[hg] galaxy 3593: Add rgtest.sh to generate test outputs

16 Apr 2010

details:   http://www.bx.psu.edu/hg/galaxy/rev/e1b63ac74b35
changeset: 3593:e1b63ac74b35
user:      fubar: ross Lazarus at gmail period com
date:      Thu Apr 01 14:25:27 2010 -0400
description:
Add rgtest.sh to generate test outputs
Minor changes to rgManQQ tool documentation
Minor fixes to rgQQ

diffstat:

 tools/rgenetics/rgManQQ.py  |   41 ++++++---
 tools/rgenetics/rgManQQ.xml |    3 +
 tools/rgenetics/rgQC.py     |   14 +++
 tools/rgenetics/rgtest.sh   |  182 ++++++++++++++++++++++++++++++++++++++++++++
 4 files changed, 227 insertions(+), 13 deletions(-)

diffs (343 lines):

diff -r 40e8c99829e0 -r e1b63ac74b35 tools/rgenetics/rgManQQ.py

--- a/tools/rgenetics/rgManQQ.py	Thu Apr 01 13:08:48 2010 -0400
+++ b/tools/rgenetics/rgManQQ.py	Thu Apr 01 14:25:27 2010 -0400
@@ -70,8 +70,9 @@
                            }
 
                 if (max.y=="max") maxy=ceiling(max(d$logp)) else maxy=max.y
-                if (maxy<8) maxy=8
-
+                maxy = max(maxy,1.1*genomewideline)
+                # if (maxy<8) maxy=8
+                # only makes sense if genome wide is assumed - we could have a fine mapping region?  
                 if (annotate) d.annotate=d[as.numeric(substr(d$SNP,3,100)) %in% SNPlist, ]
 
                 plot=qplot(pos,logp,data=d, ylab=expression(-log[10](italic(p))) , colour=factor(CHR))
@@ -83,11 +84,13 @@
                 plot=plot + opts(title=title)
                 plot=plot+opts(
                         panel.background=theme_blank(), 
-                        panel.grid.minor=theme_blank(),
                         axis.text.x=theme_text(size=size.x.labels, colour="grey50"), 
                         axis.text.y=theme_text(size=size.y.labels, colour="grey50"), 
                         axis.ticks=theme_segment(colour=NA)
                 )
+                #plot = plot + opts(panel.grid.y.minor=theme_blank(),panel.grid.y.major=theme_blank())
+                #plot = plot + opts(panel.grid.major=theme_blank())
+                 
                 if (suggestiveline) plot=plot+geom_hline(yintercept=suggestiveline,colour="blue", alpha=I(1/3))
                 if (genomewideline) plot=plot+geom_hline(yintercept=genomewideline,colour="red")
                 plot
@@ -120,11 +123,11 @@
 # instantiate rcode2 string with infile,chromcol,offsetcol,pvalscols,title before saving and running
 
 rcode2 = """rgqqMan = function(infile="%s",chromcolumn=%d, offsetcolumn=%d, pvalscolumns=%s, 
-     title="%s",grey=%d) {
-  d = read.table(infile,head=T,sep='\t')
-  print(paste('###',length(d[,1]),'values read from',infile,'read - now running plots',sep=' '))
-  for (pvalscolumn in pvalscolumns) {
-  if (pvalscolumn > 0) 
+title="%s",grey=%d) {
+d = read.table(infile,head=T,sep='\t')
+print(paste('###',length(d[,1]),'values read from',infile,'read - now running plots',sep=' '))
+for (pvalscolumn in pvalscolumns) {
+if (pvalscolumn > 0) 
      {
      cname = names(d)[pvalscolumn]
      mytitle = paste('p=',cname,', ',title,sep='')
@@ -154,12 +157,24 @@
 """
 
 
+def doManQQ(input_fname,chrom_col,offset_col,pval_cols,title,grey,ctitle,outdir):
+    """ draw a qq for pvals and a manhattan plot if chrom/offset <> 0
+    contains some R scripts as text strings - we substitute defaults into the calls
+    to make them do our bidding - and save the resulting code for posterity
+    this can be called externally, I guess...for QC eg?
+    """
+    
+    rcmd = '%s%s' % (rcode,rcode2 % (input_fname,chrom_col,offset_col,pval_cols,title,grey))
+    rlog,flist = RRun(rcmd=rcmd,title=ctitle,outdir=outdir)
+    return rlog,flist
+  
+
 def main():
     u = """<command interpreter="python">
         rgManQQ.py '$input_file' "$name" '$out_html' '$out_html.files_path' '$chrom_col' '$offset_col' '$pval_col'
     </command>
     """
-    print >> sys.stdout,'## rgManQQ.py. cl=',sys.argv
+    print >> sys.stdout,'## rgManQQ.py. cl= \n%s' % ' '.join(['"%s"' % x for x in sys.argv])
     npar = 8
     if len(sys.argv) < npar:
             print >> sys.stdout, '## error - too few command line parameters - wanting %d' % npar
@@ -177,13 +192,13 @@
     except:
          chrom_col = 0
     try:
-	offset_col = int(sys.argv[6]) + 1
+        offset_col = int(sys.argv[6]) + 1
     except:
         offset_col = 0
     p = sys.argv[7].strip().split(',')
     try:
         p = [int(x)+1 for x in p]
-	pval_cols = 'c(%s)' % ','.join(map(str,p))
+        pval_cols = 'c(%s)' % ','.join(map(str,p))
     except:
         pval_cols = 'c(0)'
     if chrom_col == 1 or offset_col == 1: # was passed as zero - do not do manhattan plots
@@ -192,8 +207,7 @@
     grey = 0
     if (sys.argv[8].lower() in ['1','true']):
        grey = 1
-    rcmd = '%s%s' % (rcode,rcode2 % (input_fname,chrom_col,offset_col,pval_cols,title,grey))
-    rlog,flist = RRun(rcmd=rcmd,title=ctitle,outdir=outdir)
+    rlog,flist = doManQQ(input_fname,chrom_col,offset_col,pval_cols,title,grey,ctitle,outdir)
     flist.sort()
     html = [galhtmlprefix % progname,]
     html.append('<h1>%s</h1>' % title)
@@ -221,6 +235,7 @@
     htmlf.write('\n')
     htmlf.close()
     
+  
 
 if __name__ == "__main__":
     main()
diff -r 40e8c99829e0 -r e1b63ac74b35 tools/rgenetics/rgManQQ.xml
--- a/tools/rgenetics/rgManQQ.xml	Thu Apr 01 13:08:48 2010 -0400
+++ b/tools/rgenetics/rgManQQ.xml	Thu Apr 01 14:25:27 2010 -0400
@@ -66,6 +66,9 @@
 - **Offset Column** contains the offset within the chromosome
 - **P Value Column** contains the (untransformed) p values at that locus - choose multiple columns if needed
 
+NOTE - plotting millions of p values may take tens of minutes depending on 
+how busy the server is - be patient please. 
+
 -----
 
 .. class:: infomark
diff -r 40e8c99829e0 -r e1b63ac74b35 tools/rgenetics/rgQC.py
--- a/tools/rgenetics/rgQC.py	Thu Apr 01 13:08:48 2010 -0400
+++ b/tools/rgenetics/rgQC.py	Thu Apr 01 14:25:27 2010 -0400
@@ -37,12 +37,25 @@
 # note no ped file passed so had to remove the -l option
 # for plinkParse.py that makes a heterozygosity report from the ped
 # file - needs fixing...
+# new: importing manhattan/qqplot plotter
+# def doManQQ(input_fname,chrom_col,offset_col,pval_cols,title,grey,ctitle,outdir):
+#    """ draw a qq for pvals and a manhattan plot if chrom/offset <> 0
+#    contains some R scripts as text strings - we substitute defaults into the calls
+#    to make them do our bidding - and save the resulting code for posterity
+#    this can be called externally, I guess...for QC eg?
+#    """
+#
+#    rcmd = '%s%s' % (rcode,rcode2 % (input_fname,chrom_col,offset_col,pval_cols,title,grey))
+#    rlog,flist = RRun(rcmd=rcmd,title=ctitle,outdir=outdir)
+#    return rlog,flist
+  
 
 from optparse import OptionParser
 
 import sys,os,shutil, glob, math, subprocess, time, operator, random, tempfile, copy, string
 from os.path import abspath
 from rgutils import galhtmlprefix, galhtmlpostfix, RRun, timenow, plinke, rexe, runPlink, pruneLD
+import rgManQQ
 
 prog = os.path.split(sys.argv[0])[1]
 vers = '0.4 april 2009 rml'
@@ -57,6 +70,7 @@
 mogresize = "x300" # this controls the width for jpeg thumbnails
 
 
+
             
 def makePlots(markers=[],subjects=[],newfpath='.',basename='test',nbreaks='20',nup=3,height=10,width=8,rgbin=''):
     """
diff -r 40e8c99829e0 -r e1b63ac74b35 tools/rgenetics/rgtest.sh
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tools/rgenetics/rgtest.sh	Thu Apr 01 14:25:27 2010 -0400
@@ -0,0 +1,182 @@
+#!/bin/sh
+# script to generate all functional test outputs for each rgenetics tool
+# could be run at installation to ensure all dependencies are in place?
+GALAXYROOT=`pwd`
+echo "using $GALAXYROOT"
+# change this as needed for your local install
+INPATH="${GALAXYROOT}/test-data"
+BINPATH="${GALAXYROOT}/tool-data/rg/bin"
+TOOLPATH="${GALAXYROOT}/tools/rgenetics"
+OROOT="${GALAXYROOT}/test-data/rgtestouts"
+NORMALOROOT="${GALAXYROOT}/test-data"
+mkdir -p $OROOT
+rm -rf $OROOT/*
+# needed for testing - but tool versions should be bumped if this is rerun?
+TOOL="rgManQQ"
+NPRE=${TOOL}test1
+OUTPATH="$OROOT/$TOOL"
+mkdir $OUTPATH
+CL="python $TOOLPATH/$TOOL.py "$INPATH/smallwgaP.xls" $NPRE ${OUTPATH}/${NPRE}.html $OUTPATH 1 2 5,7 0"
+# rgManQQ.py '$input_file' "$name" '$out_html' '$out_html.files_path' '$chrom_col' '$offset_col' 
+# '$pval_col'
+#python /opt/galaxy/tools/rgenetics/rgManQQ.py /opt/galaxy/test-data/smallwgaP.xls rgManQQtest1 
+#/opt/galaxy/test-data/rgtestouts/rgManQQ/rgManQQtest1.html /opt/galaxy/test-data/rgtestouts/rgManQQ 1 2 5,7 
+echo "Testing $TOOL using $CL"
+python $TOOLPATH/$TOOL.py "$INPATH/smallwgaP.xls" $NPRE ${OUTPATH}/${NPRE}.html $OUTPATH 1 2 5,7 0
+TOOL="rgfakePhe"
+NPRE=${TOOL}test1
+OUTPATH="$OROOT/$TOOL"
+mkdir $OUTPATH
+PSSCRIPT="$OUTPATH/script_file"
+echo "{'pN':'normtest','pT':'rnorm','pP':\"{'Mean':'100', 'SD':'10'}\"}" > $PSSCRIPT
+echo "{'pN':'cattest','pT':'cat','pP':\"{'values':'red,green,blue'}\"}" >> $PSSCRIPT
+echo "{'pN':'uniftest','pT':'$f.series.phetype','pP':\"{'low':'1','hi':'100'}\"}" >> $PSSCRIPT
+echo "{'pN':'gammatest','pT':'rgamma','pP':\"{'Alpha':'1', 'Beta':'0.1'}\"}" >> $PSSCRIPT
+echo "{'pN':'poissontest','pT':'poisson','pP':\"{'lamb':'1.0',}\"}" >> $PSSCRIPT
+echo "{'pN':'exptest','pT':'exponential','pP':\"{'Mean':'100.0',}\"}" >> $PSSCRIPT
+echo "{'pN':'weibtest','pT':'weibull','pP':\"{'Alpha':'1.0', 'Beta':'0.1'}\"}" >> $PSSCRIPT
+echo "now doing $TOOL"
+python $TOOLPATH/$TOOL.py ${INPATH}/tinywga $NPRE $NPRE.pphe $OUTPATH $PSSCRIPT
+#   <command interpreter="python">rgfakePhe.py '$infile1.extra_files_path/$infile1.metadata.base_name'
+#   "$title1" '$ppheout' '$ppheout.files_path' '$script_file'
+#
+#
+TOOL="rgQC"
+NPRE=${TOOL}test1
+echo "now doing $TOOL"
+OUTPATH="$OROOT/$TOOL"
+mkdir $OUTPATH
+python $TOOLPATH/$TOOL.py -i "$INPATH/tinywga" -o $NPRE -s ${OUTPATH}/${NPRE}.html -p $OUTPATH
+# rgQC.py -i '$input_file.extra_files_path/$input_file.metadata.base_name' -o "$out_prefix" 
+# -s '$html_file' -p '$html_file.files_path' 
+#
+TOOL="rgGRR"
+NPRE=${TOOL}test1
+echo "now doing $TOOL"
+OUTPATH="$OROOT/$TOOL"
+mkdir $OUTPATH
+python $TOOLPATH/$TOOL.py "$INPATH/tinywga" "tinywga" $OUTPATH/${NPRE}.html $OUTPATH "$NPRE" '100' '6' 
+# rgGRR.py $i.extra_files_path/$i.metadata.base_name "$i.metadata.base_name"
+#'$out_file1' '$out_file1.files_path' "$title"  '$n' '$Z' 
+#
+TOOL="rgLDIndep"
+NPRE=${TOOL}test1
+OUTPATH="$OROOT/$TOOL"
+mkdir $OUTPATH
+python $TOOLPATH/$TOOL.py "$INPATH" "tinywga" "$NPRE" 1 1 0 0 1 1 $OUTPATH/${NPRE}.pbed $OUTPATH 10000 5000 0.1 
+#rgLDIndep.py '$input_file.extra_files_path' '$input_file.metadata.base_name' '$title' '$mind'
+# '$geno' '$hwe' '$maf' '$mef' '$mei' '$out_file1'
+#'$out_file1.files_path'  '$window' '$step' '$r2' 
+TOOL="rgPedSub"
+NPRE=${TOOL}test1
+OUTPATH="$OROOT/$TOOL"
+mkdir $OUTPATH
+PSSCRIPT="$OUTPATH/pedsub.script"
+echo "title~~~~$NPRE" > $PSSCRIPT
+echo "output1~~~~${OUTPATH}/${NPRE}.lped" >> $PSSCRIPT
+echo "outformat~~~~lped" >> $PSSCRIPT
+echo "basename~~~~tinywga" >> $PSSCRIPT
+echo "inped~~~~$INPATH/tinywga" >> $PSSCRIPT
+echo "outdir~~~~$OUTPATH" >> $PSSCRIPT
+echo "region~~~~" >> $PSSCRIPT
+echo "relfilter~~~~all" >> $PSSCRIPT
+echo "rslist~~~~rs2283802Xrs2267000Xrs16997606Xrs4820537Xrs3788347Xrs756632Xrs4820539Xrs2283804Xrs2267006Xrs4822363X" >> $PSSCRIPT
+echo "now doing $TOOL"
+python $TOOLPATH/$TOOL.py $PSSCRIPT
+rm -rf $PSSCRIPT
+#
+TOOL="rgfakePhe"
+NPRE=${TOOL}test1
+OUTPATH="$OROOT/$TOOL"
+mkdir $OUTPATH
+PSSCRIPT="$OUTPATH/script_file"
+echo "{'pN':'normtest','pT':'rnorm','pP':\"{'Mean':'100', 'SD':'10'}\"}" > $PSSCRIPT
+echo "{'pN':'cattest','pT':'cat','pP':\"{'values':'red,green,blue'}\"}" >> $PSSCRIPT
+echo "{'pN':'uniftest','pT':'$f.series.phetype','pP':\"{'low':'1','hi':'100'}\"}" >> $PSSCRIPT
+echo "{'pN':'gammatest','pT':'rgamma','pP':\"{'Alpha':'1', 'Beta':'0.1'}\"}" >> $PSSCRIPT
+echo "{'pN':'poissontest','pT':'poisson','pP':\"{'lamb':'1.0',}\"}" >> $PSSCRIPT
+echo "{'pN':'exptest','pT':'exponential','pP':\"{'Mean':'100.0',}\"}" >> $PSSCRIPT
+echo "{'pN':'weibtest','pT':'weibull','pP':\"{'Alpha':'1.0', 'Beta':'0.1'}\"}" >> $PSSCRIPT
+echo "now doing $TOOL"
+python $TOOLPATH/$TOOL.py $PSSCRIPT
+#
+echo "Now doing rgclean"
+TOOL="rgClean"
+NPRE=${TOOL}test1
+OUTPATH="$OROOT/$TOOL"
+mkdir $OUTPATH
+python $TOOLPATH/$TOOL.py $INPATH "tinywga" "$NPRE" 1 1 0 0 1 1 $OUTPATH/${NPRE}.pbed $OUTPATH 0 0 0 0
+# rgClean.py '$input_file.extra_files_path' '$input_file.metadata.base_name' '$title' '$mind'
+#        '$geno' '$hwe' '$maf' '$mef' '$mei' '$out_file1' '$out_file1.files_path'
+#        '${GALAXY_DATA_INDEX_DIR}/rg/bin/plink' '$relfilter' '$afffilter' '$sexfilter' '$fixaff'
+#
+echo "Now doing rgEigPCA"
+TOOL="rgEigPCA"
+NPRE=${TOOL}test1
+OUTPATH="$OROOT/$TOOL"
+mkdir $OUTPATH
+python $TOOLPATH/$TOOL.py "$INPATH/tinywga" "$NPRE" ${OUTPATH}/${NPRE}.html $OUTPATH 4 2 2 2 $OUTPATH/rgEigPCAtest1.txt
+#    rgEigPCA.py "$i.extra_files_path/$i.metadata.base_name" "$title" "$out_file1"
+#    "$out_file1.files_path" "$k" "$m" "$t" "$s" "$pca" 
+#
+TOOL="rgfakePed"
+NPRE=${TOOL}test1
+OUTPATH="$OROOT/$TOOL"
+mkdir $OUTPATH
+echo "now doing $TOOL"
+python $TOOLPATH/$TOOL.py --title "$NPRE" -o $OUTPATH/${NPRE}.lped -p $OUTPATH -c "20" -n "40" -s "10" -w "0" -v "0" -l "pbed" -d "T" -m "0" -M "0"
+#rgfakePed.py --title '$title1' 
+#  -o '$out_file1' -p '$out_file1.extra_files_path' -c '$ncases' -n '$ntotal'
+#  -s '$nsnp'  -w '$lowmaf' -v '$missingValue' -l '$outFormat'
+#  -d '$mafdist' -m '$missingRate' -M '$mendelRate'
+#
+TOOL="rgHaploView"
+NPRE=${TOOL}test1
+OUTPATH="$OROOT/$TOOL"
+mkdir $OUTPATH
+echo "now doing $TOOL"
+python $TOOLPATH/$TOOL.py ""  "rs2283802Xrs2267000Xrs16997606Xrs4820537Xrs3788347Xrs756632Xrs4820539Xrs2283804Xrs2267006Xrs4822363X" \
+"$NPRE" $OUTPATH/${NPRE}.html  "$INPATH" "tinywga" 0.0 200000 "RSQ" "lo" "2048" "$OUTPATH" "noinfo" "0.8" \
+"YRI" $BINPATH/haploview.jar
+#  rgHaploView.py "$ucsc_region" "$rslist" "$title" "$output1"  
+#  "$lhistIn.extra_files_path" "$lhistIn.metadata.base_name"
+#  "$minmaf" "$maxdist" "$ldtype" "$hires" "$memsize" "$output1.files_path" 
+#  "$infoTrack" "$tagr2" "$hmpanel" ${GALAXY_DATA_INDEX_DIR}/rg/bin/haploview.jar
+# note these statistical tools do NOT generate composite outputs
+TOOL="rgGLM"
+NPRE=${TOOL}test1
+OUTPATH=$NORMALOROOT
+echo "now doing $TOOL"
+python $TOOLPATH/$TOOL.py "$INPATH/tinywga" $INPATH/tinywga "$NPRE" "c1" "" $OUTPATH/${NPRE}_GLM.xls \
+$OUTPATH/${NPRE}_GLM_log.txt "tinywga" "" "" "" 1 1 0 0 $OUTPATH/${NPRE}_GLM_topTable.gff 
+##        rgGLM.py '$i.extra_files_path/$i.metadata.base_name' '$phef.extra_files_path/$phef.metadata.base_name'
+##        "$title1" '$predvar' '$covar' '$out_file1' '$logf' '$dbkey' '$i.metadata.base_name'
+##        '$inter' '$cond' '$gender' '$mind' '$geno' '$maf' '$logistic' '$gffout'
+#
+TOOL="rgTDT"
+NPRE=${TOOL}test1
+OUTPATH=$NORMALOROOT
+echo "now doing $TOOL"
+python $TOOLPATH/$TOOL.py -i "$INPATH/tinywga"  -o "$NPRE" -r $OUTPATH/${NPRE}_TDT.xls \
+-l $OUTPATH/${NPRE}_TDT_log.txt -g $OUTPATH/${NPRE}_TDT_topTable.gff
+##        rgTDT.py -i '$infile.extra_files_path/$infile.metadata.base_name' -o '$title'
+##        -r '$out_file1' -l '$logf' -x '${GALAXY_DATA_INDEX_DIR}/rg/bin/plink'
+##        -g '$gffout'
+#
+TOOL="rgCaCo"
+NPRE=${TOOL}test1
+OUTPATH=$NORMALOROOT
+echo "now doing $TOOL"
+python $TOOLPATH/rgCaCo.py $INPATH/tinywga "$NPRE" $OUTPATH/${NPRE}_CaCo.xls $OUTPATH/${NPRE}_CaCo_log.txt $OUTPATH $OUTPATH/${NPRE}_CaCo_topTable.gff
+# echo tp=$TOOLPATH t=$TOOL op=$OUTPATH b=$BINPATH
+# rgCaCo.py '$i.extra_files_path/$i.metadata.base_name' "$name"  '$out_file1' '$logf' '$logf.files_path' '$gffout'
+#
+TOOL="rgQQ"
+echo "now doing $TOOL"
+NPRE=${TOOL}test1
+OUTPATH=$NORMALOROOT
+CL="python $TOOLPATH/$TOOL.py "$INPATH/tinywga.pphe" "$NPRE" 1 3 $OUTPATH/$NPRE.pdf 8 10 "false" 1 $OUTPATH"
+echo "running $TOOL using $CL"
+python $TOOLPATH/$TOOL.py "$INPATH/tinywga.pphe" "$NPRE" 1 3 $OUTPATH/$NPRE.pdf 8 10 "false" 1 $OUTPATH
+# rgQQ.py "$input1" "$name" $sample "$cols" $allqq $height $width $log $allqq.id $__new_file_path__ 
+#

    

Greg Von Kuster

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