annotate test-data/ceas_out1.log.re_match @ 3:df54f8fcc7a7 draft

Version 1.0.2-3: move to conda-based dependency resolution.

ceas\ \-\-\ 0\.9\.9\.7\ \(package\ version\ 1\.0\.2\)
INFO\ \ \@\ .*
\#\ ARGUMENTS\:\ 
\#\ name\ \=\ ceas
\#\ gene\ annotation\ table\ \=\ .*galGal3\.refGene
\#\ BED\ file\ \=\ .*
\#\ WIG\ file\ \=\ None
\#\ extra\ BED\ file\ \=\ None
\#\ ChIP\ annotation\ \=\ On
\#\ gene\-centered\ annotation\ \=\ \ On
\#\ average\ profiling\ \=\ Off
\#\ dump\ profiles\ \=\ Off
\#\ re\-annotation\ for\ genome\ background\ \(ChIP\ region\ annotation\)\ \=\ False
\#\ promoter\ sizes\ \(ChIP\ region\ annotation\)\ \=\ 1000\,2000\,3000\ bp
\#\ downstream\ sizes\ \(ChIP\ region\ annotation\)\ \=\ 1000\,2000\,3000\ bp
\#\ bidrectional\ promoter\ sizes\ \(ChIP\ region\ annotation\)\ \=\ 2500\,5000\ bp
\#\ span\ size\ \(gene\-centered\ annotation\)\ \=\ 3000\ bp\ 
INFO\ \ \@\ .*\ \#1\ read\ the\ gene\ table\.\.\.\ 
INFO\ \ \@\ .*\ \#2\ read\ the\ bed\ file\ of\ ChIP\ regions\.\.\.\ 
INFO\ \ \@\ .*\ \#3\ perform\ gene\-centered\ annotation\.\.\.\ 
INFO\ \ \@\ .*\ \#4\ See\ ceas\.xls\ for\ gene\-centered\ annotation\!\ 
INFO\ \ \@\ .*\ \#5\ read\ the\ pre\-computed\ genome\ bg\ annotation\.\.\.\ 
INFO\ \ \@\ .*\ \#6\ perform\ ChIP\ region\ annotation\.\.\.\ 
INFO\ \ \@\ .*\ \#7\ write\ a\ R\ script\ of\ ChIP\ region\ annotation\.\.\.\ 

R\ version\ .*
Copyright\ \(C\)\ 20(\d\d)\ The\ R\ Foundation\ for\ Statistical\ Computing
Platform\:\ .*

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You\ are\ welcome\ to\ redistribute\ it\ under\ certain\ conditions\.
Type\ \'license\(\)\'\ or\ \'licence\(\)\'\ for\ distribution\ details\.

\ \ Natural\ language\ support\ but\ running\ in\ an\ English\ locale

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Type\ \'contributors\(\)\'\ for\ more\ information\ and
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\>\ \#\ ARGUMENTS\:\ 
\>\ \#\ name\ \=\ ceas
\>\ \#\ gene\ annotation\ table\ \=\ .*galGal3\.refGene
\>\ \#\ BED\ file\ \=\ .*
\>\ \#\ WIG\ file\ \=\ None
\>\ \#\ extra\ BED\ file\ \=\ None
\>\ \#\ ChIP\ annotation\ \=\ On
\>\ \#\ gene\-centered\ annotation\ \=\ \ On
\>\ \#\ average\ profiling\ \=\ Off
\>\ \#\ dump\ profiles\ \=\ Off
\>\ \#\ re\-annotation\ for\ genome\ background\ \(ChIP\ region\ annotation\)\ \=\ False
\>\ \#\ promoter\ sizes\ \(ChIP\ region\ annotation\)\ \=\ 1000\,2000\,3000\ bp
\>\ \#\ downstream\ sizes\ \(ChIP\ region\ annotation\)\ \=\ 1000\,2000\,3000\ bp
\>\ \#\ bidrectional\ promoter\ sizes\ \(ChIP\ region\ annotation\)\ \=\ 2500\,5000\ bp
\>\ \#\ span\ size\ \(gene\-centered\ annotation\)\ \=\ 3000\ bp
\>\ pdf\(\"ceas\.pdf\"\,height\=11\.5\,width\=8\.5\)
\>\ 
\>\ \#\ .*
\>\ \#\ 
\>\ \#\ ChIP\ annotation
\>\ \#\ 
\>\ 
\>\ 
\>\ \#\ 
\>\ \#\ Chromosomal\ Distribution
\>\ \#\ 
\>\ 
\>\ par\(mar\=c\(4\,\ 4\,\ 5\,\ 3\.8\)\,oma\=c\(4\,\ 2\,\ 4\,\ 2\)\)
\>\ r0\<\-c\(100\.0\)
\>\ r1\<\-c\(100\.0\)
\>\ height\<\-rbind\(r0\,r1\)
\>\ names\=c\(\"26\"\)
\>\ mp\<\-barplot\(height\=height\,names\=names\,beside\=TRUE\,horiz\=TRUE\,col\=c\(\"\#5FA1C1\"\,\"\#EB9D86\"\)\,main\=\"Chromosomal\ Distribution\ of\ ChIP\ Regions\"\,xlab\=\"Percentage\ \%\"\,ylab\=\"Chromosome\"\,border\=FALSE\,xlim\=c\(0\.000000\,183\.333333\)\,cex\.names\=1\)
\>\ text\(x\=c\(100\.0\)\,y\=mp\[1\,\]\,label\=c\(\"100\.0\ \%\"\)\,pos\=4\,offset\=0\.2\,cex\=0\.9\)
\>\ text\(x\=c\(100\.0\)\,y\=mp\[2\,\]\,label\=c\(\"100\.0\ \%\ \(\<\=4\.9e\-324\)\"\)\,pos\=4\,offset\=0\.2\,cex\=0\.9\)
\>\ legend\(\"right\"\,legend\=c\(\"Genome\"\,\"ChIP\ \(p\-value\)\"\)\,col\=c\(\"\#5FA1C1\"\,\"\#EB9D86\"\)\,pch\=15\,bty\=\"n\"\)
\>\ 
\>\ \#\ 
\>\ \#\ Promoter\,Bipromoter\,Downstream\,\ Gene\ and\ Regions\ of\ interest
\>\ \#\ 
\>\ 
\>\ par\(mfrow\=c\(4\,\ 1\)\,mar\=c\(4\,\ 4\,\ 5\,\ 3\.8\)\,oma\=c\(4\,\ 2\,\ 4\,\ 2\)\)
\>\ r0\<\-c\(1\.8532425688606797\,\ 3\.616851183410451\,\ 5\.322318854623416\)
\>\ r1\<\-c\(0\.0\,\ 0\.0\,\ 0\.0\)
\>\ height\<\-rbind\(r0\,r1\)
\>\ names\=c\(\"\<\=1000\ bp\"\,\"\<\=2000\ bp\"\,\"\<\=3000\ bp\"\)
\>\ mp\<\-barplot\(height\=height\,names\=names\,beside\=TRUE\,horiz\=FALSE\,col\=c\(\"\#5FA1C1\"\,\"\#EB9D86\"\)\,main\=\"Promoter\"\,ylab\=\"Percentage\ \%\"\,border\=FALSE\,ylim\=c\(0\.000000\,9\.757585\)\,cex\.names\=1\)
\>\ text\(x\=mp\[1\,\]\,y\=c\(1\.8532425688606797\,\ 3\.616851183410451\,\ 5\.322318854623416\)\,label\=c\(\"1\.9\ \%\"\,\"3\.6\ \%\"\,\"5\.3\ \%\"\)\,pos\=3\,offset\=0\.2\)
\>\ text\(x\=mp\[2\,\]\,y\=c\(0\.0\,\ 0\.0\,\ 0\.0\)\,label\=c\(\"0\.000\ \%
\+\ \(0\.981\)\"\,\"0\.000\ \%
\+\ \(0\.964\)\"\,\"0\.000\ \%
\+\ \(0\.947\)\"\)\,pos\=3\,offset\=0\.2\)
\>\ legend\(\"topleft\"\,legend\=c\(\"Genome\"\,\"ChIP\ \(p\-value\)\"\)\,col\=c\(\"\#5FA1C1\"\,\"\#EB9D86\"\)\,pch\=15\,bty\=\"n\"\)
\>\ r0\<\-c\(0\.03876062889120376\,\ 0\.03876062889120376\)
\>\ r1\<\-c\(0\.0\,\ 0\.0\)
\>\ height\<\-rbind\(r0\,r1\)
\>\ names\=c\(\"\<\=2500\ bp\"\,\"\<\=5000\ bp\"\)
\>\ mp\<\-barplot\(height\=height\,names\=names\,beside\=TRUE\,horiz\=FALSE\,col\=c\(\"\#5FA1C1\"\,\"\#EB9D86\"\)\,main\=\"Bidirectional\ Promoter\"\,ylab\=\"Percentage\ \%\"\,border\=FALSE\,ylim\=c\(0\.000000\,0\.071061\)\,cex\.names\=1\)
\>\ text\(x\=mp\[1\,\]\,y\=c\(0\.03876062889120376\,\ 0\.03876062889120376\)\,label\=c\(\"0\.04\ \%\"\,\"0\.04\ \%\"\)\,pos\=3\,offset\=0\.2\)
\>\ text\(x\=mp\[2\,\]\,y\=c\(0\.0\,\ 0\.0\)\,label\=c\(\"0\.000\ \%
\+\ \(1\.000\)\"\,\"0\.000\ \%
\+\ \(1\.000\)\"\)\,pos\=3\,offset\=0\.2\)
\>\ legend\(\"topleft\"\,legend\=c\(\"Genome\"\,\"ChIP\ \(p\-value\)\"\)\,col\=c\(\"\#5FA1C1\"\,\"\#EB9D86\"\)\,pch\=15\,bty\=\"n\"\)
\>\ r0\<\-c\(1\.8290171758036773\,\ 3\.4690762857627364\,\ 4\.980740812519683\)
\>\ r1\<\-c\(0\.0\,\ 0\.0\,\ 0\.0\)
\>\ height\<\-rbind\(r0\,r1\)
\>\ names\=c\(\"\<\=1000\ bp\"\,\"\<\=2000\ bp\"\,\"\<\=3000\ bp\"\)
\>\ mp\<\-barplot\(height\=height\,names\=names\,beside\=TRUE\,horiz\=FALSE\,col\=c\(\"\#5FA1C1\"\,\"\#EB9D86\"\)\,main\=\"Downstream\"\,ylab\=\"Percentage\ \%\"\,border\=FALSE\,ylim\=c\(0\.000000\,9\.131358\)\,cex\.names\=1\)
\>\ text\(x\=mp\[1\,\]\,y\=c\(1\.8290171758036773\,\ 3\.4690762857627364\,\ 4\.980740812519683\)\,label\=c\(\"1\.8\ \%\"\,\"3\.5\ \%\"\,\"5\.0\ \%\"\)\,pos\=3\,offset\=0\.2\)
\>\ text\(x\=mp\[2\,\]\,y\=c\(0\.0\,\ 0\.0\,\ 0\.0\)\,label\=c\(\"0\.000\ \%
\+\ \(0\.982\)\"\,\"0\.000\ \%
\+\ \(0\.965\)\"\,\"0\.000\ \%
\+\ \(0\.950\)\"\)\,pos\=3\,offset\=0\.2\)
\>\ legend\(\"topleft\"\,legend\=c\(\"Genome\"\,\"ChIP\ \(p\-value\)\"\)\,col\=c\(\"\#5FA1C1\"\,\"\#EB9D86\"\)\,pch\=15\,bty\=\"n\"\)
\>\ r0\<\-c\(0\.2034933016788197\,\ 1\.3978051793890356\,\ 2\.359553283752029\,\ 19\.734005184234114\,\ 23\.694856949054\)
\>\ r1\<\-c\(0\.0\,\ 0\.0\,\ 0\.0\,\ 0\.0\,\ 0\.0\)
\>\ height\<\-rbind\(r0\,r1\)
\>\ names\=c\(\"5\'UTR\"\,\"3\'UTR\"\,\"Coding\ Exon\"\,\"Intron\"\,\"All\"\)
\>\ mp\<\-barplot\(height\=height\,names\=names\,beside\=TRUE\,horiz\=FALSE\,col\=c\(\"\#5FA1C1\"\,\"\#EB9D86\"\)\,main\=\"Gene\"\,ylab\=\"Percentage\ \%\"\,border\=FALSE\,ylim\=c\(0\.000000\,43\.440571\)\,cex\.names\=1\)
\>\ text\(x\=mp\[1\,\]\,y\=c\(0\.2034933016788197\,\ 1\.3978051793890356\,\ 2\.359553283752029\,\ 19\.734005184234114\,\ 23\.694856949054\)\,label\=c\(\"0\.2\ \%\"\,\"1\.4\ \%\"\,\"2\.4\ \%\"\,\"19\.7\ \%\"\,\"23\.7\ \%\"\)\,pos\=3\,offset\=0\.2\)
\>\ text\(x\=mp\[2\,\]\,y\=c\(0\.0\,\ 0\.0\,\ 0\.0\,\ 0\.0\,\ 0\.0\)\,label\=c\(\"0\.000\ \%
\+\ \(0\.998\)\"\,\"0\.000\ \%
\+\ \(0\.986\)\"\,\"0\.000\ \%
\+\ \(0\.976\)\"\,\"0\.000\ \%
\+\ \(0\.803\)\"\,\"0\.000\ \%
\+\ \(0\.763\)\"\)\,pos\=3\,offset\=0\.2\)
\>\ legend\(\"topleft\"\,legend\=c\(\"Genome\"\,\"ChIP\ \(p\-value\)\"\)\,col\=c\(\"\#5FA1C1\"\,\"\#EB9D86\"\)\,pch\=15\,bty\=\"n\"\)
\>\ 
\>\ \#\ 
\>\ \#\ Distribution\ of\ Genome\ and\ ChIP\ regions\ over\ cis\-regulatory\ element
\>\ \#\ Note\ that\ the\ x\ may\ be\ modified\ for\ better\ graphics\ in\ case\ a\ value\ is\ too\ small
\>\ \#\ Thus\,\ look\ at\ the\ labels\ of\ the\ pie\ chart\ to\ get\ the\ real\ percentage\ values
\>\ \#\ 
\>\ 
\>\ par\(mfcol\=c\(2\,\ 2\)\,mar\=c\(3\,\ 3\,\ 4\,\ 2\.8\)\,oma\=c\(4\,\ 2\,\ 4\,\ 2\)\)
\>\ x\<\-c\(0\.018532\,0\.017055\,0\.016037\,0\.017830\,0\.015092\,0\.014051\,0\.010000\,0\.013833\,0\.023014\,0\.192592\,0\.670292\)
\>\ pie\(x\=x\,labels\=c\(\"1\.9\ \%\"\,\"1\.7\ \%\"\,\"1\.6\ \%\"\,\"1\.8\ \%\"\,\"1\.5\ \%\"\,\"1\.4\ \%\"\,\"0\.2\ \%\"\,\"1\.4\ \%\"\,\"2\.3\ \%\"\,\"19\.3\ \%\"\,\"67\.0\ \%\"\)\,main\=\"Genome\"\,col\=c\(\"\#445FA2\"\,\"\#EB9D86\"\,\"\#799F7A\"\,\"\#6C527F\"\,\"\#5FA1C1\"\,\"\#E8BB77\"\,\"\#A8C5EF\"\,\"\#FDCDB9\"\,\"\#C6E6B5\"\,\"\#F1D5EE\"\,\"\#B4E1F6\"\)\,clockwise\=TRUE\,border\=FALSE\,radius\=0\.9\,cex\=0\.8\,init\.angle\=90\,density\=100\)
\>\ x\<\-c\(0\.000000\,1\.000000\)
\>\ y\<\-c\(0\.000000\,1\.000000\)
\>\ plot\(x\,\ y\,type\=\"n\"\,main\=\"\"\,xlab\=\"\"\,ylab\=\"\"\,frame\=FALSE\,axes\=FALSE\,xaxt\=\"s\"\,yaxt\=\"s\"\)
\>\ legend\(\"top\"\,legend\=c\(\"Promoter\ \(\<\=1000\ bp\)\:\ 1\.9\ \%\"\,\"Promoter\ \(1000\-2000\ bp\)\:\ 1\.7\ \%\"\,\"Promoter\ \(2000\-3000\ bp\)\:\ 1\.6\ \%\"\,\"Downstream\ \(\<\=1000\ bp\)\:\ 1\.8\ \%\"\,\"Downstream\ \(1000\-2000\ bp\)\:\ 1\.5\ \%\"\,\"Downstream\ \(2000\-3000\ bp\)\:\ 1\.4\ \%\"\,\"5\'UTR\:\ 0\.2\ \%\"\,\"3\'UTR\:\ 1\.4\ \%\"\,\"Coding\ exon\:\ 2\.3\ \%\"\,\"Intron\:\ 19\.3\ \%\"\,\"Distal\ intergenic\:\ 67\.0\ \%\"\)\,col\=c\(\"\#445FA2\"\,\"\#EB9D86\"\,\"\#799F7A\"\,\"\#6C527F\"\,\"\#5FA1C1\"\,\"\#E8BB77\"\,\"\#A8C5EF\"\,\"\#FDCDB9\"\,\"\#C6E6B5\"\,\"\#F1D5EE\"\,\"\#B4E1F6\"\)\,pch\=15\,bty\=\"n\"\)
\>\ x\<\-c\(0\.010000\,0\.010000\,0\.010000\,0\.010000\,0\.010000\,0\.010000\,0\.010000\,0\.010000\,0\.010000\,0\.010000\,1\.000000\)
\>\ pie\(x\=x\,labels\=c\(\"0\.000\ \%\"\,\"0\.000\ \%\"\,\"0\.000\ \%\"\,\"0\.000\ \%\"\,\"0\.000\ \%\"\,\"0\.000\ \%\"\,\"0\.000\ \%\"\,\"0\.000\ \%\"\,\"0\.000\ \%\"\,\"0\.000\ \%\"\,\"100\.0\ \%\"\)\,main\=\"ChIP\"\,col\=c\(\"\#445FA2\"\,\"\#EB9D86\"\,\"\#799F7A\"\,\"\#6C527F\"\,\"\#5FA1C1\"\,\"\#E8BB77\"\,\"\#A8C5EF\"\,\"\#FDCDB9\"\,\"\#C6E6B5\"\,\"\#F1D5EE\"\,\"\#B4E1F6\"\)\,clockwise\=TRUE\,border\=FALSE\,radius\=0\.9\,cex\=0\.8\,init\.angle\=90\,density\=100\)
\>\ x\<\-c\(0\.000000\,1\.000000\)
\>\ y\<\-c\(0\.000000\,1\.000000\)
\>\ plot\(x\,\ y\,type\=\"n\"\,main\=\"\"\,xlab\=\"\"\,ylab\=\"\"\,frame\=FALSE\,axes\=FALSE\,xaxt\=\"s\"\,yaxt\=\"s\"\)
\>\ legend\(\"top\"\,legend\=c\(\"Promoter\ \(\<\=1000\ bp\)\:\ 0\.000\ \%\"\,\"Promoter\ \(1000\-2000\ bp\)\:\ 0\.000\ \%\"\,\"Promoter\ \(2000\-3000\ bp\)\:\ 0\.000\ \%\"\,\"Downstream\ \(\<\=1000\ bp\)\:\ 0\.000\ \%\"\,\"Downstream\ \(1000\-2000\ bp\)\:\ 0\.000\ \%\"\,\"Downstream\ \(2000\-3000\ bp\)\:\ 0\.000\ \%\"\,\"5\'UTR\:\ 0\.000\ \%\"\,\"3\'UTR\:\ 0\.000\ \%\"\,\"Coding\ exon\:\ 0\.000\ \%\"\,\"Intron\:\ 0\.000\ \%\"\,\"Distal\ intergenic\:\ 100\.0\ \%\"\)\,col\=c\(\"\#445FA2\"\,\"\#EB9D86\"\,\"\#799F7A\"\,\"\#6C527F\"\,\"\#5FA1C1\"\,\"\#E8BB77\"\,\"\#A8C5EF\"\,\"\#FDCDB9\"\,\"\#C6E6B5\"\,\"\#F1D5EE\"\,\"\#B4E1F6\"\)\,pch\=15\,bty\=\"n\"\)
\>\ 
\>\ \#\ 
\>\ \#\ ChIP\ regions\ over\ the\ genome
\>\ \#\ 
\>\ 
\>\ par\(mar\=c\(4\,\ 4\,\ 5\,\ 3\.8\)\,oma\=c\(4\,\ 2\,\ 4\,\ 2\)\)
\>\ layout\(matrix\(c\(1\,\ 0\,\ 2\,\ 2\)\,\ 2\,\ 2\,\ byrow\ \=\ TRUE\)\,widths\=c\(1\,\ 1\)\,heights\=c\(1\,\ 5\)\)
\>\ x\<\-c\(0\.000000\,2\.515610\)
\>\ y\<\-c\(0\.000000\,1\.000000\)
\>\ plot\(x\,\ y\,type\=\"n\"\,main\=\"Distribution\ of\ Peak\ Heights\"\,xlab\=\"\"\,ylab\=\"\"\,xlim\=c\(0\.000000\,2\.515610\)\,ylim\=c\(0\.000000\,1\.000000\)\,frame\=FALSE\,xaxt\=\"s\"\,yaxt\=\"n\"\,cex\=0\.9\)
\>\ x\<\-c\(0\.000000\,2\.515610\,2\.515610\,0\.000000\)
\>\ y\<\-c\(0\.000000\,0\.000000\,1\.000000\,1\.000000\)
\>\ polygon\(x\,y\,col\=c\(\"black\"\)\)
\>\ x\ \<\-\ c\(0\.000000\,0\.169726\,0\.339451\,0\.509177\,0\.678903\,0\.848628\,1\.018354\,1\.188079\,1\.357805\,1\.527531\,1\.697256\,1\.866982\,2\.036708\,2\.206433\,2\.376159\)
\>\ y\<\-c\(0\.000000\,0\.000000\,0\.000000\,0\.000000\,0\.000000\,0\.000000\,0\.000000\,0\.000000\,0\.000000\,0\.000000\,0\.000000\,0\.000000\,0\.000000\,0\.000000\,0\.800000\)
\>\ lines\(x\,\ y\,xlim\=c\(0\,\ 2\.51561\)\,ylim\=c\(0\,\ 1\)\,type\=\"l\"\,col\=c\(\"cyan\"\)\,lwd\=2\)
\>\ x\<\-c\(4119129\.000000\,4119130\.000000\)
\>\ y\<\-c\(0\.855556\,1\.144444\)
\>\ plot\(x\,\ y\,type\=\"n\"\,main\=\"ChIP\ Regions\ \(Peaks\)\ over\ Chromosomes\"\,xlab\=\"Chromosome\ Size\ \(bp\)\"\,ylab\=\"Chromosome\"\,xlim\=c\(4119129\.000000\,4119130\.000000\)\,ylim\=c\(0\.855556\,1\.144444\)\,frame\=FALSE\,xaxt\=\"s\"\,yaxt\=\"n\"\)
\>\ start\ \<\-\ c\(4119129\)
\>\ end\ \<\-\ c\(4119130\)
\>\ vals\ \<\-\ c\(2\.51561\)
\>\ vals\[vals\ \>\ 2\.51561\]\ \<\-\ 2\.51561
\>\ vals\[vals\ \<\ 0\]\ \<\-\ 0
\>\ heights\ \<\-\ 0\.288889\ \*\ \(\(vals\ \-\ 0\)\/\(2\.51561\ \-\ 0\)\)\ \+\ 0\.855555555556
\>\ for\ \(i\ in\ 1\:length\(heights\)\)\ \{
\+\ \	polygon\(x\=c\(start\[i\]\,\ end\[i\]\,\ end\[i\]\,\ start\[i\]\)\,\ y\=c\(0\.855555555556\,\ 0\.855555555556\,\ heights\[i\]\,\ heights\[i\]\)\,\ col\=c\(\"\#CC0000\"\)\,\ border\=c\(\"\#CC0000\"\)\)
\+\ \}
\>\ mtext\(\"26\"\,side\=2\,line\=0\,outer\=FALSE\,at\=1\.0\)
\>\ dev\.off\(\)
null\ device\ 
\ \ \ \ \ \ \ \ \ \ 1\ 
\>\ 
INFO\ \ \@\ .*\ \#\.\.\.\ cong\!\ See\ ceas\.pdf\ for\ the\ graphical\ results\ of\ CEAS\!\