340_1 1340_9 1.400000 0.894427 -1.639614 0.715736 5 5
-1340_1 1341_1 1.400000 0.894427 1.029902 -0.619941 5 5
-1340_1 1341_11 1.400000 0.894427 -0.636142 -0.195857 5 5
-1340_1 1341_12 1.400000 0.894427 0.196880 -0.195857 5 5
-1340_1 1341_13 1.400000 0.894427 0.196880 -0.195857 5 5
-1340_1 1341_14 1.400000 0.894427 0.196880 -0.195857 5 5
-1340_1 1341_2 1.400000 0.894427 0.196880 -0.195857 5 5
-1340_1 1344_1 1.400000 0.894427 -2.302185 0.476644 5 5
-1340_1 1344_12 1.400000 0.894427 -0.636142 -0.195857 5 5
-1340_1 1344_13 1.400000 0.894427 -0.636142 -0.195857 5 5
-1340_1 1345_12 1.400000 0.894427 0.196880 -0.195857 5 5
-1340_10 1340_11 1.400000 0.894427 -0.132290 0.048238 5 5
-1340_10 1340_12 1.400000 0.894427 0.875635 -0.416708 5 5
-1340_10 1340_2 1.400000 0.894427 -1.140216 0.048238 5 5
-1340_10 1340_9 1.400000 0.894427 -1.140216 0.048238 5 5
-1340_10 1341_1 1.400000 0.894427 1.029902 -0.619941 5 5
-1340_10 1341_11 1.400000 0.894427 -0.636142 -0.195857 5 5
-1340_10 1341_12 1.400000 0.894427 0.196880 -0.195857 5 5
-1340_10 1341_13 1.400000 0.894427 0.196880 -0.195857 5 5
-1340_10 1341_14 1.400000 0.894427 0.196880 -0.195857 5 5
-1340_10 1341_2 1.400000 0.894427 0.196880 -0.195857 5 5
-1340_10 1344_1 1.400000 0.894427 -2.302185 0.476644 5 5
-1340_10 1344_12 1.400000 0.894427 -0.636142 -0.195857 5 5
-1340_10 1344_13 1.400000 0.894427 -0.636142 -0.195857 5 5
-1340_10 1345_12 1.400000 0.894427 0.196880 -0.195857 5 5
-1340_11 1340_12 1.400000 0.894427 0.875635 -0.416708 5 5
-1340_11 1340_2 1.400000 0.894427 0.354770 0.285726 5 5
-1340_11 1340_9 1.400000 0.894427 -1.140216 0.048238 5 5
-1340_11 1341_1 1.400000 0.894427 1.029902 -0.619941 5 5
-1340_11 1341_11 1.400000 0.894427 -0.636142 -0.195857 5 5
-1340_11 1341_12 1.400000 0.894427 0.196880 -0.195857 5 5
-1340_11 1341_13 1.400000 0.894427 0.196880 -0.195857 5 5
-1340_11 1341_14 1.400000 0.894427 0.196880 -0.195857 5 5
-1340_11 1341_2 1.400000 0.894427 0.196880 -0.195857 5 5
-1340_11 1344_1 1.400000 0.894427 -0.636142 -0.195857 5 5
-1340_11 1344_12 1.400000 0.894427 1.029902 -0.619941 5 5
-1340_11 1344_13 1.400000 0.894427 1.029902 -0.619941 5 5
-1340_11 1345_12 1.400000 0.894427 0.196880 -0.195857 5 5
-1340_12 1340_2 1.400000 0.894427 -0.642422 0.715736 5 5
-1340_12 1340_9 1.400000 0.894427 -0.132290 0.048238 5 5
-1340_12 1341_1 1.400000 0.894427 1.862924 -2.506901 5 5
-1340_12 1341_11 1.400000 0.894427 0.196880 -0.195857 5 5
-1340_12 1341_12 1.400000 0.894427 1.029902 -0.619941 5 5
-1340_12 1341_13 1.400000 0.894427 1.029902 -0.619941 5 5
-1340_12 1341_14 1.400000 0.894427 1.029902 -0.619941 5 5
-1340_12 1341_2 1.400000 0.894427 1.029902 -0.619941 5 5
-1340_12 1344_1 1.400000 0.894427 -1.469163 1.023277 5 5
-1340_12 1344_12 1.400000 0.894427 0.196880 -0.195857 5 5
-1340_12 1344_13 1.400000 0.894427 0.196880 -0.195857 5 5
-1340_12 1345_12 1.400000 0.894427 1.029902 -0.619941 5 5
-1340_2 1340_9 1.400000 0.894427 -2.148141 1.384838 5 5
-1340_2 1341_1 1.400000 0.894427 0.196880 -0.195857 5 5
-1340_2 1341_11 1.400000 0.894427 0.196880 -0.195857 5 5
-1340_2 1341_12 1.400000 0.894427 -0.636142 1.267018 5 5
-1340_2 1341_13 1.400000 0.894427 -0.636142 -0.195857 5 5
-1340_2 1341_14 1.400000 0.894427 -0.636142 -0.195857 5 5
-1340_2 1341_2 1.400000 0.894427 -0.636142 -0.195857 5 5
-1340_2 1344_1 1.400000 0.894427 0.196880 -0.195857 5 5
-1340_2 1344_12 1.400000 0.894427 1.862924 -2.506901 5 5
-1340_2 1344_13 1.400000 0.894427 1.862924 -2.506901 5 5
-1340_2 1345_12 1.400000 0.894427 -0.636142 1.267018 5 5
-1340_9 1341_1 1.400000 0.894427 0.196880 -0.195857 5 5
-1340_9 1341_11 1.400000 0.894427 0.196880 1.267018 5 5
-1340_9 1341_12 1.400000 0.894427 1.029902 -0.619941 5 5
-1340_9 1341_13 1.400000 0.894427 1.029902 -0.619941 5 5
-1340_9 1341_14 1.400000 0.894427 1.029902 -0.619941 5 5
-1340_9 1341_2 1.400000 0.894427 1.029902 -0.619941 5 5
-1340_9 1344_1 1.400000 0.894427 -3.135207 2.115187 5 5
-1340_9 1344_12 1.400000 0.894427 -1.469163 1.023277 5 5
-1340_9 1344_13 1.400000 0.894427 -1.469163 1.023277 5 5
-1340_9 1345_12 1.400000 0.894427 1.029902 -0.619941 5 5
-1341_1 1341_11 1.400000 0.894427 -0.642422 0.715736 5 5
-1341_1 1341_12 1.400000 0.894427 0.354770 0.285726 5 5
-1341_1 1341_13 1.400000 0.894427 0.875635 -0.416708 5 5
-1341_1 1341_14 1.400000 0.894427 0.875635 -0.416708 5 5
-1341_1 1341_2 1.400000 0.894427 0.875635 -0.416708 5 5
-1341_1 1344_1 1.400000 0.894427 -1.469163 1.023277 5 5
-1341_1 1344_12 1.400000 0.894427 0.196880 -0.195857 5 5
-1341_1 1344_13 1.400000 0.894427 0.196880 -0.195857 5 5
-1341_1 1345_12 1.400000 0.894427 1.029902 -0.619941 5 5
-1341_11 1341_12 1.400000 0.894427 -1.140216 1.652064 5 5
-1341_11 1341_13 1.400000 0.894427 0.875635 -0.416708 5 5
-1341_11 1341_14 1.400000 0.894427 0.875635 -0.416708 5 5
-1341_11 1341_2 1.400000 0.894427 0.875635 -0.416708 5 5
-1341_11 1344_1 1.400000 0.894427 -1.469163 2.115187 5 5
-1341_11 1344_12 1.400000 0.894427 0.196880 -0.195857 5 5
-1341_11 1344_13 1.400000 0.894427 0.196880 -0.195857 5 5
-1341_11 1345_12 1.400000 0.894427 -0.636142 1.267018 5 5
-1341_12 1341_13 1.400000 0.894427 -0.132290 0.048238 5 5
-1341_12 1341_14 1.400000 0.894427 -0.132290 0.048238 5 5
-1341_12 1341_2 1.400000 0.894427 -0.132290 0.048238 5 5
-1341_12 1344_1 1.400000 0.894427 -2.302185 1.712469 5 5
-1341_12 1344_12 1.400000 0.894427 -0.636142 1.267018 5 5
-1341_12 1344_13 1.400000 0.894427 -0.636142 1.267018 5 5
-1341_12 1345_12 1.400000 0.894427 1.862924 -2.506901 5 5
-1341_13 1341_14 1.400000 0.894427 1.883560 -2.485480 5 5
-1341_13 1341_2 1.400000 0.894427 1.351962 -1.627597 5 5
-1341_13 1344_1 1.400000 0.894427 -2.302185 1.712469 5 5
-1341_13 1344_12 1.400000 0.894427 -0.636142 -0.195857 5 5
-1341_13 1344_13 1.400000 0.894427 -0.636142 -0.195857 5 5
-1341_13 1345_12 1.400000 0.894427 0.196880 -0.195857 5 5
-1341_14 1341_2 1.400000 0.894427 1.351962 -1.627597 5 5
-1341_14 1344_1 1.400000 0.894427 -2.302185 1.712469 5 5
-1341_14 1344_12 1.400000 0.894427 -0.636142 -0.195857 5 5
-1341_14 1344_13 1.400000 0.894427 -0.636142 -0.195857 5 5
-1341_14 1345_12 1.400000 0.894427 0.196880 -0.195857 5 5
-1341_2 1344_1 1.400000 0.894427 -2.302185 1.712469 5 5
-1341_2 1344_12 1.400000 0.894427 -0.636142 -0.195857 5 5
-1341_2 1344_13 1.400000 0.894427 -0.636142 -0.195857 5 5
-1341_2 1345_12 1.400000 0.894427 0.196880 -0.195857 5 5
-1344_1 1344_12 1.400000 0.894427 -0.642422 0.715735 5 5
-1344_1 1344_13 1.400000 0.894427 -0.642422 0.715735 5 5
-1344_1 1345_12 1.400000 0.894427 -2.302185 1.712469 5 5
-1344_12 1344_13 1.400000 0.894427 1.883560 -2.485480 5 5
-1344_12 1345_12 1.400000 0.894427 -0.636142 1.267018 5 5
-1344_13 1345_12 1.400000 0.894427 -0.636142 1.267018 5 5
+fid1_iid1 fid2_iid2 mean sdev zmean zsdev geno relcode pid1 mid1 pid2 mid2
+101_1 101_2 1.200000 0.577350 1.693329 -2.011511 25 parentchild 3 2 0 0
+101_1 101_3 1.200000 0.577350 -0.717628 0.612530 25 parentchild 3 2 0 0
+101_1 105_1 1.200000 0.577350 0.670010 -0.504142 25 unrelated 3 2 3 2
+101_1 105_2 1.200000 0.577350 0.870921 -0.566551 25 unrelated 3 2 0 0
+101_1 105_3 1.200000 0.577350 1.071833 -0.655899 25 unrelated 3 2 0 0
+101_1 112_1 1.200000 0.577350 -0.736371 0.779435 25 unrelated 3 2 3 2
+101_1 112_2 1.200000 0.577350 -0.937282 0.679102 25 unrelated 3 2 0 0
+101_1 112_3 1.200000 0.577350 -0.535459 -0.655899 25 unrelated 3 2 0 0
+101_1 117_1 1.200000 0.577350 0.067275 0.077804 25 unrelated 3 2 3 2
+101_1 117_2 1.200000 0.577350 0.469098 -0.467231 25 unrelated 3 2 0 0
+101_1 117_3 1.200000 0.577350 0.469098 0.077804 25 unrelated 3 2 0 0
+101_1 12_1 1.200000 0.577350 0.469098 -0.467230 25 unrelated 3 2 3 2
+101_1 12_2 1.200000 0.577350 0.469098 -0.467230 25 unrelated 3 2 0 0
+101_1 12_3 1.200000 0.577350 1.071833 -0.655899 25 unrelated 3 2 0 0
+101_1 13_1 1.200000 0.577350 -0.133637 -0.504142 25 unrelated 3 2 3 2
+101_1 13_2 1.200000 0.577350 -0.255930 0.042025 25 unrelated 3 2 0 0
+101_1 13_3 1.200000 0.577350 1.071832 -0.655899 25 unrelated 3 2 0 0
+101_1 1334_1 1.200000 0.577350 -0.133636 0.045908 25 unrelated 3 2 10 11
+101_1 1334_10 1.200000 0.577350 -0.334548 -0.566551 25 unrelated 3 2 0 0
+101_1 1334_11 1.200000 0.577350 -0.937282 0.679102 25 unrelated 3 2 0 0
+101_1 1334_12 1.200000 0.577350 -0.334548 -0.007823 25 unrelated 3 2 0 0
+101_1 1334_13 1.200000 0.577350 -0.133636 -0.504142 25 unrelated 3 2 0 0
+101_1 1334_2 1.200000 0.577350 -0.736370 1.194476 25 unrelated 3 2 12 13
+101_1 1340_1 1.200000 0.577350 -0.535459 -0.084293 25 unrelated 3 2 9 10
+101_1 1340_10 1.200000 0.577350 -0.535459 -0.084293 25 unrelated 3 2 0 0
+101_1 1340_11 1.200000 0.577350 -0.133636 -0.504142 25 unrelated 3 2 0 0
+101_1 1340_12 1.200000 0.577350 0.469098 -0.467231 25 unrelated 3 2 0 0
+101_1 1340_2 1.200000 0.577350 0.469098 -0.467231 25 unrelated 3 2 11 12
+101_1 1340_9 1.200000 0.577350 -2.142751 0.999931 25 unrelated 3 2 0 0
+101_1 1341_1 1.200000 0.577350 0.163363 -0.455013 25 unrelated 3 2 11 12
+101_1 1341_11 1.200000 0.577350 -0.334549 0.481281 25 unrelated 3 2 0 0
+101_1 1341_12 1.200000 0.577350 -0.937282 -0.925605 25 unrelated 3 2 0 0
+101_1 1341_13 1.200000 0.577350 -0.736371 0.779435 25 unrelated 3 2 0 0
+101_1 1341_14 1.200000 0.577350 -0.736371 0.779435 25 unrelated 3 2 0 0
+101_1 1341_2 1.200000 0.577350 -0.736371 0.779435 25 unrelated 3 2 13 14
+101_1 1344_1 1.200000 0.577350 -0.535459 0.413356 25 unrelated 3 2 12 13
+101_1 1344_12 1.200000 0.577350 0.469098 -0.467231 25 unrelated 3 2 0 0
+101_1 1344_13 1.200000 0.577350 0.469098 -0.467231 25 unrelated 3 2 0 0
+101_1 1345_12 1.200000 0.577350 -0.736370 -0.774446 25 unrelated 3 2 0 0
+101_2 101_3 1.200000 0.577350 0.236040 -0.228179 25 parents 0 0 0 0
+101_2 105_1 1.200000 0.577350 0.670010 -0.504142 25 unrelated 0 0 3 2
+101_2 105_2 1.200000 0.577350 0.943250 -0.598443 25 unrelated 0 0 0 0
+101_2 105_3 1.200000 0.577350 1.136125 -0.693367 25 unrelated 0 0 0 0
+101_2 112_1 1.200000 0.577350 -0.599751 0.780517 25 unrelated 0 0 3 2
+101_2 112_2 1.200000 0.577350 -0.792626 0.696771 25 unrelated 0 0 0 0
+101_2 112_3 1.200000 0.577350 -0.406876 -0.598443 25 unrelated 0 0 0 0
+101_2 117_1 1.200000 0.577350 0.171750 0.062100 25 unrelated 0 0 3 2
+101_2 117_2 1.200000 0.577350 0.557499 -0.483424 25 unrelated 0 0 0 0
+101_2 117_3 1.200000 0.577350 0.557499 0.042491 25 unrelated 0 0 0 0
+101_2 12_1 1.200000 0.577350 0.557499 -0.483423 25 unrelated 0 0 3 2
+101_2 12_2 1.200000 0.577350 0.557499 -0.483423 25 unrelated 0 0 0 0
+101_2 12_3 1.200000 0.577350 1.136124 -0.693367 25 unrelated 0 0 0 0
+101_2 13_1 1.200000 0.577350 -0.021126 -0.483423 25 unrelated 0 0 3 2
+101_2 13_2 1.200000 0.577350 -0.255930 0.042025 25 unrelated 0 0 0 0
+101_2 13_3 1.200000 0.577350 1.136124 -0.693367 25 unrelated 0 0 0 0
+101_2 1334_1 1.200000 0.577350 -0.021125 0.042491 25 unrelated 0 0 10 11
+101_2 1334_10 1.200000 0.577350 -0.214001 -0.528970 25 unrelated 0 0 0 0
+101_2 1334_11 1.200000 0.577350 -0.792626 0.696771 25 unrelated 0 0 0 0
+101_2 1334_12 1.200000 0.577350 -0.214001 0.002982 25 unrelated 0 0 0 0
+101_2 1334_13 1.200000 0.577350 -0.021126 -0.483424 25 unrelated 0 0 0 0
+101_2 1334_2 1.200000 0.577350 -0.599751 1.178851 25 unrelated 0 0 12 13
+101_2 1340_1 1.200000 0.577350 -0.406876 -0.057030 25 unrelated 0 0 9 10
+101_2 1340_10 1.200000 0.577350 -0.406876 -0.057030 25 unrelated 0 0 0 0
+101_2 1340_11 1.200000 0.577350 -0.021126 -0.483424 25 unrelated 0 0 0 0
+101_2 1340_12 1.200000 0.577350 0.557499 -0.483423 25 unrelated 0 0 0 0
+101_2 1340_2 1.200000 0.577350 0.557499 -0.483423 25 unrelated 0 0 11 12
+101_2 1340_9 1.200000 0.577350 -1.949876 1.086115 25 unrelated 0 0 0 0
+101_2 1341_1 1.200000 0.577350 0.268187 -0.455013 25 unrelated 0 0 11 12
+101_2 1341_11 1.200000 0.577350 -0.214002 0.471641 25 unrelated 0 0 0 0
+101_2 1341_12 1.200000 0.577350 -0.792626 -0.816040 25 unrelated 0 0 0 0
+101_2 1341_13 1.200000 0.577350 -0.599751 0.780517 25 unrelated 0 0 0 0
+101_2 1341_14 1.200000 0.577350 -0.599751 0.780517 25 unrelated 0 0 0 0
+101_2 1341_2 1.200000 0.577350 -0.599751 0.780517 25 unrelated 0 0 13 14
+101_2 1344_1 1.200000 0.577350 -0.406876 0.418047 25 unrelated 0 0 12 13
+101_2 1344_12 1.200000 0.577350 0.557499 -0.483423 25 unrelated 0 0 0 0
+101_2 1344_13 1.200000 0.577350 0.557499 -0.483423 25 unrelated 0 0 0 0
+101_2 1345_12 1.200000 0.577350 -0.599751 -0.693367 25 unrelated 0 0 0 0
+101_3 105_1 1.200000 0.577350 -1.540017 1.879362 25 unrelated 0 0 3 2
+101_3 105_2 1.200000 0.577350 0.171750 -0.460872 25 unrelated 0 0 0 0
+101_3 105_3 1.200000 0.577350 -0.792627 -0.242861 25 unrelated 0 0 0 0
+101_3 112_1 1.200000 0.577350 -0.599750 0.780517 25 unrelated 0 0 3 2
+101_3 112_2 1.200000 0.577350 -0.792626 2.157894 25 unrelated 0 0 0 0
+101_3 112_3 1.200000 0.577350 -0.021126 -0.483423 25 unrelated 0 0 0 0
+101_3 117_1 1.200000 0.577350 -0.599751 1.178851 25 unrelated 0 0 3 2
+101_3 117_2 1.200000 0.577350 1.329000 -0.816040 25 unrelated 0 0 0 0
+101_3 117_3 1.200000 0.577350 0.171750 0.062100 25 unrelated 0 0 0 0
+101_3 12_1 1.200000 0.577350 2.486250 -2.592124 25 unrelated 0 0 3 2
+101_3 12_2 1.200000 0.577350 2.486250 -2.592124 25 unrelated 0 0 0 0
+101_3 12_3 1.200000 0.577350 1.136124 -0.693367 25 unrelated 0 0 0 0
+101_3 13_1 1.200000 0.577350 1.521875 -0.969866 25 unrelated 0 0 3 2
+101_3 13_2 1.200000 0.577350 -0.255930 0.546459 25 unrelated 0 0 0 0
+101_3 13_3 1.200000 0.577350 1.136125 -0.693367 25 unrelated 0 0 0 0
+101_3 1334_1 1.200000 0.577350 -0.021126 -0.483424 25 unrelated 0 0 10 11
+101_3 1334_10 1.200000 0.577350 -0.599750 -0.693367 25 unrelated 0 0 0 0
+101_3 1334_11 1.200000 0.577350 -0.792626 2.157894 25 unrelated 0 0 0 0
+101_3 1334_12 1.200000 0.577350 -0.599751 0.345553 25 unrelated 0 0 0 0
+101_3 1334_13 1.200000 0.577350 -0.406876 -0.598443 25 unrelated 0 0 0 0
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diff -r 7f95e51e06f7 -r 2d49a94c8d28 test-data/rgtestouts/rgHaploView/1_rgHaploViewtest1.pdf
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diff -r 7f95e51e06f7 -r 2d49a94c8d28 test-data/rgtestouts/rgHaploView/2_HapMap_YRI_22.pdf
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diff -r 7f95e51e06f7 -r 2d49a94c8d28 test-data/rgtestouts/rgHaploView/Chromosome22YRI.LD.PNG
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diff -r 7f95e51e06f7 -r 2d49a94c8d28 test-data/rgtestouts/rgHaploView/Log_rgHaploViewtest1.txt
--- a/test-data/rgtestouts/rgHaploView/Log_rgHaploViewtest1.txt Wed May 19 10:28:41 2010 -0400
+++ b/test-data/rgtestouts/rgHaploView/Log_rgHaploViewtest1.txt Thu May 20 12:38:35 2010 -0400
@@ -1,7 +1,7 @@
-PATH=/share/apps:/share/shared/lx26-amd64/bin:/udd/rerla/bin:/share/shared/lx26-amd64/bin:/opt/gridengine/bin/lx26-amd64:/opt/gridengine/bin/lx26-amd64:/usr/kerberos/bin:/usr/java/latest/bin:/usr/local/bin:/bin:/usr/bin:/opt/eclipse:/opt/ganglia/bin:/opt/ganglia/sbin:/opt/maven/bin:/opt/openmpi/bin/:/opt/rocks/bin:/opt/rocks/sbin:/opt/gridengine/bin:/opt/gridengine:/bin/lx26-amd64:/usr/X11R6/bin
+PATH=/usr/kerberos/bin:/usr/local/bin:/bin:/usr/bin:/home/rerla/bin
## rgHaploView.py looking for 10 rs (['rs2283802', 'rs2267000', 'rs16997606', 'rs4820537', 'rs3788347'])## rgHaploView.py: wrote 10 markers, 40 subjects for region
-## executing java -jar /share/shared/galaxy/tool-data/rg/bin/haploview.jar -n -memory 2048 -pairwiseTagging -pedfile /share/shared/galaxy/test-data/rgtestouts/rgHaploView/rgHaploViewtest1.ped -info /share/shared/galaxy/test-data/rgtestouts/rgHaploView/rgHaploViewtest1.info -tagrsqcounts -tagrsqcutoff 0.8 -ldcolorscheme RSQ -log /share/shared/galaxy/test-data/tinywga.log -maxDistance 200000 -compressedpng -chromosome 22 returned 0
+## executing java -jar /opt/galaxy/tool-data/rg/bin/haploview.jar -n -memory 2048 -pairwiseTagging -pedfile /opt/galaxy/test-data/rgtestouts/rgHaploView/rgHaploViewtest1.ped -info /opt/galaxy/test-data/rgtestouts/rgHaploView/rgHaploViewtest1.info -tagrsqcounts -tagrsqcutoff 0.8 -ldcolorscheme RSQ -log /opt/galaxy/test-data/tinywga.log -maxDistance 200000 -compressedpng -chromosome 22 returned 0
## executing mogrify -resize 800x400! *.PNG returned 0
## executing convert -resize 800x400! rgHaploViewtest1.ped.LD.PNG rgHaploViewtest1.tmp.png returned 0
## executing convert -pointsize 25 -fill maroon -draw "text 10,300 'rgHaploViewtest1'" rgHaploViewtest1.tmp.png 1_rgHaploViewtest1.png returned 0
@@ -12,16 +12,16 @@
## executing pdfjoin "*.pdf" --fitpaper true --outfile alljoin.pdf returned 0
## executing pdfnup alljoin.pdf --nup 1x2 --outfile allnup.pdf returned 0
*****************************************************
-Haploview 4.2 Java Version: 1.6.0_13
+Haploview 4.2 Java Version: 1.6.0_03
*****************************************************
-Arguments: -n -pairwiseTagging -pedfile /share/shared/galaxy/test-data/rgtestouts/rgHaploView/rgHaploViewtest1.ped -info /share/shared/galaxy/test-data/rgtestouts/rgHaploView/rgHaploViewtest1.info -tagrsqcounts -tagrsqcutoff 0.8 -ldcolorscheme RSQ -log /share/shared/galaxy/test-data/tinywga.log -maxDistance 200000 -compressedpng -chromosome 22
+Arguments: -n -pairwiseTagging -pedfile /opt/galaxy/test-data/rgtestouts/rgHaploView/rgHaploViewtest1.ped -info /opt/galaxy/test-data/rgtestouts/rgHaploView/rgHaploViewtest1.info -tagrsqcounts -tagrsqcutoff 0.8 -ldcolorscheme RSQ -log /opt/galaxy/test-data/tinywga.log -maxDistance 200000 -compressedpng -chromosome 22
Max LD comparison distance = 200000kb
-Using data file: /share/shared/galaxy/test-data/rgtestouts/rgHaploView/rgHaploViewtest1.ped
-Using marker information file: /share/shared/galaxy/test-data/rgtestouts/rgHaploView/rgHaploViewtest1.info
+Using data file: /opt/galaxy/test-data/rgtestouts/rgHaploView/rgHaploViewtest1.ped
+Using marker information file: /opt/galaxy/test-data/rgtestouts/rgHaploView/rgHaploViewtest1.info
10 out of 10 markers passed the MAF threshold.
10 out of 10 markers passed the Mendel threshold.
10 out of 10 markers passed the genotyping threshold.
@@ -33,11 +33,11 @@
Writing output to rgHaploViewtest1.ped.TESTS
Writing output to rgHaploViewtest1.ped.CHAPS
*****************************************************
-Haploview 4.2 Java Version: 1.6.0_13
+Haploview 4.2 Java Version: 1.6.0_03
*****************************************************
-Arguments: -n -chromosome 22 -panel YRI -hapmapDownload -startpos 21784 -endpos 21905 -ldcolorscheme RSQ -log /share/shared/galaxy/test-data/tinywga.log -maxDistance 200000 -compressedpng
+Arguments: -n -chromosome 22 -panel YRI -hapmapDownload -startpos 21784 -endpos 21905 -ldcolorscheme RSQ -log /opt/galaxy/test-data/tinywga.log -maxDistance 200000 -compressedpng
Max LD comparison distance = 200000kb
diff -r 7f95e51e06f7 -r 2d49a94c8d28 test-data/rgtestouts/rgHaploView/alljoin.pdf
Binary file test-data/rgtestouts/rgHaploView/alljoin.pdf has changed
diff -r 7f95e51e06f7 -r 2d49a94c8d28 test-data/rgtestouts/rgHaploView/allnup.pdf
Binary file test-data/rgtestouts/rgHaploView/allnup.pdf has changed
diff -r 7f95e51e06f7 -r 2d49a94c8d28 test-data/rgtestouts/rgHaploView/rgHaploViewtest1.html
--- a/test-data/rgtestouts/rgHaploView/rgHaploViewtest1.html Wed May 19 10:28:41 2010 -0400
+++ b/test-data/rgtestouts/rgHaploView/rgHaploViewtest1.html Thu May 20 12:38:35 2010 -0400
@@ -23,13 +23,13 @@
<li><a href="rgHaploViewtest1.ped.LD.PNG">rgHaploViewtest1.ped.LD.PNG - rgHaploViewtest1.ped.LD.PNG</a></li>
<li><a href="rgHaploViewtest1.ped.TAGS">rgHaploViewtest1.ped.TAGS - rgHaploViewtest1.ped.TAGS Tagger output</a></li>
<li><a href="rgHaploViewtest1.ped.TESTS">rgHaploViewtest1.ped.TESTS - rgHaploViewtest1.ped.TESTS Tagger output</a></li>
-</ol><br></div><div><hr>Job Log follows below (see Log_rgHaploViewtest1.txt)<pre>PATH=/share/apps:/share/shared/lx26-amd64/bin:/udd/rerla/bin:/share/shared/lx26-amd64/bin:/opt/gridengine/bin/lx26-amd64:/opt/gridengine/bin/lx26-amd64:/usr/kerberos/bin:/usr/java/latest/bin:/usr/local/bin:/bin:/usr/bin:/opt/eclipse:/opt/ganglia/bin:/opt/ganglia/sbin:/opt/maven/bin:/opt/openmpi/bin/:/opt/rocks/bin:/opt/rocks/sbin:/opt/gridengine/bin:/opt/gridengine:/bin/lx26-amd64:/usr/X11R6/bin
+</ol><br></div><div><hr>Job Log follows below (see Log_rgHaploViewtest1.txt)<pre>PATH=/usr/kerberos/bin:/usr/local/bin:/bin:/usr/bin:/home/rerla/bin
## rgHaploView.py looking for 10 rs (['rs2283802', 'rs2267000', 'rs16997606', 'rs4820537', 'rs3788347'])## rgHaploView.py: wrote 10 markers, 40 subjects for region
-## executing java -jar /share/shared/galaxy/tool-data/rg/bin/haploview.jar -n -memory 2048 -pairwiseTagging -pedfile /share/shared/galaxy/test-data/rgtestouts/rgHaploView/rgHaploViewtest1.ped -info /share/shared/galaxy/test-data/rgtestouts/rgHaploView/rgHaploViewtest1.info -tagrsqcounts -tagrsqcutoff 0.8 -ldcolorscheme RSQ -log /share/shared/galaxy/test-data/tinywga.log -maxDistance 200000 -compressedpng -chromosome 22 returned 0
+## executing java -jar /opt/galaxy/tool-data/rg/bin/haploview.jar -n -memory 2048 -pairwiseTagging -pedfile /opt/galaxy/test-data/rgtestouts/rgHaploView/rgHaploViewtest1.ped -info /opt/galaxy/test-data/rgtestouts/rgHaploView/rgHaploViewtest1.info -tagrsqcounts -tagrsqcutoff 0.8 -ldcolorscheme RSQ -log /opt/galaxy/test-data/tinywga.log -maxDistance 200000 -compressedpng -chromosome 22 returned 0
## executing mogrify -resize 800x400! *.PNG returned 0
@@ -51,7 +51,7 @@
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