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CSBB-v3.0_Linux.pl
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CSBB-v3.0_Linux.pl
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#!/usr/bin/perl
use Capture::Tiny ':all';
use English qw' -no_match_vars ';
print "\nOperating System is $OSNAME\n";
##### Computational Suite For Bioinformaticians and Biologists ########
print "\n\=\=\=\=\=\=\=\=\=\=\=\=\=\=\=\=\=\=\=\=\=\=\=\=\=\=\=\=\=\=\=\=\=\=\=\=\=\=\=\=\=\=\=\=\=\n";
print "\nCSBB \- Computational Suite For Bioinformaticians and Biologists\n";
print "\n\=\=\=\=\=\=\=\=\=\=\=\=\=\=\=\=\=\=\=\=\=\=\=\=\=\=\=\=\=\=\=\=\=\=\=\=\=\=\=\=\=\=\=\=\=\n";
print "\nVersion\_3.0\n";
print "\nDeveloped and maintained by Praneet Chaturvedi\!\!\n";
print "\nPlease report issues and bugs on https://github.com/csbbcompbio/CSBB-v3.0\n";
################# TIME STAMP START ##################
my @timestamp;
open(TS,"TimeStamp_CSBB-v3.0.txt");
while(my $data = <TS>)
{
chomp $data;
push(@timestamp,$data);
}
close TS;
my $lastruncsbb=pop(@timestamp);
if($lastruncsbb eq "")
{
my $timestamp_first = localtime(time);
print "\nCSBB-v3.0 First run on $timestamp_first\n";
}
else
{
print "\nCSBB-v3.0 Last run \: $lastruncsbb\n";
}
open(TS,">>TimeStamp_CSBB-v3.0.txt");
my $timestamp = localtime(time);
print "\nCurrent Run: $timestamp\n";
print TS "$timestamp\n";
close TS;
################# TIME STAMP END ##################
################ Log Directory ###################
use Cwd;
my $cwd = getcwd;
my $log_dir=$cwd."\/".'CSBB-v3.0_Logs';
if(-d $log_dir)
{
print "\n$log_dir directory is already present\, CSBB will use the same to write module logs\n";
sleep(1);
}
else
{
mkdir($log_dir);
print "\n$log_dir directory is created\, CSBB will use this directory to write module logs\n";
sleep(1);
}
############### Log Directory End ###############
###Asking user input###
my $user_input=$ARGV[0]; chomp $user_input; ###user input through command line ##
#######################################################################
#######################################################################
############ CALLING MODULES BASED ON USER INPUT ###########
if(($user_input eq "--install")||($user_input eq "install"))
{
&install;
}
if(($user_input eq "--help")||($user_input eq "help"))
{
&help;
}
if(($user_input eq "UpperQuantile")||($user_input eq "--UpperQuantile")||($user_input eq "UQ"))
{
my $file=$ARGV[1];
&upperquantile($file);
}
if(($user_input eq "ExpressionToZscore")||($user_input eq "--ExpressionToZscore")||($user_input eq "E2Z"))
{
my $file=$ARGV[1];
&expressiontozscore($file);
}
if(($user_input eq "BasicStats")||($user_input eq "--BasicStats")||($user_input eq "BS"))
{
my $file=$ARGV[1];
&basicstats($file);
}
if(($user_input eq "ExtractGeneInfo")||($user_input eq "--ExtractGeneInfo")||($user_input eq "EGI"))
{
my $file=$ARGV[1];
my $file1=$ARGV[2];
&extractgeneinfo($file,$file1);
}
if(($user_input eq "ExpressionPlot")||($user_input eq "--ExpressionPlot")||($user_input eq "EP"))
{
my $file=$ARGV[1];
&expressionplot($file);
}
if(($user_input eq "InteractiveHeatmap")||($user_input eq "--InteractiveHeatmap")||($user_input eq "IH"))
{
my $file=$ARGV[1];
my $clustering_type=$ARGV[2];
my $color_theme=$ARGV[3];
&interactiveheatmap($file,$clustering_type,$color_theme);
}
if(($user_input eq "CorrelationProfiles")||($user_input eq "--CorrelationProfiles")||($user_input eq "CP"))
{
my $file=$ARGV[1];
my $threshold=$ARGV[2];
my $genesofinterest=$ARGV[3];
my $typeOfCorr=$ARGV[4];
&correlationprofile($file,$threshold,$genesofinterest,$typeOfCorr);
}
if(($user_input eq "Biogrid-Gene-Protein-Search")||($user_input eq "--Biogrid-Gene-Protein-Search")||($user_input eq "Biogrid"))
{
my $organism=$ARGV[1];
my $file=$ARGV[2];
&biogrid($organism,$file);
}
if(($user_input eq "DifferentialExpression")||($user_input eq "--DifferentialExpression")||($user_input eq "DE"))
{
my $file=$ARGV[1];
my $numbercontrol=$ARGV[2];
my $numbertreatment=$ARGV[3];
my $countsthreshold=$ARGV[4];
my $numbersamples=$ARGV[5];
my $typeOfNormalization=$ARGV[6];
&de($file,$numbercontrol,$numbertreatment,$countsthreshold,$numbersamples,$typeOfNormalization);
}
if(($user_input eq "PCA")||($user_input eq "--PCA"))
{
my $file=$ARGV[1];
&pca($file);
}
if(($user_input eq "NMF")||($user_input eq "--NMF"))
{
my $file=$ARGV[1];
&nmf($file);
}
if(($user_input eq "ProcessPublicData")||($user_input eq "--ProcessPublicData"))
{
my $file=$ARGV[1];
my $path=$ARGV[2];
&ProcessPublic($file,$path);
}
if(($user_input eq "InteractiveScatterPlot")||($user_input eq "--InteractiveScatterPlot")||($user_input eq "IPS"))
{
$file=$ARGV[1];
$colx=$ARGV[2];
$coly=$ARGV[3];
$colenrichment=$ARGV[4];
&interactivesp($file,$colx,$coly,$colenrichment);
}
if(($user_input eq "Process-RNASeq_SingleEnd")||($user_input eq "--Process-RNASeq_SingleEnd")||($user_input eq "RNASeq-Single"))
{
my $file=$ARGV[1]; ####### Fastq File
my $species=$ARGV[2]; ########### Works for human, mouse, frog and zebrafish
my $Output_folder_name=$ARGV[3]; ######## Output folder name
my $phred_qual=$ARGV[4]; #### Phred quality 33 or 64 [[[[ 33 if Ilumina encoding 1.8+ and rest 64]
&ProcessRNASeqSingle($file,$species,$Output_folder_name,$phred_qual);
}
if(($user_input eq "Process-RNASeq_PairedEnd")||($user_input eq "--Process-RNASeq_PairedEnd")||($user_input eq "RNASeq-Paired"))
{
my $file1=$ARGV[1]; ####### Fastq File pair 1
my $file2=$ARGV[2]; ####### Fastq File pair 2
my $species=$ARGV[3]; ########### Works for human, mouse, frog and zebrafish
my $Output_folder_name=$ARGV[4]; ######## Output folder name
my $phred_qual=$ARGV[5]; #### Phred quality 33 or 64 [[[[ 33 if Ilumina encoding 1.8+ and rest 64]
&ProcessRNASeqPaired($file1,$file2,$species,$Output_folder_name,$phred_qual);
}
if(($user_input eq "Process-ChIP-ATAC_SingleEnd")||($user_input eq "--Process-ChIP-ATAC_SingleEnd")||($user_input eq "ChIP-ATAC-Single"))
{
my $file=$ARGV[1]; ####### Fastq File
my $species=$ARGV[2]; ########### Works for human, mouse, frog and zebrafish
my $Output_folder_name=$ARGV[3]; ######## Output folder name
my $phred_qual=$ARGV[4]; #### Phred quality 33 or 64 [[[[ 33 if Ilumina encoding 1.8+ and rest 64]
my $exp_type=$ARGV[5]; #### Experiment type : ATAC, CHIP-TF or CHIP-EPIGENETIC
&ProcessChIPATACSingleEnd($file,$species,$Output_folder_name,$phred_qual,$exp_type);
}
if(($user_input eq "Process-ChIP-ATAC_PairedEnd")||($user_input eq "--Process-ChIP-ATAC_PairedEnd")||($user_input eq "ChIP-ATAC-Paired"))
{
my $file1=$ARGV[1]; ####### Fastq File pair 1
my $file2=$ARGV[2]; ####### Fastq File pair 2
my $species=$ARGV[3]; ########### Works for human, mouse, frog and zebrafish
my $Output_folder_name=$ARGV[4]; ######## Output folder name
my $phred_qual=$ARGV[5]; #### Phred quality 33 or 64 [[[[ 33 if Ilumina encoding 1.8+ and rest 64]
my $exp_type=$ARGV[6]; #### Experiment type : ATAC, CHIP-TF or CHIP-EPIGENETIC
&ProcessChIPATACPairedEnd($file1,$file2,$species,$Output_folder_name,$phred_qual,$exp_type);
}
if(($user_input eq "Generate-TPM-Counts-Matrix")||($user_input eq "--Generate-TPM-Counts-Matrix")||($user_input eq "GenerateMatrix"))
{
my $RSEM_res_dir=$ARGV[1];
my $Species=$ARGV[2];
my $output_dir=$ARGV[3];
&GenerateTPMCounts($RSEM_res_dir,$Species,$output_dir);
}
if($user_input eq "")
{
sleep(1);
&help;
}
if($user_input eq "Citation")
{
&cite;
}
#########################################################################
#########################################################################
##### MODULES CODE DOWN HERE ##########
##################### HELP MODULE ####################
sub help
{
print "\nPlease See README and White-Paper for getting detailed instructions on running CSBB-v3.0\n";
print "\n\=\=\=\=\=\=\=\=\=\=\=\=\=\=\=\=\=\=\=\=\=\=\=\=\=\=\=\=\=\=\=\=\=\=\=\=\=\=\=\=\=\=\=\=\=\n";
print "\n Please See \: Please run install module if using CSBB\-v3\.0 for first time \[just one time process\] \n";
sleep(2);
print "\nPlease use options below to run CSBB \- Computational Suite For Bioinformaticians and Biologists\n";
print "\nOptions\:\:\n";
print "\nCitation \-\-\-\> for citing CSBB please use url : https://github.com/csbbcompbio/CSBB-v3.0\n\n";
print "\ninstall \-\-\-\> for installing all the required dependencies for Pipelines \:\:only one time process\n\n";
print "\nUpperQuantile \-\-\-\> for performing upper quantile normalization\n\n";
print "\nBasicStats \-\-\-\> for obtaining stats like mean\, median\, standard deviation\, variance\, Sum\, min and max for each Gene Expression profile\n\n";
print "\nExpressionToZscore \-\-\-\> for obtaining z-scores for Gene Expression in samples\n\n";
print "\nExtractGeneInfo \-\-\-\> for obtaining info\/expression of list genes from a huge matrix gene info\/expression\n\n";
print "\nExpressionPlot \-\-\-\> for generating line plot visualizing expression\/information of genes\/entities across samples\/objects\n\n";
print "\nInteractiveHeatmap \-\-\-\> for generating interactive heatmaps for expression data\. User has three options on clustering type and four choices on color theme\. Please read README for descriptions and run command\.\n\n";
print "\nCorrelationProfiles \-\-\-\> for obtaining genes correlation profile termed as positively and negatively correlated based on User threshold\. One can obtain profile for all genes or just genes of interest \(For genes of interest user needs to provide the path to gene list file\)\. Heatmap will only be displayed for genes of interest\n\n";
print "\nBiogrid\-Gene\-Protein\-Search \-\-\-\> for obtaining gene\-protein interactions for Human and Mouse for genes of interest\n\n";
print "\nDifferentialExpression \-\-\-\> for obtaining DE genes in RNA-SEQ expriments\. Uses RUVSeq package in R\n\n";
print "\nPCA \-\-\-\> for performing Principal Component Analysis\n";
print "\nNMF \-\-\-\> for performing Nonnegative Matrix Factorization on Samples in Expression dataset\n";
print "\nProcessPublicData \-\-\-\> for processing public data \[Includes downloading .sra files from SRA, mapping to reference genome and running processing pipelines based on Assay Type for human, mouse, frog and zebrafish\]\n";
print "\nInteractiveScatterPlot \-\-\-\> for generating Interactive Scatter plot based on user preference\. User needs to provide path to the file\, Column number for x\-axis values\, Column number for y\-axis values and Column number which user needs for color factorization \(If users provides No color factorization will not be done\) Please see README for extensive explanation\n";
print "\nProcess\-RNASeq\_SingleEnd \-\-\-\> for processing Single End RNASeq data using RSEM for human, mouse, frog and zebrafish\n";
print "\nProcess\-RNASeq\_PairedEnd \-\-\-\> for processing Paired End RNASeq data using RSEM for human, mouse, frog and zebrafish\n";
print "\nGenerate-TPM-Counts-Matrix \-\-\-\> for generating TPM and Counts Matrix for Both Isoforms and Genes using CSBB RNA-seq result directory and species of interest\n";
print "\nProcess-ChIP-ATAC_SingleEnd \-\-\-\> for processing Single End ChIP and ATAC Seq data for human, mouse and frog\n";
print "\nProcess-ChIP-ATAC_PairedEnd \-\-\-\> for processing Paired End ChIP and ATAC Seq data for human, mouse and frog\n";
}
##################### MODULE END #####################
##################### Log Module Start #####################
sub logCSBB
{
my $stdout=@_[0];chomp $stdout; my $stderr=@_[1]; chomp $stderr; my $exit=@_[2]; chomp $exit; my $module_name=@_[3]; chomp $module_name;
my $outfile1="CSBB"."\_".$module_name."\_"."LOG"; my $outfile2="CSBB"."\_".$module_name."\_"."ERROR"; my $outfile3="CSBB"."\_".$module_name."\_"."EXIT-STATUS";
open(LOG,">>CSBB-v3.0_Logs/$outfile1.txt"); open(ERROR,">>CSBB-v3.0_Logs/$outfile2.txt"); open(EXIT,">>CSBB-v3.0_Logs/$outfile3.txt");
print LOG "$stdout\n"; print ERROR "$stderr\n"; print EXIT "$exit\n";
close LOG; close ERROR; close EXIT;
}
##################### MODULE END #####################
#################### MODULE CITATION #################
sub cite
{
print "Please CITE CSBB using following url : https://github.com/csbbcompbio/CSBB-v3.0\n";
}
##################### MODULE END #####################
#################### Install MODULE ##################
sub install
{
use Cwd;
my $cwd = getcwd;
print "\nInstalling Required dependencies on your system \.\.\. Please allow access to CSBB when prompted \.\. This is one time installation\n";
sleep(0.5);
print "\nPlease Provide your Linux OS type \:\: Ubuntu or Redhat\n";
my $takeOS=<stdin>; chomp $takeOS;
if($takeOS eq "Ubuntu")
{
my $scripttoinstall=$cwd."\/"."Modules"."\/"."getbrew_Linux.pl";
my $dirto_install=$cwd."\/"."Modules";
system("perl","$scripttoinstall","$dirto_install") ==0 or die "\nExcecution Stopped because of errors \.\.\. Contact Praneet Chaturvedi for bugs and issues on github\n";
print "\nRequired modules successfully insatlled\n";
}
if($takeOS eq "Redhat")
{
my $scripttoinstall=$cwd."\/"."Modules"."\/"."getbrew_Linux_Redhat.pl";
my $dirto_install=$cwd."\/"."Modules";
system("perl","$scripttoinstall","$dirto_install") ==0 or die "\nExcecution Stopped because of errors \.\.\. Contact Praneet Chaturvedi for bugs and issues on github\n";
print "\nRequired modules successfully insatlled\n";
}
}
##################### MODULE END #####################
#################### UPPER QUANTILE MODULE ##################
sub upperquantile
{
use Cwd;
my $cwd = getcwd;
print "\nUpper Quantile Normalization module loaded\n";
my $file=@_[0];chomp $file;
if($file eq "")
{
print "\nPlease provide the path to the file \.\. You can drag and drop the file from finder window \.\. Please remove space at the end and quotes\n";
$file=<stdin>;chomp $file;
}
my $start_time=time();
my $header;my $path;
my $counter=0;
my $counter1=0;
open(F,$file);
while(my $data = <F>)
{
$data =~ s/^\s+|\s+$//g;
chomp $data;
$counter++;
if($counter==1)
{
$header=$data;
}
}
close F;
print "\nStored Header Info\n";
print "\nRunning R in Background \(please be patient\)\.\.\.\.\.\n";
my @filepath=split(/\//,$file);
my $filename=pop(@filepath);
foreach my $m(@filepath)
{
if($m eq "")
{}
else
{
$path=$path."\/".$m;
}
}
my $dirtoR=$cwd."\/"."Modules"."\/"."Uquantile_normalization.r";
print "\nPerforming Upper Quantile Normalization\n";
($stdout, $stderr, $exit) = capture {
system(sudo,Rscript,$dirtoR,$path,$filename) ==0 or die "\nExcecution Stopped because of errors \.\.\. Contact Praneet Chaturvedi for bugs and issues on github\n";
};
&logCSBB($stdout,$stderr,$exit,$user_input);
print "\nR Run complete \.\.\. Now writing header with perl\n";
my $Rfile = $path."\/"."temporaryfile"."\."."txt";
my $outfile = "Quantile"."\_"."Normalized"."\_".$filename;
open(OUT,">$path/$outfile");
my $newhead=$header;
print OUT "$header\n";
open(F,"$Rfile");
while(my $data = <F>)
{
$data =~ s/^\s+|\s+$//g;
chomp $data;
$counter1++;
if($counter1==1)
{}
else
{
print OUT "$data\n";
}
}
close F;
close OUT;
unlink $Rfile;
my $end_time=time();
my $total_time=$end_time-$start_time;
print "\nRun Complete in $total_time seconds \.\.\.\n";
print "\nPlease see file $outfile for results in $path\n";
}
############################ MODULE END ############################
########################### EXPRESSIONTOZSCORE MODULE ##################
sub expressiontozscore
{
print "\nExpressionToZscore module loaded\n";
use Cwd;
my $cwd = getcwd;
my $file=@_[0];chomp $file;
if($file eq "")
{
print "\nPlease provide the path to the file \.\. You can drag and drop the file from finder window \.\. Please remove space at the end and quotes\n";
$file=<stdin>;chomp $file;
}
my $start_time=time();
my $header;my $path;
my $counter=0;
my $counter1=0;
open(F,$file);
while(my $data = <F>)
{
$data =~ s/^\s+|\s+$//g;
chomp $data;
$counter++;
if($counter==1)
{
$header=$data;
}
}
close F;
print "\nStored Header Info\n";
print "\nRunning R in Background \(please be patient\)\.\.\.\.\.\n";
my @filepath=split(/\//,$file);
my $filename=pop(@filepath);
foreach my $m(@filepath)
{
if($m eq "")
{}
else
{
$path=$path."\/".$m;
}
}
my $dirtoR=$cwd."\/"."Modules"."\/"."Zscore_Calculator.r";
print "\nPerforming Zscore Normalization\n";
($stdout, $stderr, $exit) = capture {
system(sudo,Rscript,$dirtoR,$path,$filename) ==0 or die "\nExcecution Stopped because of errors \.\.\. Contact Praneet Chaturvedi for bugs and issues on github\n";
};
&logCSBB($stdout,$stderr,$exit,$user_input);
print "\nR Run complete \.\.\. Now writing header with perl\n";
my $Rfile = $path."\/"."temporaryfile"."\."."txt";
my $outfile = "Zscores"."\_".$filename;
open(OUT,">$path/$outfile");
my $newhead=$header;
print OUT "$header\n";
open(F,"$Rfile");
while(my $data = <F>)
{
$data =~ s/^\s+|\s+$//g;
chomp $data;
$counter1++;
if($counter1==1)
{}
else
{
print OUT "$data\n";
}
}
close F;
close OUT;
unlink $Rfile;
my $end_time=time();
my $total_time=$end_time-$start_time;
print "\nRun Complete in $total_time seconds \.\.\.\n";
print "\nPlease see file $outfile for results in $path\n";
}
################################## MODULE END #############################
################################# BASICSTATS MODULE ########################
sub basicstats
{
print "\nBasicStats module loaded\n";
use Cwd;
my $cwd = getcwd;
my $file=@_[0];chomp $file;
if($file eq "")
{
print "\nPlease provide the path to the file \.\. You can drag and drop the file from finder window \.\. Please remove space at the end and quotes\n";
$file=<stdin>;chomp $file;
}
my $start_time=time();
my $path;
my $counter1=0;
print "\nRunning R in Background \(please be patient\)\.\.\.\.\.\n";
my @filepath=split(/\//,$file);
my $filename=pop(@filepath);
foreach my $m(@filepath)
{
if($m eq "")
{}
else
{
$path=$path."\/".$m;
}
}
my $dirtoR=$cwd."\/"."Modules"."\/"."BasicStats.r";
print "\nCalculating Basic Stats for all entities in the $file\n";
($stdout, $stderr, $exit) = capture {
system(sudo,Rscript,$dirtoR,$path,$filename) ==0 or die "\nExcecution Stopped because of errors \.\.\. Contact Praneet Chaturvedi for bugs and issues on github\n";
};
&logCSBB($stdout,$stderr,$exit,$user_input);
print "\nR Run complete \.\.\. Now writing header with perl\n";
my $Rfile = $path."\/"."temporaryfile"."\."."txt";
my $outfile = "BasicStats"."\_".$filename;
open(OUT,">$path/$outfile");
print OUT "Gene\tMean\tMedian\tMedian Adjusted Deviation\tStandard Deviation\tVariance\tMinimum\tMaximum\tSum\n";
open(F,"$Rfile");
while(my $data = <F>)
{
$data =~ s/^\s+|\s+$//g;
chomp $data;
$counter1++;
if($counter1==1)
{}
else
{
print OUT "$data\n";
}
}
close F;
close OUT;
unlink $Rfile;
my $end_time=time();
my $total_time=$end_time-$start_time;
print "\nRun Complete in $total_time seconds \.\.\.\n";
print "\nPlease see file $outfile for results in $path\n";
}
###################################### MODULE END ################################
############################### EXTRACTGENEINFO MODULE ##########################
sub extractgeneinfo
{
use Cwd;
my $cwd = getcwd;
print "\nExtractGeneInfo module loaded\n";
my $file1=@_[0];chomp $file1;
my $file2=@_[1];chomp $file2;
if($file1 eq "")
{
print "\nPlease provide the path to the Expression\/Info file \.\. You can drag and drop the file from finder window \.\. Please remove space at the end and quotes\n";
$file1=<stdin>;chomp $file1;
}
if($file2 eq "")
{
print "\nPlease provide the path to the Gene List file \.\. Please use header in the file CSBB assumes first line as header\.\. You can drag and drop the file from finder window \.\. Please remove space at the end and quotes\n";
$file2=<stdin>;chomp $file2;
}
my $start_time=time();
print "\nRunning Extract Gene Info Module\n";
my $dirtoperl=$cwd."\/"."Modules"."\/"."extract_gene_info.pl";
($stdout, $stderr, $exit) = capture {
system("perl","$dirtoperl","$file1","$file2") ==0 or die "\nExcecution Stopped because of errors \.\.\. Contact Praneet Chaturvedi for bugs and issues on github\n";
};
&logCSBB($stdout,$stderr,$exit,$user_input);
my $end_time=time();
my $total_time=$end_time-$start_time;
print "\nRun Complete in $total_time seconds \.\.\.\n";
print "\nPlease see file $outfile for results\n";
}
##################################### MODULE END ##################################
##################################### MODULE EXPRESSION PLOT START ###########################
sub expressionplot
{
print "\nExpressionPlot Module loaded\n";
use Cwd;
my $cwd = getcwd;
my $file=@_[0];chomp $file;
if($file eq "")
{
print "\nPlease provide the path to the file \.\. You can drag and drop the file from finder window \.\. Please remove space at the end and quotes\n";
$file=<stdin>;chomp $file;
}
my $start_time=time();
my $path;
my @filepath=split(/\//,$file);
my $filename=pop(@filepath);
foreach my $m(@filepath)
{
if($m eq "")
{}
else
{
$path=$path."\/".$m;
}
}
my $dirtoR=$cwd."\/"."Modules"."\/"."Line_Graph.r";
print "\nGenerating Expression Plots\n";
($stdout, $stderr, $exit) = capture {
system(sudo,Rscript,$dirtoR,$path,$filename) ==0 or die "\nExcecution Stopped because of errors \.\.\. Contact Praneet Chaturvedi for bugs and issues on github\n";
};
&logCSBB($stdout,$stderr,$exit,$user_input);
print "\nR Run Complete\n";
my $end_time=time();
my $total_time=$end_time-$start_time;
print "\nRun Complete in $total_time seconds\n";
print "\nExpression plot is generated and is saved in $path\n";
}
######################################### MODULE END ###############################
#################################### INTERACTIVE HEATMAP MODULE ###################
sub interactiveheatmap
{
print "\nInteractive Heatmap module loaded\n";
use Cwd;
my $cwd = getcwd;
my $file=@_[0];chomp $file;my $clustering_type=@_[1];chomp $clustering_type;my $color_theme=@_[2];chomp $color_theme;
if($file eq "")
{
print "\nPlease provide the path to the Expression file \.\. You can drag and drop the file from finder window \.\. Please remove space at the end and quotes\n";
$file=<stdin>;chomp $file;
}
if($clustering_type eq "")
{
print "\nPlease provide Clustering type\. Options are 1\. Row\_Clust for only row clustering 2\. Col\_Clust for Column CLustering 3\. Row\_Col\_Clust for both way clustering\n";
$clustering_type=<stdin>;chomp $clustering_type;
}
if($color_theme eq "")
{
print "\nPlease provide Color theme\. Options are 1\. YellowGreenOrange 2\. BlueWhiteRed 3\. YellowBlackBlue 4\. GreenWhitePurple\n";
$color_theme=<stdin>;chomp $color_theme;
}
my $start_time=time();
my $path;
my @filepath=split(/\//,$file);
my $filename=pop(@filepath);
foreach my $m(@filepath)
{
if($m eq "")
{}
else
{
$path=$path."\/".$m;
}
}
print "\nRunning R in Background\n";
print "\n$file\n";
if($clustering_type eq "Row_Clust")
{
print "runing\n";
my $dirtoR=$cwd."\/"."Modules"."\/"."Row_Clust.r";
print "\nRunning Interactive Heatmap Module with Row Clust and $color_theme color theme\n";
($stdout, $stderr, $exit) = capture {
system(sudo,Rscript,$dirtoR,$path,$filename,$color_theme) ==0 or die "\nExcecution Stopped because of errors \.\.\. Contact Praneet Chaturvedi for bugs and issues on github\n";
};
&logCSBB($stdout,$stderr,$exit,$user_input);
print "\nR Run Complete\n";
my $end_time=time();
my $total_time=$end_time-$start_time;
print "\nRun Complete in $total_time seconds\n";
print "\nBoth Interactive and Static Heatmaps are saved in the folder $path\n";
}
if($clustering_type eq "Col_Clust")
{
my $dirtoR=$cwd."\/"."Modules"."\/"."Col_Clust.r";
print "\nRunning Interactive Heatmap Module with Col Clust and $color_theme color theme\n";
($stdout, $stderr, $exit) = capture {
system(sudo,Rscript,$dirtoR,$path,$filename,$color_theme) ==0 or die "\nExcecution Stopped because of errors \.\.\. Contact Praneet Chaturvedi for bugs and issues on github\n";
};
&logCSBB($stdout,$stderr,$exit,$user_input);
print "\nR Run Complete\n";
my $end_time=time();
my $total_time=$end_time-$start_time;
print "\nRun Complete in $total_time seconds\n";
print "\nBoth Interactive and Static Heatmaps are saved in the folder $path\n";
}
if($clustering_type eq "Row_Col_Clust")
{
my $dirtoR=$cwd."\/"."Modules"."\/"."Row_Col_Clust.r";
print "\nRunning Interactive Heatmap Module with Row-Col Clust and $color_theme color theme\n";
($stdout, $stderr, $exit) = capture {
system(sudo,Rscript,$dirtoR,$path,$filename,$color_theme) ==0 or die "\nExcecution Stopped because of errors \.\.\. Contact Praneet Chaturvedi for bugs and issues on github\n";
};
&logCSBB($stdout,$stderr,$exit,$user_input);
print "\nR Run Complete\n";
my $end_time=time();
my $total_time=$end_time-$start_time;
print "\nRun Complete in $total_time seconds\n";
print "\nBoth Interactive and Static Heatmaps are saved in the folder $path\n";
}
}
############################# MODULE END ######################################
############################# CORRELATION PROFILES ############################
sub correlationprofile
{
print "\nCorrelationProfiles module loaded\n";
use Cwd;
my $cwd = getcwd;
my $file=@_[0];my $threshold=@_[1];my $genesofinterest=@_[2];chomp $file;chomp $threshold;chomp $genesofinterest;my $negativethreshold=-1*$threshold; my $typeOfCorr=@_[3]; chomp ;$typeOfCorr;
if($file eq "")
{
print "\nPlease provide the path to the Gene Expression file \.\. You can drag and drop the file from finder window \.\. Please remove space at the end and quotes\n";
$file = <stdin>;chomp $file;
}
if($threshold eq "")
{
print "\nPlease provide correlation threshold \.\. Threshold Range is -1 to 1\n";
$threshold = <stdin>;chomp $threshold;
}
if($genesofinterest eq "")
{
print "\nPlease provide genes of interest\. Options are all or Path to gene list file \.\. You can drag and drop from finder window \.\. Please remove space at the end\n";
$genesofinterest = <stdin>;chomp $genesofinterest;
}
if($typeOfCorr eq "")
{
print "\nPlease provide Correlation type\. Options are pearson or spearman or kendall\n";
$typeOfCorr = <stdin>;chomp $typeOfCorr;
}
my $start_time=time();
my $path;
my @filepath=split(/\//,$file);
my $filename=pop(@filepath);
foreach my $m(@filepath)
{
if($m eq "")
{}
else
{
$path=$path."\/".$m;
}
}
if($genesofinterest eq "all")
{
print "\nRunning R in background to perform correlations \.\.\. please be patient\.\.\.\n";
my $dirtoR=$cwd."\/"."Modules"."\/"."Correlation_for_Matrix.r";
($stdout, $stderr, $exit) = capture {
system(sudo,Rscript,$dirtoR,$path,$filename,$typeOfCorr) ==0 or die "\nExcecution Stopped because of errors \.\.\. Contact Praneet Chaturvedi for bugs and issues on github\n";
};
&logCSBB($stdout,$stderr,$exit,$user_input);
print "\nR Run complete \.\.\. Now writing header with perl\n";
my $Rfile = $path."\/"."temporaryfile"."\."."txt";
my $counter=0;my $header;my $counter1=0;
open(F,"$Rfile");
while(my $data = <F>)
{
chomp $data;
$counter++;
if($counter==1)
{
$header=$data;
}
}
close F;
my $mainhead="Entity"."\t".$header;
my $correlation_file_R=$path."\/"."Correlation"."\_"."Profiles"."\_".$filename;
open(OUT,">$correlation_file_R");
open(F,"$Rfile");
print OUT "$mainhead\n";
while(my $data = <F>)
{
chomp $data;
$counter1++;
if($counter1==1)
{}
else
{
print OUT "$data\n";
}
}
close OUT;
close F;
unlink $Rfile;
print "\nCorrelation Profiles outputted\.\. Now obtaining positive and negative correlated entities\n";
my $dirtoperl=$cwd."\/"."Modules"."\/"."obtain_positive_negative_correlation_set.pl";
($stdout, $stderr, $exit) = capture {
system("perl","$dirtoperl","$path","$filename","$correlation_file_R","$threshold") ==0 or die "\nExcecution Stopped because of errors \.\.\. Contact Praneet Chaturvedi for bugs and issues on github\n";
};
&logCSBB($stdout,$stderr,$exit,$user_input);
print "\nPositive and Negative correlation profiles obtained\n";
my $end_time=time();
my $total_time=$end_time-$start_time;
print "\nRun Complete in $total_time seconds\n";
print "\nCorrelation Profiles results are saved in $path\n";
}
if($genesofinterest =~/.txt/)
{
&extractgeneinfo($file,$genesofinterest);
my @filepath_new=split(/\//,$genesofinterest);
my $filename_new=pop(@filepath_new);
my $path_new;
foreach my $m(@filepath_new)
{
if($m eq "")
{}
else
{
$path_new=$path_new."\/".$m;
}
}
my $extractinfo_result="Expression"."\_".$filename_new;
my $temp=$path_new."\/".$extractinfo_result;
print "\nRunning R in background to perform correlations \.\.\. please be patient\.\.\.\n";
my $dirtoR=$cwd."\/"."Modules"."\/"."Correlation_for_Matrix.r";
($stdout, $stderr, $exit) = capture {
system(sudo,Rscript,$dirtoR,$path_new,$extractinfo_result,$typeOfCorr) ==0 or die "\nExcecution Stopped because of errors \.\.\. Contact Praneet Chaturvedi for bugs and issues on github\n";
};
&logCSBB($stdout,$stderr,$exit,$user_input);
unlink $temp;
print "\nR Run complete \.\.\. Now writing header with perl\n";
my $Rfile = $path_new."\/"."temporaryfile"."\."."txt";
my $counter=0;my $header;my $counter1=0;
open(F,"$Rfile");
while(my $data = <F>)
{
chomp $data;
$counter++;
if($counter==1)
{
$header=$data;
}
}
close F;
my $mainhead="Entity"."\t".$header;
my $correlation_file_R=$path."\/"."Correlation"."\_"."Profiles"."\_".$filename_new;
open(OUT,">$correlation_file_R");
open(F,"$Rfile");
print OUT "$mainhead\n";
while(my $data = <F>)
{
chomp $data;
$counter1++;
if($counter1==1)
{}
else
{
print OUT "$data\n";
}
}
close OUT;
close F;
unlink $Rfile;
my $dirtoR1=$cwd."\/"."Modules"."\/"."Row_Col_Clust_Correlation_input.r";
print "\nInteractive Heatmap Module loaded\n";
print "\nRunning R for generating heatmap using Correlation values\n";
($stdout, $stderr, $exit) = capture {
system(sudo,Rscript,$dirtoR1,$path_new,$correlation_file_R) ==0 or die "\nExcecution Stopped because of errors \.\.\. Contact Praneet Chaturvedi for bugs and issues on github\n";
};
&logCSBB($stdout,$stderr,$exit,$user_input);
print "\nR run complete \.\.\.\. Heatmap generated now finding positively and negatively correlated entity sets using perl\n";
my $dirtoperl=$cwd."\/"."Modules"."\/"."obtain_positive_negative_correlation_set.pl";
($stdout, $stderr, $exit) = capture {
system("perl","$dirtoperl","$path_new","$filename_new","$correlation_file_R","$threshold") ==0 or die "\nExcecution Stopped because of errors \.\.\. Contact Praneet Chaturvedi for bugs and issues on github\n";
};
&logCSBB($stdout,$stderr,$exit,$user_input);
my $end_time=time();
my $total_time=$end_time-$start_time;
print "\nRun Complete in $total_time seconds\n";
print "\nCorrelation Profiles files are saved in $path_new\n";
}
}
####################################### MODULE END ####################################
###################################### BIOGRID MODULE START ##########################
sub biogrid
{
print "\nBiogrid\-Gene\-Protein\-Search Module loaded\n";
use Cwd;
my $cwd = getcwd;
my $organism=@_[0];chomp $organism;my $file=@_[1]; chomp $file;
if($organism eq "")
{
print "\nPlease provide Oraganism of interest\.Options are 1\. Human 2\. Mouse\n";
$organism=<stdin>;chomp $organism;
}
if($file eq "")
{
print "\nPlease provide the path to the Gene list file \.\. You can drag and drop the file from finder window \.\. Please remove space at the end and quotes\n";
$file=<stdin>;chomp $file;
}
my $start_time=time();
my $path;
my @filepath=split(/\//,$file);
my $filename=pop(@filepath);
foreach my $m(@filepath)
{
if($m eq "")
{}
else
{
$path=$path."\/".$m;
}
}
if($organism eq "Human")
{
my $dirtoperl=$cwd."\/"."Modules"."\/"."Biogrid_ppi_Human.pl";
print "\nRunning BioGrid PPI extraction module\n";
($stdout, $stderr, $exit) = capture {
system("perl","$dirtoperl","$path","$filename") ==0 or die "\nExcecution Stopped because of errors \.\.\. Contact Praneet Chaturvedi for bugs and issues on github\n";
};
&logCSBB($stdout,$stderr,$exit,$user_input);
my $end_time=time();
my $total_time=$end_time-$start_time;
print "\nRun Complete in $total_time seconds\n";
print "\nGene Protein interaction results are saved in $path\n";
}
if($organism eq "Mouse")
{
my $dirtoperl=$cwd."\/"."Modules"."\/"."Biogrid_ppi_Mouse.pl";
print "\nRunning BioGrid PPI extraction module\n";
($stdout, $stderr, $exit) = capture {
system("perl","$dirtoperl","$path","$filename") ==0 or die "\nExcecution Stopped because of errors \.\.\. Contact Praneet Chaturvedi for bugs and issues on github\n";
};
&logCSBB($stdout,$stderr,$exit,$user_input);
my $end_time=time();
my $total_time=$end_time-$start_time;
print "\nRun Complete in $total_time seconds\n";
print "\nGene Protein interaction results are saved in $path\n";
}
}
################################### MODULE END ##########################
################################## DIFFERENTIAL EXPRESSION MODULE ###############
sub de
{
print "\nDifferentialExpression Module loaded\n";
use Cwd;
my $cwd = getcwd;
my $file=@_[0];my $numbercontrol=@_[1];my $numbertreatment=@_[2];my $countsthreshold=@_[3];my $numbersamples=@_[4];my $typeOfNorm=@_[5];
chomp $file;chomp $numbercontrol;chomp $numbertreatment;chomp $countsthreshold;chomp $numbersamples;
if($file eq "")
{
print "\nPlease provide the path to the Counts file \.\. Please place the all control samples before all treatment samples \.\. You can drag and drop the file from finder window \.\. Please remove space at the end and quotes\n";
$file=<stdin>;chomp $file;
}
if($numbercontrol eq "")
{
print "\nPlease provide the Number of Control Samples\n";
$numbercontrol=<stdin>;chomp $numbercontrol;
}
if($numbertreatment eq "")
{
print "\nPlease provide the Number of Treatment Samples\n";
$numbertreatment=<stdin>;chomp $numbertreatment;
}
if($countsthreshold eq "")
{
print "\nPlease provide the Counts threshold \n";
$countsthreshold=<stdin>;chomp $countsthreshold;
}
if($numbersamples eq "")
{
print "\nPlease provide the number of samples you want to apply counts filtering\n";
$numbersamples=<stdin>;chomp $numbersamples;
}
if($typeOfNorm eq "")
{
print "\nPlease provide the Type of Normalization you want to apply options : 1) UpperQuantile 2) UpperQuantile+Empirical \[\[ PLEASE SEE \:\:\: Normalization type is based on sequencing data quality\]\]\]\n";
$typeOfNorm=<stdin>;chomp $typeOfNorm;
}
if($typeOfNorm eq "UpperQuantile")
{
my $start_time=time();
my $path;
my @filepath=split(/\//,$file);
my $filename=pop(@filepath);
foreach my $m(@filepath)
{
if($m eq "")
{}
else
{
$path=$path."\/".$m;
}
}
my $dirtoR=$cwd."\/"."Modules"."\/"."RUVseq.r";
print "\nRunning R in background to perform DE using RUVSeq \[Normalization \: UpperQuantile\] \.\.\. \(please be patient\)\n";
($stdout, $stderr, $exit) = capture {
system(sudo,Rscript,$dirtoR,$path,$filename,$numbercontrol,$numbertreatment,$countsthreshold,$numbersamples) ==0 or die "\nExcecution Stopped because of errors \.\.\. Contact Praneet Chaturvedi for bugs and issues on github\n";
};
&logCSBB($stdout,$stderr,$exit,$user_input);
print "\nR Run complete \.\.\. Now writing header with perl\n";
my $Rfile = $path."\/"."temporaryfile"."\."."txt";
my $outfile = "DE_Using_UQ_Normalization"."\_".$filename;
open(OUT,">$path/$outfile");
print OUT "Gene\tlogFC\tlogCPM\tLR\tPvalue\tFDR\n";
open(F,"$Rfile");
while(my $data = <F>)
{
$data =~ s/^\s+|\s+$//g;
chomp $data;
$counter1++;
if($counter1==1)
{}
else
{
print OUT "$data\n";
}
}
close F;
close OUT;
unlink $Rfile;
my $end_time=time();
my $total_time=$end_time-$start_time;
print "\nRun Complete in $total_time seconds \.\.\.\n";
print "\nPlease see file $outfile in $path for results\n";
}
if($typeOfNorm eq "UpperQuantile+Empirical")
{
my $start_time=time();
my $path;
my @filepath=split(/\//,$file);
my $filename=pop(@filepath);
foreach my $m(@filepath)
{
if($m eq "")
{}
else
{
$path=$path."\/".$m;
}
}
my $dirtoR=$cwd."\/"."Modules"."\/"."RUVseq_with_empirical.r";