changeset 0:8c5de60b3c04 draft

Uploaded
author vladimir-daric
date Fri, 25 Apr 2014 05:05:39 -0400
parents
children a39532e4b01b
files DESeq_diff_ann_wrapper.py DESeq_diff_ann_wrapper.xml GetOptions.R README deseq_result_html.html function_deseq.R script_deseq.R test/.svn/all-wcprops test/.svn/entries test/.svn/prop-base/A1_count.txt.svn-base test/.svn/prop-base/A2_count.txt.svn-base test/.svn/prop-base/A3_count.txt.svn-base test/.svn/prop-base/B1_count.txt.svn-base test/.svn/prop-base/B2_count.txt.svn-base test/.svn/prop-base/B3_count.txt.svn-base test/.svn/text-base/A1_count.txt.svn-base test/.svn/text-base/A2_count.txt.svn-base test/.svn/text-base/A3_count.txt.svn-base test/.svn/text-base/B1_count.txt.svn-base test/.svn/text-base/B2_count.txt.svn-base test/.svn/text-base/B3_count.txt.svn-base test/A1_count.txt test/A2_count.txt test/A3_count.txt test/B1_count.txt test/B2_count.txt test/B3_count.txt
diffstat 27 files changed, 13013 insertions(+), 0 deletions(-) [+]
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/DESeq_diff_ann_wrapper.py	Fri Apr 25 05:05:39 2014 -0400
@@ -0,0 +1,108 @@
+#!/usr/bin/env python
+# -*- coding: utf-8 -*-
+
+'''
+Created on 10 sep. 2012
+
+@author: Vladimir Daric, Rachel Legendre, Coline Billerey, Alban Ott, Claire Wallon
+@copyright: eBio ebio@igmors.u-psud.fr
+@license: GPL v3
+'''
+
+from optparse import OptionParser
+from os import path, mkdir, getcwd, walk
+from shutil import copyfile
+import subprocess
+import sys
+
+def stop_err( msg ):
+    sys.stderr.write( "%s\n" % msg )
+    sys.exit()    
+    
+def __main__():
+    #Parse Command Line
+    parser = OptionParser()
+    
+    # DESeq-count options.
+    parser.add_option( "-a", "--alpha", type="float", dest="alpha", 
+                       default = 0.05 )
+    parser.add_option( "-f", "--foldchange", type="float", dest="foldchange", 
+                       default = 0.05 )
+    parser.add_option( "-b", "--header", action="store_true", dest="header", 
+                       default = False )
+    parser.add_option( "-r", "--replicates", action="store_true", dest="replicates", 
+                       default = False )
+    parser.add_option( "-l", "--logbase", type="int", dest="logbase", 
+                       default = 10 )
+    parser.add_option( "-n", "--geneNumber", type="int", dest="geneNumber", 
+                       default = 30 )
+    parser.add_option( "-d", "--subfolder", type="string", dest="subfolder")
+    
+    parser.add_option( "-c", "--cond1", type="string", dest="cond1")
+    
+    parser.add_option( "-C", "--cond2", type="string", dest="cond2")
+    
+    parser.add_option( "-s", "--sharingMode", type="string", dest="mode", default = "fit-only"  )
+    parser.add_option( "-t", "--fitType", type="string", dest="fitType", default = "local"  )                       
+    parser.add_option( "-m", "--method", type="string", dest="method", default = "pooled" )
+    # Wrapper / Galaxy options.
+    parser.add_option( '-o', '--out', dest='outfile', help="file containing results for all counts" )
+    parser.add_option( '-u', '--up', dest='up_file', help="file containing results for up regulates counts" )
+    parser.add_option( '-w', '--down', dest='down_file', help="file containing results for down regulated counts" )
+    
+    (options, args) = parser.parse_args()
+    #make a folder for results
+    outfile = options.outfile
+    workfolder, filename = path.split(outfile)
+    #mksubdir
+    newdirname = options.subfolder
+    if path.exists(newdirname):
+        raise
+    try:
+        mkdir(newdirname)
+    except:
+        raise
+
+    #launch script_deseq in subfolder
+    exebinpath = path.join(path.dirname(__file__), 'script_deseq.R')
+
+    cmd = "%s --OutputDir=%s/DESeq_out --alpha=%f --foldchange=%f --logBase=%d --geneNumber=%d --sharingMode=%s --method=%s --fitType==%s" % (exebinpath, newdirname, options.alpha, options.foldchange, options.logbase, options.geneNumber,options.mode, options.method, options.fitType)
+    if options.replicates:
+        cmd += " --IsReplicate=TRUE"
+    if options.header:
+        cmd += " --IsHeader=TRUE"
+    for myarg in args:
+                
+        dataset, cond, rep = myarg.split(',')
+        ## replace group with correct name
+        if (cond == "1") :
+                cond = options.cond1
+        else :
+                cond = options.cond2
+        cmd += ' --condition=%s --replicate=%s --HTSeqcount=%s' % (cond, rep, dataset)
+
+    try:
+        proc = subprocess.Popen( args=cmd, shell=True, stdout=None, stderr=subprocess.PIPE )
+        returncode = proc.wait()
+        
+        stderr = ''
+        buffsize = 1048576
+        try:
+            while True:
+                stderr += proc.stderr.read( buffsize )
+                if not stderr or len( stderr ) % buffsize != 0:
+                    break
+        except OverflowError:
+            pass
+        if returncode != 0:
+            raise Exception, stderr
+    except Exception, e:
+        stop_err( 'Error running DESeq analyse: %s'% e )
+        
+    ##copy up and down files in galaxy dataset :
+    copyfile(path.join(newdirname, 'DESeq_out_up_genes.csv'), options.up_file)
+    copyfile(path.join(newdirname, 'DESeq_out_down_genes.csv'), options.down_file)
+    copyfile(path.join(path.dirname(__file__), 'deseq_result_html.html'), outfile)
+    
+if __name__=="__main__": 
+    __main__()
\ No newline at end of file
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/DESeq_diff_ann_wrapper.xml	Fri Apr 25 05:05:39 2014 -0400
@@ -0,0 +1,207 @@
+<tool id="deseq-diff-ann" name="DESeq" version="1.14.0">
+  <requirements>
+    <requirement type='binary' version="3.0.2">R</requirement>
+    <requirement type="package" version="2.14">Bioconductor</requirement>
+    <requirement type="package" version="1.14.0">DESeq</requirement>
+    <requirement type="package" version="2.12.1">gplots</requirement>
+    <requirement type="package" version="3.5-3">plotrix</requirement>
+    <requirement type="package" version="1.0-5">RColorBrewer</requirement>
+  </requirements>
+  <description>Uses DESeq R library for differential expression analysis</description>
+  <parallelism method="basic"></parallelism>
+  <command interpreter="python">
+    DESeq_diff_ann_wrapper.py
+    --alpha=$alpha
+    --out=$outhtml
+    --up=$up
+    --down=$down
+    --foldchange=$foldchange
+    --logbase=$logbase
+  	--geneNumber=$geneNumber
+    #if $params.settingsType == "yes":
+      --sharingMode=$params.mode
+      --method=$params.method
+      --fitType=$params.type
+    #end if  
+    --cond1=$cond1
+    --cond2=$cond2
+    --subfolder=$outhtml.files_path
+    #if str( $replicat_opt['options_type_selector'] ) == 'with':
+        --replicates
+        #for $i in $replicat_opt.series
+            ${i.htseq_out},${i.group},${i.label}
+        #end for
+    #else
+        #for $i in $replicat_opt.series
+            ${i.htseq_out},${i.group},${i.label}
+        #end for
+    #end if
+    
+
+  </command>
+  <inputs>
+    <param name="alpha" format="txt" type="text" value="0.05" label="Significance threshold (p-value)" help="p-value threshold for false discovery rate of significantly differentially expressed genes. See DESeq manual.">
+      <sanitizer>
+        <valid initial="string.digits">
+          <add value="." />
+        </valid>
+        <mapping initial="none">
+          <add source="," target="."/>
+        </mapping>
+      </sanitizer>
+    </param>
+    <param name="foldchange" format="txt" type="text" value="2" label="Fold change threshold" help="Fold change from condition B to A used both in graphs and selection of up or down-regulated significant genes. See DESeq manual.">
+      <sanitizer>
+        <valid initial="string.digits">
+          <add value="." />
+        </valid>
+        <mapping initial="none">
+          <add source="," target="."/>
+        </mapping>          
+      </sanitizer>
+    </param>
+    <conditional name="params">
+      <param name="settingsType" type="select" label="DESeq advanced mode" help="Use default settings or set custom values for any DESeq parameter.">
+    	<option value="no">Use Default</option>
+        <option value="yes">Full parameter list</option>
+      </param>
+        <when value="no" />
+        <!-- Full/advanced params. -->
+        <when value="yes">
+	  <param name="mode" type="select" label="DESeq mode" help="How variance estimate is computed with respect to the fitted line. See DESeq manual for more explain.">
+	    <option value="fit-only" >fit-only</option>
+	    <option value="maximum" selected="True">maximum</option>
+	    <option value="gene-est-only">gene-est-only</option>
+	  </param>
+	  <param name="method" type="select" label="DESeq method" help="How samples are pooled to estimate dispersion. If no replicates use 'blind'.">
+	    <option value="blind">blind</option>
+	    <option value="pooled" selected="True">pooled</option>
+	    <option value="per-condition">per-condition</option>
+	  </param>
+          <param name="type" type="select" label="DESeq fit type" help="refers to the model. 'Local' is the published model, 'parametric' is glm-based (may not converge).">
+            <option value="local" >local</option>
+            <option value="parametric" selected="True">parametric</option>
+          </param>
+      	</when>  <!-- full -->
+      </conditional>  <!-- params -->
+    
+    <param name="logbase" type="select" label="Select of logBase representation">
+      <option value="2">2</option>
+      <option value="10" selected="True">10</option>
+    </param>
+    
+    <param name="geneNumber" format="txt" type="text" value="30" label="Number of genes included in the heatmap of the most highly expressed genes"/>
+      
+    <param name="cond1" format="txt" type="text" value="cond1" label="Name for condition one" help="This name will be used in graphs."/>
+    <param name="cond2" format="txt" type="text" value="cond2" label="Name for condition two" help="This name will be used in graphs."/>
+    
+    <conditional name="replicat_opt">
+        <param name="options_type_selector" type="select" label="Analysis with replicates" help="NB : without replicate, the 'blind' method and 'fit-only' mode are applied, in accordance with the DESeq manual.">
+          <option value="with" selected="True">with replicates</option>
+          <option value="without">without replicates</option>
+        </param>
+        <when value="with">
+          <repeat name="series" title="replicate read count">
+            <param name="htseq_out" format="txt" type="data" label="HTSeq-count results"/>
+            <param name="group" type="select" label="Replicate condition">
+              <option value="1" selected="True">Condition one</option>
+              <option value="2">Condition two</option>
+            </param>
+            <param name="label" format="txt" type="text" value="replicate1" label="Replicate label name" help="You can specify a label for your replicates.">
+              <sanitizer>
+                <valid initial="string.letters,string.digits">
+                  <add value="_" />
+                </valid>
+                <mapping initial="none">
+                  <add source=" " target="_"/>
+                </mapping>          
+              </sanitizer>
+            </param>
+	  </repeat>
+        </when>
+      <when value="without">
+        <repeat name="series" title="Read count">
+          <param name="htseq_out" format="txt" type="data" label="HTSeq-count results"/>
+          <param name="group" type="select" label="Replicate condition">
+            <option value="1" selected="True">Condition one</option>
+            <option value="2">Condition two</option>
+          </param>
+          <param name="label" format="txt" type="text" value="label1" label="Replicate label name" help="You can specify a label for your replicates."/>
+        </repeat>
+      </when>
+    </conditional>
+  </inputs>
+  <outputs>
+    <data name="up" format="tabular" label="DE_up_genes" />
+    <data name="down" format="tabular" label="DE_down_genes" />
+    <data name="outhtml" format="html" label="deseq_result on ${on_string}" />
+  </outputs>
+  <tests>
+  	<test>
+  		<param name="params.settingsType" value="yes"/>
+  		<param name="params.type" value="local" />
+  		<param name="cond1" value="A" />
+		<param name="cond2" value="B" />
+		<param name="params.mode" value="" />
+		<param name="params.mode" value="" />
+		<param name="params.mode" value="" />	
+  		
+	</test>
+  </tests>
+  <help>
+Summary
+-------  
+
+This is a Galaxy wrapper for the DESeq package version 1.14.0 enabling full control of DESeq options (as well as additional graphical outputs/tables).
+A major task in the analysis of RNA-seq count data is the detection of differentially expressed genes. Based on read count data for each gene and each sample, the `DESeq`_ package provides methods to test for differential expression based on the negative binomial distribution and a shrinkage estimator for the distribution variance.
+
+.. _DESeq: http://bioconductor.org/packages/release/bioc/html/DESeq.html
+
+Input
+------
+Two or more count data files. Each file contains the number of reads assigned to each gene for a given sample. One may use for instance the output files of HTSeq-count.
+
+example: ::
+
+  geneA	12
+  geneB	0
+  geneC	150
+  geneD	3
+
+
+Output 
+------- 
+
+This Galaxy wrapper provides an html output and various result tables describing differentially expressed genes.
+
+.. class:: warningmark
+
+Warning note : in the absence of biological replicates : use the p-value (not the "adjusted" p-value) as the significance of differential expression.
+
+
+Dependencies
+------------
+
+.. class:: warningmark
+
+This tool depends on R (>=3.0.0), DESeq (>=1.14.0), gplots (>=2.12.1), plotrix (>=3.5-3), RColorBrewer (>=1.0-5). 
+
+
+.. class:: infomark
+
+Please contact `eBio`_ for more information
+
+.. _eBio: http://ebio.u-psud.fr/
+
+Citation 
+---------
+
+Simon Anders and Wolfgang Huber (2010): `Differential expression analysis for sequence count data`_. Genome Biology 11:R106
+
+.. _Differential expression analysis for sequence count data: http://www.ncbi.nlm.nih.gov/pubmed/20979621
+
+
+
+
+  </help>
+</tool>
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/GetOptions.R	Fri Apr 25 05:05:39 2014 -0400
@@ -0,0 +1,172 @@
+###
+# Created on 25 sep. 2012
+
+# @author: Alban Ott
+# @copyright: IGM ebio.igmors.u-psud.fr
+# @licence: GPL v3
+#
+
+# Il est interdit de mettre ARGUMENT comme argument long
+# spec contains at least 4 columns, as many as 5 columns.
+#
+# column 1: long name of flag
+#
+# column 2: short name of flag
+#
+# column 3: argument flag.  0=without argument, 1=with argument
+#
+# column 4: mode of argument.  one of "logical", "integer", "double",
+# "complex", "character", "" for arguments without value (return logical)
+#
+# column 5 (optional): description of ARGUMENT.
+#
+
+
+RetreiveAndDestroy=function(opt,root,stem,regexp,SearchNames,Out,isValue,NbFound,StockNames){
+	Bool=lapply(paste(root,SearchNames,stem,sep=""),grepl,opt)
+	names(Bool)=StockNames
+	Pos=lapply(Bool,which)
+	names(Pos)=StockNames
+	disable=c()
+	for (i in StockNames){
+		nbmatch=length(Pos[[i]])
+		if(nbmatch>0){
+			NbFound[[i]]=NbFound[[i]]+nbmatch
+			disable=c(disable,-1*Pos[[i]])
+			if(is.null(Out[[i]])){
+				if(isValue[[i]]!=0){
+					if(regexp=="next"){
+						Out[[i]]=opt[Pos[[i]]+1]
+						disable=c(disable,-1*(Pos[[i]]+1))
+					}else{
+						Out[[i]]=sub(regexp,"\\1",opt[Pos[[i]]])
+					}
+				}else{
+					Out[[i]]=TRUE
+				}
+			}else{
+				if(isValue[[i]]!=0){
+					if(regexp=="next"){
+						Out[[i]]=c(Out[[i]],opt[Pos[[i]]+1])
+						disable=c(disable,-1*(Pos[[i]]+1))
+					}else{
+						Out[[i]]=c(Out[[i]],sub(regexp,"\\1",opt[Pos[[i]]]))
+					}
+				}else{
+					Out[[i]]=c(Out[[i]],TRUE)
+				}
+			}
+		}
+	}
+	if(length(disable)>0){
+		opt=opt[disable]
+	}
+	Out[["ARGUMENT"]]=list()
+	Out[["ARGUMENT"]][["opt"]]=opt
+	Out[["ARGUMENT"]][["NbFound"]]=NbFound
+	return(Out)
+}
+
+getopt = function (spec=NULL,opt=commandArgs()) {
+	
+	FindArgs=which(opt=="--args")
+	if(length(FindArgs)!=1){
+		stop(length(FindArgs)," --args found where 1 expected.",call.=F)
+	}
+	ExecName=sub("--file=","",opt[FindArgs-1])
+	
+	if(FindArgs<length(opt)){
+		opt=opt[(FindArgs+1):length(opt)]
+	}else{
+		opt=""
+	}
+	
+	
+	min.columns=5
+	colNames=c("LongName","ShortName","Flag","Mod","Default")
+	max.columns=6
+	DimSpec=dim(spec)
+	if(DimSpec[2]>min.columns){
+		colNames=c(colNames,"Description")
+	}
+	
+	if(is.null(spec) | !is.matrix(spec) | (DimSpec[2]<min.columns | DimSpec[2]>max.columns)){
+		stop('argument "spec" is required and must be a matrix with 4|5 columns.',call.=F)
+	}
+	colnames(spec)=colNames
+	
+	spec=as.data.frame(spec,stringsAsFactors=F)
+	#spec validation
+	if(length(unique(c(spec$ShortName,"ARGUMENT","args")))!=DimSpec[1]+2 | length(unique(spec$LongName))!=DimSpec[1]){
+		stop('Long|Short names for flags must be unique (Long name : "ARGUMENT" and "args" forbidden).',
+				"\n","List of duplicated :",
+				"\n","Short: ",paste(spec$ShortName[duplicated(c(spec$ShortName,"ARGUMENT","args"))],collapse=" "),
+				"\n","Long:  ",paste(spec$ShortName[duplicated(spec$LongName)],collapse=" "),call.=F)
+	}
+	if(length(which(nchar(spec$ShortName)>1))!=0){
+		stop('Short names flags can\'t be longer than 1 character.')
+	}
+	
+	
+	#initialize 
+	Out=list()
+	Short2Long=list()
+	NbFound=list()
+	isValue=list()
+	for (i in 1:DimSpec[1]){
+		Short2Long[[spec$ShortName[i]]]=spec$LongName[i]
+		NbFound[[spec$LongName[i]]]=0
+		isValue[[spec$LongName[i]]]=spec$Flag[i]
+	}
+	
+	#Map, retreive and suppress ARGUMENTs and arguments
+	#Value ARGUMENT --example=value
+	Out=RetreiveAndDestroy(opt,"^--","=.+$",".+=(.+)$",spec$LongName,Out,isValue,NbFound,spec$LongName)
+	opt=Out[["ARGUMENT"]][["opt"]]
+	NbFound=Out[["ARGUMENT"]][["NbFound"]]
+	Out[["ARGUMENT"]]=NULL
+	#boolean ARGUMENT --example
+	Out=RetreiveAndDestroy(opt,"^--","$","$",spec$LongName,Out,isValue,NbFound,spec$LongName)
+	opt=Out[["ARGUMENT"]][["opt"]]
+	NbFound=Out[["ARGUMENT"]][["NbFound"]]
+	Out[["ARGUMENT"]]=NULL
+	#short name ARGUMENT -t value OR boolean -t
+	Out=RetreiveAndDestroy(opt,"^-","$","next",spec$ShortName,Out,isValue,NbFound,spec$LongName)
+	opt=Out[["ARGUMENT"]][["opt"]]
+	NbFound=Out[["ARGUMENT"]][["NbFound"]]
+	Out[["ARGUMENT"]]=NULL
+	#Warn about non mapped ARGUMENTs
+	if(length(opt)>0){
+		PosUnkArg=which(grepl("^-",opt))
+		if(length(PosUnkArg)){
+			message("Error, argument unreconized :","\n",paste(opt[PosUnkArg],collapse="\n"),"\n\n")
+		}
+		if(length(PosUnkArg)>0){
+			opt=opt[PosUnkArg*-1]
+		}
+	}
+	#Arguments
+	Out[["ARGUMENT"]]=opt
+	
+	#Validation of ARGUMENTs
+	for(i in 1:DimSpec[1]){
+		if(spec$Flag[i]=="0"){#verify boolean arguments
+			NbValue=length(Out[[spec$LongName[i]]])
+			if(NbValue>1){
+				message("Warning : ",spec$LongName[i]," found ",NbValue," times")
+			}
+		}
+		if(length(Out[[spec$LongName[i]]])==0){
+			Out[[spec$LongName[i]]]=spec$Default[i]
+		}
+		library("methods")
+		Out[[spec$LongName[i]]]=as(Out[[spec$LongName[i]]],spec$Mod[i])
+	}
+	
+	return(Out)
+}
+
+# column 3: argument flag.  0=no argument, 1=required argument, 2=optional argument
+
+
+
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/README	Fri Apr 25 05:05:39 2014 -0400
@@ -0,0 +1,27 @@
+
+This program uses the `DESeq`_ R library to realize a differential analysis on feature count data from RNA-Seq experiments.
+As input you have to provide a genomic features count date, such as provided by `HTSeq-count`_.
+The script performs a normalisation of data and then the differential analysis (negative binomial test).
+Several plots are produced. 
+
+
+The wrapper program (DESeq_diff_ann_wrapper.py) and R library GetOptions.R are free software; you can
+redistribute it and/or modify it under the terms of the GNU General Public License as published by the 
+Free Software Foundation; either version 3 of the License, or (at your option) any later version.
+
+Authors :
+Vladimir Daric (eBio), Rachel Legendre (eBio), Coline Billerey (eBio), Alban Ott (IGM), Claire Wallon (eBio)
+
+
+Licenses:
+
+If **DESeq** is used to obtain results for scientific publications it should be cited as [1].
+References:
+[1] Anders, S and Huber, W (2010): `Differential expression analysis for sequence count data`. 
+
+Contact:
+    ebio@igmors.u-psud.fr
+    
+.. _DESeq: http://bioconductor.org/packages/release/bioc/html/DESeq.html
+.. _HTSeq: http://www-huber.embl.de/users/anders/HTSeq/doc/count.html
+.. _eBio: http://ebio.u-psud.fr/
\ No newline at end of file
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/deseq_result_html.html	Fri Apr 25 05:05:39 2014 -0400
@@ -0,0 +1,76 @@
+<!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">
+	<head>
+		<meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
+    
+	</head>
+	<body>
+		<h1>DESeq analyse results</h1>
+		<p>
+			<ul>
+				<li>
+					Total read counts for each sample : <br />
+					<img border="0" src="DESeq_out_TotSamplePlot.png" width="50%" height="50%"/>
+				</li>
+				<li>
+					Proportion of null counts for each condition : <br />
+					<img border="0" src="DESeq_out_NullCondPlot.png" width="25%" height="50%"/><br />
+					<font color="red"> For the next graphs and calculations, all null counts are removed from data.</font> <br /><br />
+				</li>
+				<li>
+					<a href="http://en.wikipedia.org/wiki/Violin_plot">Violinplot</a> of raw counts for each sample : <br />
+					<img border="0" src="DESeq_out_RawViolin.png" width="50%" height="50%"/><br />
+					<font color="red"> For the next graphs and calculations, data are normalized.</font> <br /><br />
+				</li>
+				<li>
+					<a href="http://en.wikipedia.org/wiki/Violin_plot">ViolinPlot</a> of normalized counts for each sample : <br />
+					<img border="0" src="DESeq_out_NormViolin.png" width="50%" height="50%"/>
+				</li>
+				<li>
+					Heatmap of euclidean distances between samples : <br/> <a href="http://bioconductor.org/packages/release/bioc/vignettes/DESeq/inst/doc/DESeq.pdf#subsection.7.2"> (See DESeq manual, Heatmap of the sample-to-sample distances, figure 16) </a><br/>
+					<img border="0" src="DESeq_out_HeatDistPlot.png" width="50%" height="50%"/>
+				</li>
+				<li>
+					Heatmap of count data of the 30 most highly expressed genes :<br /> <a href="http://bioconductor.org/packages/release/bioc/vignettes/DESeq/inst/doc/DESeq.pdf#subsection.7.1"> (See DESeq manual, Heatmap of the count table, figure 15 left) </a><br />
+					<img border="0" src="DESeq_out_HeatCountPlot.png" width="50%" height="50%"/>
+				</li>
+				<li>
+					Distribution of p-values : <br /> (graph shows adjusted p-values when biological replicates are available, raw p-values otherwise)<br />
+					<img border="0" src="DESeq_out_histPval.png" width="50%" height="50%"/>
+				</li>
+				<li>
+					Control plot of dispersion estimates : <br/> <a href="http://bioconductor.org/packages/release/bioc/vignettes/DESeq/inst/doc/DESeq.pdf#section.4">(See DESeq manual)</a><br/>
+					<img border="0" src="DESeq_out_EstDispPlot.png" width="50%" height="50%"/><br />
+					Red line : regression over all data. <br /><br />
+				</li>
+				<li>
+					MAplot showing normalised mean versus log2 (fold change) for condition two versus condition one : <br /> <a href="http://bioconductor.org/packages/release/bioc/vignettes/DESeq/inst/doc/DESeq.pdf#section.3">(See DESeq manual)</a> <br /> 
+					<img border="0" src="DESeq_out_MAplot.png" width="50%" height="50%"/><br />
+					Red line indicates FoldChange = 1. <br />
+					Red points represent genes with an adjusted p-value below the p-value threshold. <br />
+					Triangles : infinite fold changes.<br/> <br/>
+				</li>
+				<li>
+					Enriched <a href="http://en.wikipedia.org/wiki/Volcano_plot_%28statistics%29">volcano plot</a> showing differentially expressed genes satisfying p-value and foldchange thresholds provided : <br /> Upper and right panels show, respectively, the projection of log fold change density and the log p-value density. <br />
+					<img border="0" src="DESeq_out_volcanoplot.png" width="50%" height="50%"/><br />
+					Red points : genes with p-value lower than the p-value threshold provided and foldchange greater than the absolute value of the foldchange threshold provided. Fold change of +Inf and -Inf are plotted on either side of volcano plot.<br /><br />
+				</li>
+				<li>
+					Complete quantitative results :
+					<a href="DESeq_out_complete.csv">DESeq_out_complete.csv</a>
+				</li>
+				<li>
+					Results for significantly over-expressed genes :
+					<a href="DESeq_out_up_genes.csv">DESeq_out_up_genes.csv</a>
+				</li>
+				<li>
+					Results for significantly sub-expressed genes :
+					<a href="DESeq_out_down_genes.csv">DESeq_out_down_genes.csv</a>
+				</li>
+			</ul>
+		</p>
+	</body>
+</html>
+
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/function_deseq.R	Fri Apr 25 05:05:39 2014 -0400
@@ -0,0 +1,448 @@
+# Home made violin plot (Alban Ott)
+
+vioplot = function(x, DensCol="#00000060", BoxplotCol="#000000FF", InfFactorSpace=0.4,BoxplotFill="#FFFFFF00", YLAB="log10(normalized count)"){ #x must be a matrix or a dataframe
+	
+	# Number of samples :
+	SampleNumber=length(colnames(x))
+	
+	if(is.vector(x)){
+		x=as.matrix(x)
+	}
+	YNormalizedDensity=list()
+	XNormalizedDensity=list()
+	
+	#Set a value to -Inf
+	xNoInfo=x[x!=-Inf]
+	OverallMinMax=c(min(xNoInfo),max(xNoInfo))
+	range=OverallMinMax[2]-OverallMinMax[1]
+	Inf2Value=OverallMinMax[1]-range*InfFactorSpace
+	breakInf=OverallMinMax[1]-range*(InfFactorSpace-.1)
+	xValInf=x
+	IsInf=xValInf==-Inf
+	if(sum(IsInf)>0){
+		xValInf[xValInf==-Inf]=Inf2Value
+	}
+	#Pre compute densities
+	for (i in 1:dim(xValInf)[2]){
+		dens=density(xValInf[,i])
+		YNormalizedDensity[[i]]=dens$x
+		#Normalize density to fit boxplot
+		XNormalizedDensity[[i]]=dens$y/max(dens$y)/5
+	}
+	
+	#Print boxplot with a range compatible with density plot
+	if(sum(IsInf)>0){
+		ylim=c(OverallMinMax[1]-range*(InfFactorSpace+0.1),OverallMinMax[2]+range*0.1)
+		if (SampleNumber > 8) {
+			boxplot(x, boxwex=0.2, ylim=ylim, border=BoxplotCol, col=BoxplotFill, notch=T, yaxt="n", las=2)
+		}else {
+			boxplot(x, boxwex=0.2, ylim=ylim, border=BoxplotCol, col=BoxplotFill, notch=T, yaxt="n")	
+		}
+		AxisTick=seq(floor(OverallMinMax[1]),round(OverallMinMax[2]),length.out=round(OverallMinMax[2])-floor(OverallMinMax[1])+1)
+		axis(2,at=c(Inf2Value,AxisTick),c("-Inf",AxisTick),las=1)
+		axis.break(2,breakInf,style="slash")
+
+	}else{
+		if (SampleNumber > 8){
+			boxplot(x, boxwex=0.2, border=BoxplotCol, col=BoxplotFill, notch=T, las=2)
+		}else {
+			boxplot(x, boxwex=0.2, border=BoxplotCol, col=BoxplotFill, notch=T)
+		}
+		
+	}
+	mtext(side = 2, YLAB, line = 2)	
+	#Plot densities
+	for (i in 1:dim(x)[2]){
+		points(i+XNormalizedDensity[[i]], YNormalizedDensity[[i]], type="l", lwd=3, col=DensCol)
+		points(i-XNormalizedDensity[[i]], YNormalizedDensity[[i]], type="l", lwd=3, col=DensCol)
+		if(sum(IsInf)>0){
+			points(i,Inf2Value,pch=8,col=DensCol,lwd=3)
+		}
+	}
+}
+
+
+
+#######################################################
+# Histogram of p-value. Use adjusted p-value if
+#             there are replicats
+#######################################################
+
+
+PlotHistPval = function(res, rep, file, ImageSize=1960, PPI=200){
+	
+	png( file=file , width=ImageSize, height=ImageSize, res=PPI )
+	if (rep){
+		hist(res$padj, breaks=100, col="black", border="black", main="",ylab="Number of elements (e.g. : genes)",xlab="adjusted p-value")
+	}else{
+		hist(res$pval, breaks=100, col="black", border="black", main="",ylab="Number of elements (e.g. : genes)",xlab="raw p-value")
+	}
+	invisible(dev.off())
+	
+}
+
+
+
+#######################################################
+# Plot violinplot of (un)normalized counts
+#######################################################
+
+PlotViolin = function(cds, norm, file, ImageSize=1960, PPI=200, logBase=10){
+	
+	png( file=file , width=ImageSize, height=ImageSize, res=PPI )
+	## probleme avec les +/-inf
+	NormCount = log(counts( cds, normalized=norm ), base=logBase)
+	## get correct ylab
+	if ( norm ){
+		YLAB=paste("log",logBase,"(normalized count)",sep="")
+	}else{
+		YLAB=paste("log",logBase,"(raw count)",sep="")
+	}	
+	color_cond1 = colorRampPalette(brewer.pal(3, "Purples"))(sum(conditions(cds)==levels(conditions(cds))[1]))
+	color_cond2 = colorRampPalette(brewer.pal(3, "RdPu"))(sum(conditions(cds)==levels(conditions(cds))[2]))
+	colors = c(as.vector(color_cond1),as.vector(color_cond2))
+	labels = colnames( NormCount )
+
+	vioplot(NormCount,BoxplotFill=colors, YLAB=YLAB)	
+	
+	invisible(dev.off())
+
+	
+}
+
+##############################################################
+# Plot volcano with density plot of foldchange and pvalues
+##############################################################
+
+PlotVolcano = function (res, cond1,cond2 ,alpha, fold, rep, file, ImageSize=1960,logBase=10, InfFactorSpace=0.4,PPI=200){
+	
+	png( file=file , width=ImageSize, height=ImageSize ,res=PPI )
+	
+	
+	if ( rep ){
+		pvalCol=8
+		YLAB=paste("-log",logBase,"(adjusted p-value)",sep="")
+	}else{
+		pvalCol=7
+		YLAB=paste("-log",logBase,"(raw p-value)",sep="")
+	}
+	
+	ThreslogAlpha = -log(alpha, logBase)
+	ThreslogFC = log(fold, logBase)
+	logPVal = -log(res[,pvalCol], logBase)
+	logFC=log(res$foldChange, logBase)
+	
+	#Set values to -/+Inf
+	MinMaxlogFC=summary(logFC[abs(logFC)!=Inf])[c("Min.","Max.")]
+	range=MinMaxlogFC[2]-MinMaxlogFC[1]
+	Inf2Value=c(MinMaxlogFC[1]-range*InfFactorSpace, MinMaxlogFC[2]+range*InfFactorSpace)
+	breakInf=c(MinMaxlogFC[1]-range*(InfFactorSpace-0.1), MinMaxlogFC[2]+range*(InfFactorSpace-0.1))
+	logFC[logFC==-Inf]=Inf2Value[1]
+	logFC[logFC== Inf]=Inf2Value[2]
+	
+	
+	#Precompute densities
+	logFCDens=density(logFC)
+	logPvalDens=density(logPVal)	
+	tmp=logPvalDens$x
+	logPvalDens$x=logPvalDens$y
+	logPvalDens$y=tmp
+	#Compute xlim and ylim to align graphics
+	marOutside=0.05
+	XLIM=c(min(logFCDens$x)-(max(logFCDens$x)-min(logFCDens$x))*marOutside,max(logFCDens$x)+(max(logFCDens$x)-min(logFCDens$x))*marOutside)
+	YLIM=c(min(logPvalDens$y)-(max(logPvalDens$y)-min(logPvalDens$y))*marOutside,max(logPvalDens$y)+(max(logPvalDens$y)-min(logPvalDens$y))*marOutside)
+	
+	
+	plot.new()
+	split.screen(rbind(
+					c(0,0.7,0,0.7),
+					c(0,0.7,0.7,1),
+					c(0.7,1,0,0.7)
+			))
+	screen(1)
+	# c(bottom, left, top, right) default : par(mar=c(5,6,3,4)+.1)
+	par(mar=c(5,6,0,0)+.1)
+	# volcano plot
+	VolcanoCol=ifelse((log(res$foldChange, logBase) > ThreslogFC  | log(res$foldChange, logBase) < -ThreslogFC)&(logPVal>ThreslogAlpha), "red","black")
+	plot(logFC,logPVal,pch=20,cex=0.3,xlim=XLIM,ylim=YLIM,xaxt="n",col=VolcanoCol,xlab=paste("log",logBase,"(FoldChange ",paste(cond2,cond1,sep="/"),")",sep=""),ylab=YLAB,bty="l")
+	
+	AxisTick=seq(floor(MinMaxlogFC[1]),round(MinMaxlogFC[2]),length.out=round(MinMaxlogFC[2])-floor(MinMaxlogFC[1])+1)
+	axis(1,at=c(Inf2Value[1],AxisTick,Inf2Value[2]),c("-Inf",AxisTick,"+Inf"),las=1)
+	axis.break(1,breakInf[1],style="slash")
+	axis.break(1,breakInf[2],style="slash")
+	
+	#pval threshold dashed line
+	abline(h=ThreslogAlpha,col="red", lty=2, lwd=2 )
+	
+	screen(2)
+	par(mar=c(0,6,3,0)+.1)
+	plot(logFCDens, col="black",main ="",xaxt="n",bty="n",ylab=paste("Density of\nlog",logBase,"(FoldChange)",sep=""),xlab="",xlim=XLIM)
+	
+	screen(3)
+	par(mar=c(5,0,0,4)+.1)
+	plot(logPvalDens,main="", col="black",yaxt="n",bty="n",xlab=paste("Density of\n",YLAB,sep=""),ylab="",ylim=YLIM)
+	
+	invisible(dev.off())
+	
+}
+
+#######################################################
+# Plot mean of normalized counts vs log2 of foldchange
+#######################################################
+
+MAPlot = function(res, OutPrefix, file, ImageSize=1960, PPI=200){
+	
+	png( file=file , width=ImageSize, height=ImageSize, res=PPI )
+	plotMA(res)
+	
+	invisible(dev.off())
+}
+
+
+#######################################################
+# Plot estimation of dispersion
+#######################################################
+
+
+EstDispPlot = function(cds, method, file, ImageSize=1960, PPI=200){
+	
+	png( file=file , width=ImageSize, height=ImageSize, res=PPI )
+	
+	if (method == "per-condition"){
+		
+		#print(ls( cds@fitInfo))
+		par(mfcol=c(1,2))
+		for (cond in (ls(cds@fitInfo))){
+			plotDispEsts(cds, name=cond,main=paste("Estimate dispersion plot for ",cond,sep=""))		
+		}
+		
+	}else{
+		plotDispEsts(cds)
+	}
+	
+	
+	invisible(dev.off())
+}
+
+#######################################################
+# Histogram of null counts proportion per condition
+#######################################################
+
+
+NullCondPlot = function(cds, file ,ImageSize=1960, PPI=200){
+
+	png( file=file , width=ImageSize/2, height=ImageSize, res=PPI )
+	
+	
+	CountsNorm_cond=list()
+	CountsNull_cond=list()
+	## for each condition 
+	for (cond in rev(levels(conditions(cds)))){
+		# we count number of feature with no count
+		CountsNorm_cond[[cond]]=counts( cds, normalized=TRUE )[ , conditions(cds)==cond ]
+		# if there are no replicate dim is null and return R error
+		if (is.null(dim(CountsNorm_cond[[cond]]))) {
+			CountsNull_cond[[cond]]=sum(CountsNorm_cond[[cond]] == 0)/length(CountsNorm_cond[[cond]])
+		}
+		else {
+			CountsNull_cond[[cond]]=sum(apply(CountsNorm_cond[[cond]],1,sum) == 0)/nrow(CountsNorm_cond[[cond]])
+		}
+
+	}
+	# we plot number of feature with no count
+	colors = c("#756bb1","#fa9fb5")
+	barplot(as.numeric(CountsNull_cond), ylab="Proportion of null count elements (e.g. : genes)", names.arg = names(CountsNull_cond), col=colors, ylim=c(0,1))
+	
+	invisible(dev.off())
+}
+
+
+#######################################################
+# Histogram of total reads count per sample
+#######################################################
+
+
+TotReadSamplePlot = function(cds, file ,ImageSize=1960, PPI=200){
+
+	png( file=file , width=ImageSize, height=ImageSize, res=PPI )
+	
+	RawCount = counts( cds, normalized=FALSE)
+	## choice of x colors according to number of replicate in Ramp palette
+	color_cond1 = colorRampPalette(brewer.pal(3, "Purples"))(sum(conditions(cds)==levels(conditions(cds))[1]))
+	color_cond2 = colorRampPalette(brewer.pal(3, "RdPu"))(sum(conditions(cds)==levels(conditions(cds))[2]))
+	colors = c(as.vector(color_cond1),as.vector(color_cond2))
+	#if there are many replicates, x labels are drawn vertically
+	if (length(sampleNames(cds)) > 8){
+		barplot(colSums(RawCount), ylab="", col=colors, ylim=c(0,max(colSums(RawCount))*1.2 ), las=2, yaxt="n")
+		## As there are millions of reads, y labels are drawn horizontally
+		axis(2, las=0)
+		mtext("Total Read Count per Sample", side=2, line=2.5)
+	}
+	else {
+		barplot(colSums(RawCount), ylab="", names.arg = colnames(RawCount), col=colors, ylim=c(0,max(colSums(RawCount))*1.2 ) )
+		## As there are millions of reads, y labels are drawn horizontally
+		axis(2, las=0)
+		mtext("Total Read Count per Sample", side=2, line=2.5)
+	}
+	invisible(dev.off())
+}
+
+
+###################################################################
+# heatmap of expression data of the 30 most highly expressed genes
+###################################################################
+
+HeatCountPlot=function(cds, vsd, file, geneNumber=30, ImageSize=1960, PPI=200){
+	
+	png( file=file , width=ImageSize, height=ImageSize, res=PPI )
+	
+	select = order(rowMeans(counts(cds)), decreasing=TRUE)[1:geneNumber]
+	hmcol = colorRampPalette(brewer.pal(9, "GnBu"))(100)
+	heatmap.2(exprs(vsd)[select,], col = hmcol, trace="none", margin=c(10, 6))
+	
+	invisible(dev.off())
+}
+
+#######################################################
+# Heatmap of Euclidean distances between the samples
+#######################################################
+
+HeatDistPlot=function(vsd, cdsBlind, file, ImageSize=1960, PPI=200){
+	
+	png( file=file , width=ImageSize, height=ImageSize, res=PPI )
+	
+	dists = dist(t(exprs(vsd)))
+	mat = as.matrix(dists)
+	rownames(mat) = colnames(mat) = with(pData(cdsBlind), paste(condition,sampleNames(cdsBlind), sep=" : "))
+	hmcol = colorRampPalette(brewer.pal(9, "GnBu"))(100)
+	heatmap.2(mat, trace="none", col = rev(hmcol), margin=c(13, 13))
+	
+	invisible(dev.off())
+}
+
+#######################################################
+# Export up and down genes according to p-value and 
+#     Foldchange, and export complete results
+#######################################################
+
+
+WriteResults = function (res, rawCounts, normCounts, cond1, cond2, alpha, foldchange, rep, OutPrefix, logBase=10){
+	
+	## re-compute logBase(FC) passed in argument
+	res[,6] = log(res[,5],base=logBase)
+	
+	## get results not failed pvalue threshold
+	if (rep == TRUE){
+		res_sig = res[res$padj < alpha,]
+	}else{
+		res_sig = res[res$pval < alpha,]
+	}
+	
+	# select up genes
+	up = res_sig[res_sig$foldChange > foldchange,]
+	up = up[rev(order(up$foldChange)),]
+	
+	# select down genes
+	down = res_sig[res_sig$foldChange < 1/foldchange,]
+	down = down[order(down$foldChange),]
+	
+	# change any column names for more comprehension
+	names = colnames(res)
+	names[3] = paste("baseMean_",cond1,sep="")
+	names[4] = paste("baseMean_",cond2,sep="")
+	names[5] = paste("foldChange_",paste(cond2,cond1,sep="/"),sep="")
+	names[6] = paste("log",logBase,"FoldChange",sep="")
+	colnames(res) = names
+	colnames(up) = names
+	colnames(down) = names
+	
+	# export up genes
+	write.table( format(up,scientific=FALSE,digits=3,dec=','), file=paste(OutPrefix,"_up_genes.csv",sep=""), sep="\t", row.names=F, quote=F)
+	# export down genes
+	write.table( format(down,scientific=FALSE,digits=3,dec=','), file=paste(OutPrefix,"_down_genes.csv",sep=""), sep="\t", row.names=F, quote=F)
+	
+	#rename col names of raw counts
+	names = NULL
+	for(name in colnames(rawCounts)){
+		names = c(names,paste("raw_",name,sep=""))
+	} 
+	colnames(rawCounts) = names
+	
+	#rename col names of normalized counts
+	names = NULL
+	for(name in colnames(normCounts)){
+		names = c(names,paste("norm_",name,sep=""))
+	} 
+	colnames(normCounts) = names	
+	
+	## merge raw and normalized counts	
+	counts = merge(rawCounts, normCounts,by="row.names",all=T)
+	all_results = data.frame(res$id, counts[,2:ncol(counts)], res[,3:ncol(res)])
+	colnames(all_results)[1] <- "ID"
+	## export complete results
+	write.table( format(all_results,scientific=FALSE,digits=3,dec=','), file=paste(OutPrefix,"_complete.csv",sep=""), sep="\t", row.names=F, quote=F)
+	
+	
+}
+
+#######################################################
+# create a raw count matrix from argument's sample 
+#######################################################
+
+
+CreateCountMatrix = function(sample, header, rep){
+	
+	#Read the HTseq-count files dans concatenate them in different columns.
+	names = sample$files
+	rawCounts=data.frame(Id=character(),stringsAsFactors=T)
+	for (i in 1:length(names)){
+		tmp = read.table(names[i], sep="\t", header=header, as.is=T,col.names=c("Id", sample$replicate[i]))#read
+		rawCounts = merge(rawCounts, tmp, by="Id", all=T)#concatenate
+	}
+	colnames(rawCounts) = c("Id", sample$replicate)#rename
+	
+	rawCounts[is.na(rawCounts)] = 0  
+	
+	#Clean up the HTseq-count from overview lines
+	row2remove = c("alignment_not_unique", "ambiguous", "no_feature", "not_aligned", "too_low_aQual")
+	rawCounts = rawCounts[!rawCounts$Id %in% row2remove,]
+	rawCounts[is.na(rawCounts)] = 0 
+	
+	#convert Id columns to row names
+	rownames(rawCounts)=rawCounts[,1]
+	rawCounts=rawCounts[,-1]
+	
+	return(rawCounts)
+}
+
+
+
+#######################################################
+# Launch DE analysis with(out) replicates
+#######################################################
+# parameters: 
+# method: how samples are pooled to estimate dispersion. If no replicates use "blind"
+# sharingMode: how variance estimate is computed with respect to the fitted line. 
+# 				"Maximum" is the most conservative (takes care of outliers, i.e., genes with dispersion much larger than the fitted values), 
+#					"fit-only" keeps the estimated value. Use this only with very few replicates, and when you are not too concerned about false positives from dispersion outliers, i.e. genes with an unusually high variability.
+# 				"gene-est-only" : No fitting or sharing, use only the empirical value.
+#sharingMode = c( "maximum", "fit-only", "gene-est-only" )
+# fitType: refers to the model. "Local" is the published model, "parametric" is glm-based (may not converge)
+#in this case, without replicates
+#fitType = c("parametric", "local")
+
+
+DE_analysis = function(countTable, design, rep, mode="maximum", method="pooled", fitType="parametric"){
+
+	cds = newCountDataSet( countTable, design$condition)
+	cds = estimateSizeFactors( cds )
+	
+	if (rep){
+		cds = estimateDispersions( cds, fitType=fitType, sharingMode=mode, method=method)
+	# If there are no replicates, we force Mode and method as described in DESeq manual
+	} else {
+		cds = estimateDispersions( cds, fitType=fitType, sharingMode="fit-only", method="blind")
+	}
+	return(cds)
+}
+
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/script_deseq.R	Fri Apr 25 05:05:39 2014 -0400
@@ -0,0 +1,140 @@
+#!/usr/bin/env Rscript
+
+###################################
+# @author: Vladimir Daric, Rachel Legendre, Coline Billerey, Alban Ott, Claire Wallon
+# @copyright: eBio ebio@igmors.u-psud.fr
+# @license: GPL v3
+
+
+
+#######################################################
+# GetExecutingDirectory (for galaxy)
+#######################################################
+
+getScriptDirectory = function() {
+  cheminScript = unlist(strsplit(commandArgs()[4],split="="))[2]
+  cheminScriptSplit = unlist(strsplit(cheminScript,split="/"))
+  return(paste(cheminScriptSplit[1:(length(cheminScriptSplit)-1)],collapse="/"))
+}
+
+
+####################################################
+#						MAIN PROGRAM 
+####################################################
+
+
+scriptDirectory = getScriptDirectory()
+source(paste(scriptDirectory,"/GetOptions.R",sep=""))
+source(paste(scriptDirectory,"/function_deseq.R",sep=""))
+
+optArgs=getopt(
+		rbind(
+				c('IsReplicate'     , 'r', 0, 'logical'  , "FALSE"      , "Is there any replicates ?"),
+				c('help'            , 'h', 0, 'logical'  , "FALSE"      , "Display help"),
+				c('IsHeader'        , 'b', 0, 'logical'  , "FALSE"      , "Is there a header in the HTSeq-count file ?"),
+				c('alpha'           , 'a', 1, 'numeric'  , "0.05"       , "p-value threshold"),
+				c('foldchange'      , 'f', 1, 'numeric'  , "2"          , "foldchange threshold"),
+				c('HTSeqcount'      , 'c', 1, 'character', ""           , "HTSeq-count files"),
+				c('condition'       , 'g', 1, 'character', ""           , "Biological conditions"),
+				c('replicate'       , 'l', 1, 'character', ""           , "Names of each replicate"),
+				c('OutputDir'       , 'p', 1, 'character', "DESeq_out"  , "Output directory"),
+				c('ImageSize'       , 's', 1, 'numeric'  , "1960"       , "Image size"),
+				c('PPI'             , 'i', 1, 'numeric'  , "200"        , "Image resolution"),
+				c('logBase'         , 'o', 1, 'numeric'  , "10"         , "log base for image and result"),
+				c('geneNumber'      , 'z', 1, 'numeric'  , "30"         , "Gene number for heatmap of most highly expressed genes."),
+				c('sharingMode'     , 'v', 1, 'character', "maximum"    , "Sharing mode of estimate dispersion fonction (maximum, fit-only, gene-est-only)"),
+				c('method'	    	, 'w', 1, 'character', "pooled"   	, "Method of estimate dispersion fonction (pooled, per-condition or blind)"),
+				c('fitType'         , 't', 1, 'character', "parametric" , "Fit type of estimate dispersion fonction (local or parametric)")
+		)
+)
+attach(optArgs)
+sample = data.frame(replicate=replicate, files=HTSeqcount, condition=condition,stringsAsFactors=F)
+
+if (help) {
+	#AO : deprecated
+	cat("DESeqTools version eBio
+					Commande : script_deseq.R [options] file1 file2 file3 file4 .... 
+					Exemple: ./script_deseq.R --condition=Cond1 --replicate=replicate1 -HTSeqcount=file_count1.txt
+					--condition=Cond1 --replicate=replicate2 -HTSeqcount=file_count2.txt  
+					--condition=Cond2 --replicate=replicate1 -HTSeqcount=file_count3.txt 
+					--condition=Cond2 --replicate=replicate2 -HTSeqcount=file_count4.txt")
+	stop("",call.=F)
+}
+
+## Supress warning
+options(warn=-1)
+
+if (length(unique(condition))!=2){
+	stop("Please specify exactly TWO and ONLY two diferent condition names",call.=F)
+}
+
+if (length(condition)!=length(HTSeqcount) || length(replicate) != length(HTSeqcount)){
+	stop("You must specify as many conditions and replicates as files. In your input I\'ve found ",
+			length(HTSeqcount)," files, ",
+			length(condition)," conditions, ",
+			length(replicate)," replicates", call.=F)
+}
+
+# Chargement des packages et des fonctions
+suppressPackageStartupMessages(library("DESeq"))
+suppressPackageStartupMessages(library("RColorBrewer"))
+suppressPackageStartupMessages(library("gplots"))
+suppressPackageStartupMessages(library("plotrix"))
+
+
+## conditions
+conds <- unique(sample$condition)
+
+########################################################
+# Counts matrix creation
+countTable = CreateCountMatrix(sample, IsHeader, IsReplicate)
+
+# suppress non expressed transcript in all conditions
+countTable=countTable[apply(countTable,1,sum)!=0,]
+
+# Make relations between names and conditions
+design = data.frame(names = sample$replicate, condition = sample$condition )
+ 
+# DESeq main analysis, NB : type of analysis depend on IsReplicate
+cds = DE_analysis(countTable,design,IsReplicate,mode=sharingMode, method=method, fitType=fitType)
+DESeqResults = nbinomTest( cds,conds[1],conds[2])
+
+# Plot hist of null counts
+NullCondPlot(cds,file=paste(OutputDir,"_NullCondPlot.png", sep=""),ImageSize=ImageSize, PPI=PPI)
+
+# plot of total read count per sample
+TotReadSamplePlot(cds, file=paste(OutputDir,"_TotSamplePlot.png", sep="") ,ImageSize=ImageSize, PPI=PPI)
+
+# plot hist of pvalues
+#	|_->if there is replicate    : adjusted pvalue
+#	|_->if there is no replicate : raw pvalue
+PlotHistPval(DESeqResults,IsReplicate,file=paste(OutputDir,"_histPval.png", sep=""),ImageSize=ImageSize, PPI=PPI)
+
+## Violin plot for raw data
+PlotViolin(cds, FALSE, paste(OutputDir,"_RawViolin.png", sep=""), ImageSize=ImageSize, PPI=PPI, logBase=logBase)
+
+## Violin plot for raw data
+PlotViolin(cds, TRUE, paste(OutputDir,"_NormViolin.png", sep=""), ImageSize=ImageSize, PPI=PPI, logBase=logBase)
+
+# plot volcano
+PlotVolcano(res=DESeqResults, cond1=conds[1], cond2=conds[2], alpha=alpha, fold=foldchange, rep=IsReplicate, file=paste(OutputDir,"_volcanoplot.png", sep=""), ImageSize=ImageSize, PPI=PPI, logBase=logBase)
+
+# plot MA and dispersion
+MAPlot(DESeqResults,file=paste(OutputDir,"_MAplot.png", sep=""), ImageSize=ImageSize, PPI=PPI)
+EstDispPlot(cds, method, file=paste(OutputDir,"_EstDispPlot.png", sep=""), ImageSize=ImageSize, PPI=PPI)
+
+# compute clustering
+if (IsReplicate){
+	cdsBlind = estimateDispersions( cds, method = "blind",sharingMode=sharingMode, fitType=fitType  )
+}else{
+	cdsBlind = estimateDispersions( cds, method = "blind",sharingMode='fit-only', fitType=fitType  )
+}
+vsd = varianceStabilizingTransformation( cdsBlind )
+
+# plot clustering and correlation
+HeatCountPlot(cds,vsd,file=paste(OutputDir,"_HeatCountPlot.png", sep=""), geneNumber, ImageSize=ImageSize, PPI=PPI)
+HeatDistPlot(vsd,cdsBlind,file=paste(OutputDir,"_HeatDistPlot.png", sep=""), ImageSize=ImageSize, PPI=PPI)
+
+## export result
+WriteResults (DESeqResults, countTable, counts( cds, normalized=TRUE ), conds[1], conds[2], alpha, foldchange, IsReplicate, OutputDir, logBase=logBase)
+
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test/.svn/all-wcprops	Fri Apr 25 05:05:39 2014 -0400
@@ -0,0 +1,41 @@
+K 25
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+END
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test/.svn/entries	Fri Apr 25 05:05:39 2014 -0400
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+http://svn.igmors.u-psud.fr/depot
+
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
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+zur	276
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test/.svn/text-base/A2_count.txt.svn-base	Fri Apr 25 05:05:39 2014 -0400
@@ -0,0 +1,961 @@
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+yjcE	69
+zur	166
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test/.svn/text-base/A3_count.txt.svn-base	Fri Apr 25 05:05:39 2014 -0400
@@ -0,0 +1,961 @@
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+viuB	240
+xerC	33
+yajC	373
+yjcE	63
+zur	171
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test/.svn/text-base/B1_count.txt.svn-base	Fri Apr 25 05:05:39 2014 -0400
@@ -0,0 +1,961 @@
+35kd_ag	2007
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+Rv2577	114
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+zur	585
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test/.svn/text-base/B2_count.txt.svn-base	Fri Apr 25 05:05:39 2014 -0400
@@ -0,0 +1,961 @@
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test/.svn/text-base/B3_count.txt.svn-base	Fri Apr 25 05:05:39 2014 -0400
@@ -0,0 +1,961 @@
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+relG	55
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+sirR	132
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+subI	118
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+ung	66
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+valU	1
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+vapB21	10
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+vapC42	8
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+virS	91
+viuB	40
+xerC	24
+yajC	90
+yjcE	29
+zur	228
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test/A1_count.txt	Fri Apr 25 05:05:39 2014 -0400
@@ -0,0 +1,961 @@
+35kd_ag	2021
+PE23	406
+PE24	145
+PE25	736
+PE26	578
+PE27	62
+PE27A	7
+PE29	19
+PE_PGRS39	405
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+PE_PGRS41	1280
+PE_PGRS42	47
+PE_PGRS43	146
+PE_PGRS44	156
+PE_PGRS45	241
+PE_PGRS46	211
+PE_PGRS47	427
+PE_PGRS48	290
+PPE38	124
+PPE39	120
+PPE40	1887
+PPE41	1219
+PPE42	237
+PPE43	75
+PPE44	255
+PPE45	94
+PPE46	81
+PPE47	66
+PPE48	3
+PPE49	187
+Rv2227	148
+Rv2228c	253
+Rv2229c	156
+Rv2230c	185
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+Rv2237	296
+Rv2237A	260
+Rv2239c	832
+Rv2240c	333
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+Rv2250c	53
+Rv2251	177
+Rv2252	99
+Rv2253	59
+Rv2254c	32
+Rv2255c	32
+Rv2256c	937
+Rv2257c	162
+Rv2258c	567
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+Rv2262c	89
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+Rv2272	74
+Rv2273	21
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+Rv2277c	52
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+Rv2279	71
+Rv2280	1620
+Rv2282c	58
+Rv2283	15
+Rv2285	328
+Rv2286c	124
+Rv2288	377
+Rv2292c	100
+Rv2293c	94
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+Rv2295	233
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+Rv2300c	144
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+Rv2303c	389
+Rv2304c	42
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+Rv2307c	78
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+Rv2309c	165
+Rv2310	7
+Rv2311	62
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+Rv2314c	389
+Rv2315c	485
+Rv2319c	32
+Rv2323c	89
+Rv2324	75
+Rv2325c	248
+Rv2326c	942
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+vapB21	25
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+vapB41	102
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+vapC39	99
+vapC40	65
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+vapC42	36
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+virS	112
+viuB	436
+xerC	349
+yajC	527
+yjcE	171
+zur	276
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test/A2_count.txt	Fri Apr 25 05:05:39 2014 -0400
@@ -0,0 +1,961 @@
+35kd_ag	1395
+PE23	167
+PE24	63
+PE25	320
+PE26	363
+PE27	26
+PE27A	2
+PE29	5
+PE_PGRS39	168
+PE_PGRS40	16
+PE_PGRS41	462
+PE_PGRS42	16
+PE_PGRS43	35
+PE_PGRS44	57
+PE_PGRS45	65
+PE_PGRS46	58
+PE_PGRS47	177
+PE_PGRS48	169
+PPE38	71
+PPE39	14
+PPE40	487
+PPE41	575
+PPE42	86
+PPE43	52
+PPE44	67
+PPE45	39
+PPE46	45
+PPE47	32
+PPE48	2
+PPE49	74
+Rv2227	50
+Rv2228c	62
+Rv2229c	64
+Rv2230c	73
+Rv2235	93
+Rv2237	112
+Rv2237A	57
+Rv2239c	425
+Rv2240c	162
+Rv2242	99
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+Rv2250A	22
+Rv2250c	20
+Rv2251	51
+Rv2252	21
+Rv2253	7
+Rv2254c	6
+Rv2255c	9
+Rv2256c	236
+Rv2257c	56
+Rv2258c	288
+Rv2260	57
+Rv2261c	30
+Rv2262c	26
+Rv2263	81
+Rv2264c	94
+Rv2265	10
+Rv2267c	56
+Rv2269c	9
+Rv2271	171
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+virS	68
+viuB	176
+xerC	29
+yajC	266
+yjcE	69
+zur	166
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test/A3_count.txt	Fri Apr 25 05:05:39 2014 -0400
@@ -0,0 +1,961 @@
+35kd_ag	1646
+PE23	197
+PE24	73
+PE25	404
+PE26	509
+PE27	43
+PE27A	3
+PE29	6
+PE_PGRS39	184
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+PE_PGRS42	22
+PE_PGRS43	65
+PE_PGRS44	68
+PE_PGRS45	109
+PE_PGRS46	84
+PE_PGRS47	235
+PE_PGRS48	229
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+vapC21	14
+vapC22	63
+vapC23	11
+vapC38	157
+vapC39	36
+vapC40	25
+vapC41	118
+vapC42	12
+vapC43	40
+virS	84
+viuB	240
+xerC	33
+yajC	373
+yjcE	63
+zur	171
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test/B1_count.txt	Fri Apr 25 05:05:39 2014 -0400
@@ -0,0 +1,961 @@
+35kd_ag	2007
+PE23	288
+PE24	108
+PE25	296
+PE26	448
+PE27	56
+PE27A	5
+PE29	13
+PE_PGRS39	759
+PE_PGRS40	61
+PE_PGRS41	1785
+PE_PGRS42	50
+PE_PGRS43	96
+PE_PGRS44	193
+PE_PGRS45	182
+PE_PGRS46	136
+PE_PGRS47	395
+PE_PGRS48	375
+PPE38	80
+PPE39	64
+PPE40	685
+PPE41	629
+PPE42	155
+PPE43	72
+PPE44	199
+PPE45	103
+PPE46	57
+PPE47	46
+PPE48	2
+PPE49	104
+Rv2227	81
+Rv2228c	157
+Rv2229c	114
+Rv2230c	182
+Rv2235	208
+Rv2237	231
+Rv2237A	268
+Rv2239c	873
+Rv2240c	287
+Rv2242	216
+Rv2248	174
+Rv2250A	21
+Rv2250c	35
+Rv2251	97
+Rv2252	39
+Rv2253	18
+Rv2254c	17
+Rv2255c	23
+Rv2256c	944
+Rv2257c	69
+Rv2258c	268
+Rv2260	234
+Rv2261c	56
+Rv2262c	83
+Rv2263	96
+Rv2264c	166
+Rv2265	35
+Rv2267c	90
+Rv2269c	22
+Rv2271	157
+Rv2272	64
+Rv2273	14
+Rv2275	99
+Rv2277c	23
+Rv2278	19
+Rv2279	59
+Rv2280	899
+Rv2282c	24
+Rv2283	7
+Rv2285	241
+Rv2286c	61
+Rv2288	169
+Rv2292c	117
+Rv2293c	71
+Rv2294	120
+Rv2295	231
+Rv2296	284
+Rv2297	103
+Rv2298	365
+Rv2300c	140
+Rv2302	362
+Rv2303c	406
+Rv2304c	94
+Rv2305	191
+Rv2306A	31
+Rv2306B	19
+Rv2307A	23
+Rv2307B	54
+Rv2307D	19
+Rv2307c	46
+Rv2308	118
+Rv2309A	11
+Rv2309c	148
+Rv2310	6
+Rv2311	37
+Rv2312	88
+Rv2313c	212
+Rv2314c	297
+Rv2315c	302
+Rv2319c	30
+Rv2323c	117
+Rv2324	42
+Rv2325c	265
+Rv2326c	1107
+Rv2327	280
+Rv2331	118
+Rv2331A	36
+Rv2336	310
+Rv2337c	173
+Rv2342	217
+Rv2345	1042
+Rv2348c	1053
+Rv2354	21
+Rv2355	64
+Rv2360c	125
+Rv2365c	42
+Rv2366c	216
+Rv2367c	155
+Rv2369c	9
+Rv2370c	59
+Rv2372c	692
+Rv2375	534
+Rv2387	282
+Rv2390c	460
+Rv2395	308
+Rv2401	70
+Rv2401A	25
+Rv2402	629
+Rv2405	810
+Rv2406c	159
+Rv2407	56
+Rv2409c	222
+Rv2410c	325
+Rv2411c	670
+Rv2413c	334
+Rv2414c	131
+Rv2415c	46
+Rv2417c	71
+Rv2418c	79
+Rv2420c	72
+Rv2422	4
+Rv2423	130
+Rv2424c	56
+Rv2425c	185
+Rv2426c	281
+Rv2432c	151
+Rv2433c	13
+Rv2434c	77
+Rv2435c	139
+Rv2437	51
+Rv2438A	21
+Rv2446c	42
+Rv2449c	495
+Rv2451	93
+Rv2452c	25
+Rv2454c	2047
+Rv2455c	4998
+Rv2456c	91
+Rv2459	510
+Rv2464c	168
+Rv2466c	1025
+Rv2468A	191
+Rv2468c	301
+Rv2469c	188
+Rv2472	64
+Rv2473	71
+Rv2474c	117
+Rv2475c	128
+Rv2477c	2223
+Rv2478c	42
+Rv2479c	77
+Rv2480c	28
+Rv2481c	47
+Rv2484c	1091
+Rv2488c	129
+Rv2489c	11
+Rv2491	17
+Rv2492	35
+Rv2499c	128
+Rv2506	91
+Rv2507	384
+Rv2508c	237
+Rv2509	327
+Rv2510c	97
+Rv2512c	146
+Rv2513	108
+Rv2514c	25
+Rv2515c	82
+Rv2516c	234
+Rv2517c	205
+Rv2520c	104
+Rv2522c	186
+Rv2525c	392
+Rv2529	49
+Rv2532c	119
+Rv2536	429
+Rv2541	65
+Rv2542	222
+Rv2548A	440
+Rv2551c	28
+Rv2553c	433
+Rv2554c	273
+Rv2556c	562
+Rv2557	3689
+Rv2558	3996
+Rv2559c	750
+Rv2560	114
+Rv2561	113
+Rv2562	51
+Rv2563	146
+Rv2565	358
+Rv2566	173
+Rv2567	284
+Rv2568c	76
+Rv2569c	97
+Rv2570	80
+Rv2571c	81
+Rv2573	24
+Rv2574	205
+Rv2575	319
+Rv2576c	888
+Rv2577	114
+Rv2578c	116
+Rv2581c	395
+Rv2585c	477
+Rv2597	139
+Rv2598	18
+Rv2599	19
+Rv2600	50
+Rv2603c	606
+Rv2609c	117
+Rv2611c	113
+Rv2613c	95
+Rv2614A	25
+Rv2616	825
+Rv2617c	1481
+Rv2618	1611
+Rv2619c	1607
+Rv2620c	1550
+Rv2621c	7153
+Rv2622	1034
+Rv2624c	497
+Rv2625c	340
+Rv2627c	252
+Rv2628	124
+Rv2629	1247
+Rv2630	373
+Rv2631	576
+Rv2632c	401
+Rv2633c	1312
+Rv2635	4
+Rv2636	63
+Rv2638	406
+Rv2639c	152
+Rv2640c	226
+Rv2642	109
+Rv2644c	27
+Rv2645	39
+Rv2646	52
+Rv2647	18
+Rv2648	17
+Rv2649	88
+Rv2650c	158
+Rv2651c	119
+Rv2652c	48
+Rv2653c	13
+Rv2654c	3
+Rv2655c	66
+Rv2656c	156
+Rv2657c	103
+Rv2658c	83
+Rv2659c	214
+Rv2660c	402
+Rv2661c	65
+Rv2662	47
+Rv2663	106
+Rv2664	57
+Rv2665	204
+Rv2666	28
+Rv2668	120
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+Rv2670c	58
+Rv2672	625
+Rv2675c	376
+Rv2676c	445
+Rv2680	182
+Rv2681	179
+Rv2683	180
+Rv2686c	88
+Rv2687c	73
+Rv2688c	163
+Rv2689c	132
+Rv2690c	421
+Rv2693c	272
+Rv2694c	770
+Rv2695	83
+Rv2696c	482
+Rv2698	538
+Rv2699c	690
+Rv2700	396
+Rv2704	140
+Rv2705c	165
+Rv2706c	993
+Rv2707	1274
+Rv2708c	500
+Rv2709	254
+Rv2712c	353
+Rv2714	723
+Rv2715	598
+Rv2716	138
+Rv2717c	107
+Rv2719c	370
+Rv2721c	1168
+Rv2722	58
+Rv2723	123
+Rv2728c	145
+Rv2729c	892
+Rv2730	86
+Rv2731	624
+Rv2732c	222
+Rv2733c	613
+Rv2734	331
+Rv2735c	276
+Rv2737A	62
+Rv2738c	82
+Rv2739c	64
+Rv2742c	222
+Rv2743c	536
+Rv2749	170
+Rv2750	209
+Rv2751	172
+Rv2752c	432
+Rv2762c	18
+Rv2765	77
+Rv2767c	16
+Rv2771c	83
+Rv2772c	118
+Rv2774c	72
+Rv2775	99
+Rv2776c	441
+Rv2777c	1553
+Rv2778c	577
+Rv2779c	102
+Rv2781c	2247
+Rv2787	138
+Rv2791c	2041
+Rv2792c	357
+Rv2795c	314
+Rv2797c	126
+Rv2798c	96
+Rv2799	233
+Rv2800	367
+Rv2802c	130
+Rv2803	34
+Rv2804c	44
+Rv2805	47
+Rv2806	5
+Rv2807	47
+Rv2808	52
+Rv2809	75
+Rv2810c	41
+Rv2811	5
+Rv2812	8
+Rv2813	18
+Rv2814c	74
+Rv2815c	19
+Rv2816c	93
+Rv2817c	108
+Rv2818c	126
+Rv2819c	191
+Rv2820c	167
+Rv2821c	167
+Rv2822c	82
+Rv2823c	282
+Rv2824c	148
+Rv2825c	198
+Rv2826c	70
+Rv2827c	163
+Rv2828A	151
+Rv2828c	94
+Rv2837c	358
+Rv2840c	1296
+Rv2842c	415
+Rv2843	132
+Rv2844	152
+Rv2850c	539
+Rv2851c	300
+Rv2854	110
+Rv2857c	107
+Rv2859c	92
+Rv2862c	182
+Rv2864c	178
+Rv2867c	945
+Rv2876	348
+Rv2879c	136
+Rv2880c	114
+Rv2884	683
+Rv2885c	729
+Rv2886c	425
+Rv2887	128
+Rv2891	19
+Rv2893	121
+Rv2896c	204
+Rv2897c	36
+Rv2898c	35
+Rv2901c	382
+Rv2908c	127
+Rv2910c	28
+Rv2912c	60
+Rv2913c	264
+Rv2915c	133
+Rv2917	97
+Rv2923c	102
+Rv2926c	646
+Rv2927c	1114
+Rv2929	29
+Rv2943	67
+Rv2943A	4
+Rv2944	34
+Rv2949c	1155
+Rv2951c	432
+Rv2952	187
+Rv2953	252
+Rv2954c	345
+Rv2955c	144
+Rv2956	138
+Rv2957	89
+Rv2958c	442
+Rv2959c	603
+Rv2960c	233
+Rv2961	28
+Rv2962c	291
+Rv2963	565
+Rv2966c	34
+Rv2968c	153
+Rv2969c	711
+Rv2970A	131
+Rv2971	488
+Rv2972c	85
+Rv2974c	73
+Rv2975c	120
+Rv2978c	772
+Rv2979c	400
+Rv2980	45
+Rv2983	52
+Rv2989	106
+Rv2990c	72
+Rv2991	84
+Rv2993c	237
+Rv2994	331
+Rv2997	90
+Rv2998	38
+Rv2998A	9
+Rv3000	88
+Rv3005c	533
+Rv3007c	396
+Rv3008	207
+Rv3013	39
+Rv3015c	111
+Rv3023c	162
+Rv3026c	44
+Rv3027c	47
+Rv3030	141
+Rv3031	134
+Rv3032	89
+Rv3032A	26
+Rv3033	59
+Rv3034c	190
+Rv3035	185
+Rv3037c	97
+Rv3038c	582
+Rv3040c	83
+Rv3041c	96
+Rv3046c	378
+Rv3047c	122
+Rv3049c	757
+Rv3050c	769
+Rv3054c	238
+Rv3055	77
+Rv3057c	181
+Rv3058c	360
+Rv3060c	272
+Rv3064c	54
+Rv3066	54
+Rv3067	94
+Rv3069	54
+Rv3070	29
+Rv3071	75
+Rv3072c	28
+Rv3073c	51
+Rv3074	1338
+Rv3075c	684
+Rv3076	29
+Rv3079c	135
+Rv3081	245
+Rv3083	409
+Rv3085	93
+Rv3087	425
+Rv3090	76
+Rv3091	267
+Rv3092c	507
+Rv3093c	38
+Rv3094c	67
+Rv3095	61
+Rv3096	314
+Rv3098A	157
+Rv3098c	154
+Rv3099c	706
+Rv3103c	41
+Rv3104c	276
+Rv3108	25
+Rv3113	17
+Rv3114	28
+Rv3115	150
+Rv3120	141
+Rv3122	61
+Rv3123	53
+Rv3126c	20
+Rv3127	942
+Rv3128c	344
+Rv3129	339
+Rv3131	439
+Rv3134c	17
+TB22.2	220
+TB31.7	1128
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+accD1	250
+accD6	8572
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+acyP	23
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+adi	559
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+aglA	202
+agpS	148
+ahpC	2000
+ahpD	884
+ahpE	354
+alaS	3320
+alaU	17
+ald	10918
+aldC	162
+amiA2	78
+amiC	534
+amt	158
+aprA	0
+aprB	2707
+apt	877
+argA	37
+argW	4
+aroB	167
+aroD	187
+aroE	61
+aroF	1250
+aroK	184
+arsA	102
+arsB1	105
+arsC	189
+asnT	11
+aspS	333
+atsF	154
+bcp	268
+bkdA	4021
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+bkdC	1985
+cadI	190
+cdh	301
+cdsA	342
+ceoB	249
+ceoC	308
+cfp2	1113
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+che1	1109
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+clgR	855
+clpC2	29
+clpP1	1216
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+clpX	2691
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+cobD	93
+cobO	127
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+ctaD	2902
+cut2	435
+cyp121	69
+cyp124	200
+cyp128	111
+cyp136	408
+cyp141	142
+cysA1	1021
+cysA3	3126
+cysE	155
+cysG	232
+cysH	1564
+cysK1	687
+cysT	454
+cysU	45
+cysW	175
+dacB2	125
+dapA	1268
+dapB	285
+dapF	389
+dctA	391
+ddlA	275
+dedA	69
+devR	637
+devS	569
+dfrA	93
+dgt	240
+dhaA	311
+dinF	82
+dinP	106
+dipZ	159
+dnaG	591
+dnaJ2	1448
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+echA15	101
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+efp	519
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+esxO	1404
+esxP	1005
+esxQ	86
+esxR	22
+esxS	13
+fabD	8056
+fabG5	148
+fadD13	425
+fadD22	1172
+fadD26	4081
+fadD28	4463
+fadD29	2096
+fadD35	85
+fadD9	2074
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+fadE22	297
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+gabT	410
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+glnU	15
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+gluU	7
+glyS	226
+glyT	43
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+gpsI	1248
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+hflX	513
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+hsdM	151
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+hsdS.1	22
+htpG	1049
+hupB	1295
+ideR	1798
+ilvB1	754
+ilvC	896
+ilvN	338
+infB	2309
+iscS	475
+kasA	15895
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+ldtB	2215
+lepA	260
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+leuB	528
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+leuD	136
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+lppN	17
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+lppP	58
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+lppV	39
+lppW	1033
+lppX	265
+lppY	79
+lppZ	1038
+lpqA	616
+ltp1	569
+lysU	37
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+mazE9	28
+mazF8	17
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+mbtA	386
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+mbtC	3184
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+mbtF	4479
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+mcr7	1101
+merT	307
+metV	1
+mez	226
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+mmr	19
+mmuM	101
+moaA1	50
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+moaC1	18
+moaD1	9
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+mpt53	288
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+nrdI	2636
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+phoH1	399
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+pknK	642
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+plcA	125
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+ppgK	244
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+ppk1	539
+ppsA	3802
+ppsB	1024
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+ppsD	1337
+ppsE	1449
+pptT	85
+prfB	746
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+proS	498
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+ptkA	138
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+purU	126
+pyrH	771
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+recG	89
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+ribD	103
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+rnc	854
+rne	3733
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+rplU	504
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+rpsP	485
+rpsT	640
+ruvA	128
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+secD	987
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+sirA	5055
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+smc	526
+smpB	83
+smtB	788
+snoP	68
+snzP	849
+speE	45
+sseB	742
+sseC1	747
+ssr	492125
+sthA	572
+stp	244
+subI	543
+suhB	93
+tesA	245
+tesB2	267
+tgs1	2467
+tgs4	366
+thiL	439
+thrS	481
+thyA	416
+thyX	36
+tig	959
+trmD	104
+trmU	234
+truB	111
+tsf	578
+ugpA	42
+ugpB	26
+ugpC	47
+ugpE	24
+ung	345
+uppS	161
+uspA	22
+uspB	10
+uspC	48
+valS	1133
+valT	73
+valU	5
+valV	4
+vapB16	6
+vapB17	135
+vapB18	6
+vapB19	43
+vapB20	33
+vapB21	13
+vapB22	55
+vapB23	4
+vapB38	98
+vapB39	32
+vapB40	141
+vapB41	82
+vapB42	14
+vapB43	92
+vapC16	46
+vapC17	82
+vapC18	7
+vapC19	165
+vapC20	32
+vapC21	30
+vapC22	101
+vapC23	8
+vapC38	300
+vapC39	38
+vapC40	97
+vapC41	203
+vapC42	24
+vapC43	58
+virS	145
+viuB	400
+xerC	280
+yajC	431
+yjcE	98
+zur	585
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test/B2_count.txt	Fri Apr 25 05:05:39 2014 -0400
@@ -0,0 +1,961 @@
+35kd_ag	3619
+PE23	56
+PE24	53
+PE25	46
+PE26	323
+PE27	28
+PE27A	19
+PE29	41
+PE_PGRS39	172
+PE_PGRS40	32
+PE_PGRS41	515
+PE_PGRS42	12
+PE_PGRS43	38
+PE_PGRS44	114
+PE_PGRS45	472
+PE_PGRS46	96
+PE_PGRS47	204
+PE_PGRS48	99
+PPE38	51
+PPE39	27
+PPE40	167
+PPE41	66
+PPE42	86
+PPE43	43
+PPE44	47
+PPE45	37
+PPE46	117
+PPE47	119
+PPE48	6
+PPE49	32
+Rv2227	30
+Rv2228c	56
+Rv2229c	18
+Rv2230c	27
+Rv2235	95
+Rv2237	103
+Rv2237A	70
+Rv2239c	168
+Rv2240c	18
+Rv2242	127
+Rv2248	25
+Rv2250A	10
+Rv2250c	16
+Rv2251	31
+Rv2252	33
+Rv2253	20
+Rv2254c	18
+Rv2255c	18
+Rv2256c	399
+Rv2257c	9
+Rv2258c	36
+Rv2260	27
+Rv2261c	8
+Rv2262c	15
+Rv2263	84
+Rv2264c	107
+Rv2265	17
+Rv2267c	60
+Rv2269c	8
+Rv2271	40
+Rv2272	9
+Rv2273	4
+Rv2275	24
+Rv2277c	14
+Rv2278	8
+Rv2279	53
+Rv2280	338
+Rv2282c	8
+Rv2283	3
+Rv2285	92
+Rv2286c	54
+Rv2288	29
+Rv2292c	18
+Rv2293c	25
+Rv2294	32
+Rv2295	72
+Rv2296	136
+Rv2297	82
+Rv2298	122
+Rv2300c	50
+Rv2302	420
+Rv2303c	466
+Rv2304c	36
+Rv2305	41
+Rv2306A	9
+Rv2306B	3
+Rv2307A	26
+Rv2307B	86
+Rv2307D	19
+Rv2307c	26
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+Rv2309A	4
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+Rv2310	6
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+Rv2314c	81
+Rv2315c	125
+Rv2319c	33
+Rv2323c	243
+Rv2324	146
+Rv2325c	52
+Rv2326c	268
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+Rv2331	16
+Rv2331A	10
+Rv2336	118
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+Rv2402	158
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+Rv2452c	38
+Rv2454c	1013
+Rv2455c	3524
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+Rv2481c	10
+Rv2484c	1257
+Rv2488c	65
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+Rv2491	14
+Rv2492	51
+Rv2499c	449
+Rv2506	47
+Rv2507	148
+Rv2508c	102
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+Rv2510c	37
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+Rv2513	60
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+Rv2515c	66
+Rv2516c	695
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+Rv2554c	141
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+Rv2557	2327
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+Rv2570	86
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+Rv2617c	13954
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+Rv2621c	2185
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+Rv2624c	201
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+Rv2742c	184
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+Rv2776c	156
+Rv2777c	570
+Rv2778c	95
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+Rv2791c	343
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+Rv2823c	115
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+Rv2825c	66
+Rv2826c	77
+Rv2827c	122
+Rv2828A	39
+Rv2828c	35
+Rv2837c	167
+Rv2840c	994
+Rv2842c	203
+Rv2843	37
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+Rv2850c	159
+Rv2851c	241
+Rv2854	50
+Rv2857c	24
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+Rv2862c	57
+Rv2864c	22
+Rv2867c	808
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+Rv2879c	124
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+Rv2896c	25
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+Rv2901c	232
+Rv2908c	23
+Rv2910c	33
+Rv2912c	100
+Rv2913c	582
+Rv2915c	52
+Rv2917	20
+Rv2923c	27
+Rv2926c	200
+Rv2927c	148
+Rv2929	8
+Rv2943	16
+Rv2943A	2
+Rv2944	11
+Rv2949c	110
+Rv2951c	73
+Rv2952	23
+Rv2953	30
+Rv2954c	51
+Rv2955c	25
+Rv2956	52
+Rv2957	49
+Rv2958c	53
+Rv2959c	112
+Rv2960c	25
+Rv2961	13
+Rv2962c	114
+Rv2963	253
+Rv2966c	11
+Rv2968c	60
+Rv2969c	330
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+Rv2971	150
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+Rv2974c	27
+Rv2975c	26
+Rv2978c	96
+Rv2979c	59
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+Rv2993c	38
+Rv2994	42
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+Rv2998	17
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+Rv3007c	449
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+Rv3013	6
+Rv3015c	10
+Rv3023c	77
+Rv3026c	23
+Rv3027c	18
+Rv3030	21
+Rv3031	14
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+Rv3032A	2
+Rv3033	19
+Rv3034c	49
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+Rv3049c	894
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+Rv3079c	294
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+Rv3098A	141
+Rv3098c	102
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+aprA	0
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+rbfA	312
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+recA	200
+recG	30
+recO	30
+recX	13
+relA	1673
+relF	224
+relG	43
+ribD	22
+ribF	73
+rimM	29
+rip	319
+rnc	425
+rne	991
+rnhB	162
+rnpB	128984
+rocD1	204
+rocD2	44
+rocE	71
+rpfD	131
+rpfE	6
+rpiB	266
+rplS	199
+rplU	244
+rpmA	151
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+rpsO	278
+rpsP	79
+rpsT	91
+ruvA	5
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+ruvC	13
+scoA	1387
+scoB	717
+secD	264
+secF	235
+serA1	197
+serB2	54
+sigA	766
+sigB	20498
+sirA	1487
+sirR	138
+smc	174
+smpB	14
+smtB	344
+snoP	12
+snzP	205
+speE	31
+sseB	107
+sseC1	74
+ssr	1056376
+sthA	182
+stp	115
+subI	166
+suhB	19
+tesA	58
+tesB2	61
+tgs1	982
+tgs4	697
+thiL	66
+thrS	306
+thyA	514
+thyX	11
+tig	165
+trmD	14
+trmU	39
+truB	21
+tsf	97
+ugpA	22
+ugpB	17
+ugpC	17
+ugpE	22
+ung	85
+uppS	45
+uspA	8
+uspB	11
+uspC	29
+valS	185
+valT	23
+valU	4
+valV	0
+vapB16	2
+vapB17	56
+vapB18	5
+vapB19	13
+vapB20	15
+vapB21	6
+vapB22	73
+vapB23	3
+vapB38	50
+vapB39	16
+vapB40	58
+vapB41	89
+vapB42	9
+vapB43	12
+vapC16	16
+vapC17	107
+vapC18	16
+vapC19	82
+vapC20	22
+vapC21	23
+vapC22	93
+vapC23	6
+vapC38	366
+vapC39	26
+vapC40	32
+vapC41	131
+vapC42	15
+vapC43	14
+virS	81
+viuB	62
+xerC	21
+yajC	112
+yjcE	38
+zur	222
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test/B3_count.txt	Fri Apr 25 05:05:39 2014 -0400
@@ -0,0 +1,961 @@
+35kd_ag	3697
+PE23	50
+PE24	43
+PE25	33
+PE26	227
+PE27	22
+PE27A	17
+PE29	49
+PE_PGRS39	211
+PE_PGRS40	42
+PE_PGRS41	561
+PE_PGRS42	15
+PE_PGRS43	50
+PE_PGRS44	132
+PE_PGRS45	683
+PE_PGRS46	110
+PE_PGRS47	232
+PE_PGRS48	104
+PPE38	48
+PPE39	10
+PPE40	112
+PPE41	45
+PPE42	68
+PPE43	30
+PPE44	40
+PPE45	17
+PPE46	81
+PPE47	87
+PPE48	7
+PPE49	17
+Rv2227	27
+Rv2228c	43
+Rv2229c	19
+Rv2230c	29
+Rv2235	99
+Rv2237	95
+Rv2237A	51
+Rv2239c	185
+Rv2240c	38
+Rv2242	149
+Rv2248	13
+Rv2250A	7
+Rv2250c	21
+Rv2251	25
+Rv2252	26
+Rv2253	10
+Rv2254c	13
+Rv2255c	18
+Rv2256c	429
+Rv2257c	5
+Rv2258c	32
+Rv2260	33
+Rv2261c	12
+Rv2262c	14
+Rv2263	71
+Rv2264c	107
+Rv2265	9
+Rv2267c	41
+Rv2269c	12
+Rv2271	23
+Rv2272	9
+Rv2273	1
+Rv2275	13
+Rv2277c	8
+Rv2278	13
+Rv2279	54
+Rv2280	336
+Rv2282c	7
+Rv2283	2
+Rv2285	90
+Rv2286c	61
+Rv2288	25
+Rv2292c	13
+Rv2293c	19
+Rv2294	21
+Rv2295	71
+Rv2296	146
+Rv2297	78
+Rv2298	110
+Rv2300c	58
+Rv2302	370
+Rv2303c	433
+Rv2304c	35
+Rv2305	38
+Rv2306A	9
+Rv2306B	10
+Rv2307A	11
+Rv2307B	78
+Rv2307D	11
+Rv2307c	18
+Rv2308	28
+Rv2309A	5
+Rv2309c	51
+Rv2310	0
+Rv2311	14
+Rv2312	55
+Rv2313c	36
+Rv2314c	75
+Rv2315c	99
+Rv2319c	30
+Rv2323c	257
+Rv2324	117
+Rv2325c	64
+Rv2326c	273
+Rv2327	139
+Rv2331	12
+Rv2331A	5
+Rv2336	105
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+Rv2402	120
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+Rv2454c	1017
+Rv2455c	3593
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+Rv2466c	1587
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+Rv2484c	1393
+Rv2488c	51
+Rv2489c	0
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+Rv2492	38
+Rv2499c	453
+Rv2506	58
+Rv2507	152
+Rv2508c	79
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+Rv2510c	21
+Rv2512c	76
+Rv2513	59
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+Rv2516c	662
+Rv2517c	639
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+Rv2569c	14
+Rv2570	96
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+Rv2573	13
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+Rv2575	173
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+Rv2581c	151
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+Rv2616	4802
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+Rv2621c	2145
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+Rv2633c	824
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+Rv2655c	89
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+Rv2659c	600
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+Rv2706c	1180
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+Rv2708c	211
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+Rv2739c	8
+Rv2742c	180
+Rv2743c	540
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+Rv2752c	192
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+Rv2775	57
+Rv2776c	158
+Rv2777c	478
+Rv2778c	66
+Rv2779c	63
+Rv2781c	976
+Rv2787	74
+Rv2791c	280
+Rv2792c	52
+Rv2795c	35
+Rv2797c	79
+Rv2798c	18
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+Rv2800	142
+Rv2802c	31
+Rv2803	6
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+Rv2807	6
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+Rv2822c	21
+Rv2823c	71
+Rv2824c	55
+Rv2825c	104
+Rv2826c	55
+Rv2827c	150
+Rv2828A	58
+Rv2828c	33
+Rv2837c	169
+Rv2840c	755
+Rv2842c	164
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+Rv2844	38
+Rv2850c	181
+Rv2851c	192
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+Rv2857c	21
+Rv2859c	7
+Rv2862c	66
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+Rv2867c	888
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+Rv2879c	125
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+Rv2886c	96
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+Rv2896c	36
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+Rv2901c	215
+Rv2908c	26
+Rv2910c	20
+Rv2912c	99
+Rv2913c	532
+Rv2915c	56
+Rv2917	22
+Rv2923c	24
+Rv2926c	203
+Rv2927c	150
+Rv2929	5
+Rv2943	8
+Rv2943A	0
+Rv2944	4
+Rv2949c	67
+Rv2951c	32
+Rv2952	12
+Rv2953	27
+Rv2954c	40
+Rv2955c	16
+Rv2956	41
+Rv2957	29
+Rv2958c	35
+Rv2959c	66
+Rv2960c	17
+Rv2961	14
+Rv2962c	110
+Rv2963	210
+Rv2966c	4
+Rv2968c	46
+Rv2969c	282
+Rv2970A	39
+Rv2971	125
+Rv2972c	30
+Rv2974c	18
+Rv2975c	32
+Rv2978c	104
+Rv2979c	44
+Rv2980	21
+Rv2983	16
+Rv2989	132
+Rv2990c	177
+Rv2991	20
+Rv2993c	32
+Rv2994	50
+Rv2997	22
+Rv2998	12
+Rv2998A	3
+Rv3000	22
+Rv3005c	105
+Rv3007c	446
+Rv3008	84
+Rv3013	8
+Rv3015c	18
+Rv3023c	61
+Rv3026c	13
+Rv3027c	31
+Rv3030	21
+Rv3031	8
+Rv3032	10
+Rv3032A	6
+Rv3033	20
+Rv3034c	30
+Rv3035	50
+Rv3037c	13
+Rv3038c	128
+Rv3040c	15
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+Rv3046c	275
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+Rv3049c	899
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+Rv3058c	124
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+Rv3066	52
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+Rv3069	22
+Rv3070	10
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+Rv3072c	6
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+Rv3075c	139
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+Rv3094c	45
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+Rv3098A	170
+Rv3098c	81
+Rv3099c	100
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+Rv3126c	0
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+Rv3134c	1
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+ald	5720
+aldC	43
+amiA2	16
+amiC	128
+amt	155
+aprA	0
+aprB	760
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+clpP1	965
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+cyp136	262
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