Mercurial > repos > antmarge > compgenes

changeset 8:d85d5b108937 draft

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Deleted selected files
author antmarge
date Wed, 29 Mar 2017 19:38:55 -0400
parents 9c995a9f974d
children 29b882d7b60f
files compGenes.pl compGenes.xml tool_dependencies.xml
diffstat 3 files changed, 0 insertions(+), 252 deletions(-) [+]
line wrap: on
line diff
--- a/compGenes.pl	Wed Mar 29 14:54:07 2017 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,187 +0,0 @@
-#!/usr/bin/perl -w
-
-#Margaret Antonio 17.01.06 without essentiality. For original, unmodified aggregate.pl output (where unique insertions are not included). 
-
-use Getopt::Long;
-use Statistics::Distributions;
-use strict;
-use autodie;
-no warnings;
-
-#no warnings;
-
-#ASSIGN INPUTS TO VARIABLES USING FLAGS
-our ($input1, $input2, $h, $out, $sortkey, $round, $l1, $l2, $outfile);
-
-GetOptions(
-'input1:s' => \$input1,
-'input2:s' => \$input2,
-'h' => \$h,
-'o:s' =>\$outfile,
-'r:i'=> \$round,
-
-);
-
-sub print_usage() {
-    print "\n####################################################################\n";
-    
-    print "compGenes: compare genes for an organism under different conditions\n\n";
-    print "DESCRIPTION: Takes two aggregate.pl outputs and compares them by\n";
-    print "calculating the difference in mean fitness for each gene.\n";
-    print "Example: compare organism in presence of control vs antibiotic.\n";
-    print "Note: For different strains/genomes, use compStrains.pl\n";
-    
-    print "\nUSAGE:";
-    print "perl compGenes.pl -d inputs/ \n\n";
-    
-    print "REQUIRED:\n";
-    print " -d\tDirectory containing all input files (files from\n";
-    print "   \taggregate script)\n";
-    print "   \tOR\n";
-    print "   \tIn the command line (without a flag), input the name(s) of\n";
-    print "   \ttwo files containing aggregate gene fitness values. \n\n";
-    
-    print "OPTIONAL:\n";
-    print " -h\tPrints usage and exits program\n";
-    print " -o\tOutput file for comparison data. Default: label1label2.csv\n";
-    print " -r\tRound final output numbers to this number of decimals\n";
-    print " -l1\tLabels for input files. Default: filenames\n";
-    print "   \tTwo strings, comma separated (i.e. -l expt1,expt2).\n";
-    print "   \tOrder should match file order.\n";
-    
-    print " \n~~~~Always check that file paths are correctly specified~~~~\n";
-    print "\n##################################################################\n";
-
-}
-
-# Check if help needed or if improper inputs
-
-if ($h){
-    print_usage();
-    exit;
-}
-
-if (! $outfile){
-    $outfile="geneComp.csv"
-}
-$round = '%.4f';
-
-my @files=($input1,$input2);
-
-#GET LABELS: USE (-l) OR USE FILNEAMES AS LABELS FOR COLUMNS IN OUTPUT FILE
-
-my @labels=($l1,$l2);
-
-#CHECK IF REQ. VARIABLES WERE DEFINED USING FLAGS. IF NOT THEN USE DEFAULT VALUES
-
-#$out="comp.".$labels[0].$labels[1].".csv";
-
-#READ INPUT FILES AND PUT GENE INFO FROM EACH LINE INTO HASH %all WHERE KEY=GENE_ID AND
-#VALUE=GENE INFO (MEAN FITNESS, # INSERTIONS, ETC.)
-
-my %all;
-my @header;
-
-#OPEN TWO COMPARISON FILES, ONE PER LOOP
-for (my $i=0; $i<2; $i++){
-    print "File #",$i+1,"\t";
-    my $file=$files[$i];
-    print $file,"\n";
-    
-    open(DATA, '<', $file) or die "Could not open '$file'\n";
-    
-    #EXTRACT THE HEADER (COLUMN NAMES) OF THE FILE AND KEEP FOR OUTPUT HEADER
-    #APPEND FILE NAME OR GIVEN LABEL (-l) TO COLUMN NAME SO ITS DIFFERENT FROM OTHER INPUT FILE
-    
-    my $head=<DATA>;
-    my @temp = split("\n",$head);
-    $head = $temp[0];
-    
-    my @cols=split(',',$head);
-    @cols = @cols[0,1,2,3,4,5];
-    for (my $j=0;$j<scalar @cols;$j++){
-        $cols[$j]=$cols[$j].'-'.$labels[$i];
-    }
-    push (@header,@cols);
-    while (my $entry = <DATA>) {
-        chomp $entry;
-        my @line=split(",",$entry);
-        if (!$line[5]){
-            $line[5]="NA";
-        }
-        if (!$line[6]){
-            $line[6]=0;
-        }
-        @line=@line[0,1,2,3,4,5];
-        my $gene=$line[0];
-        chomp($gene);
-        
-        #PUT GENE AND INFO INTO THE HASH FOR EXISTING KEY (1ST FILE) OR CREATE NEW KEY (2ND FILE)
-        
-        if (!exists $all{$gene}){
-            my @info;
-            push (@info,@line);
-            $all{$gene}=\@info;
-        }
-        else{
-            my @info=@{$all{$gene}};
-            push (@info,@line);
-            my $diff=sprintf("$round",($info[1]-$info[7]));
-            my $total1=$info[2];
-            my $total2=$info[8];
-            my $sd1=$info[3];
-            my $se1=$info[4];
-            my $sd2=$info[9];
-            my $se2=$info[10];
-            my $df=$total1+$total2-2;
-            my $tdist;
-            my $pval;
-            
-            # CHECK TO MAKE SURE ALL VARIABLES IN TDIST,PVAL CALCULATIONS ARE NUMBERS AND NO
-            # ZEROS (0) IN THE DENOMINATOR
-            
-            if ($se1 eq "X" or $se2 eq "X" or $sd1 eq "X" or $sd2 eq "X" or $total1==0 or $total2==0 or $sd1==0 or $sd2==0 or $df<=0){
-                ($tdist,$pval)=("NA","NA");
-            }
-            else{
-                $tdist=sqrt((($diff)/(sqrt((($sd1**2)/$total1)+(($sd2**2)/$total2))))**2);
-                
-                $pval=Statistics::Distributions::tprob($df,$tdist);
-            }
-            push (@info,$diff,$df,$tdist,$pval);
-            $all{$gene}=\@info;
-        }
-    }
-    close DATA;
-}
-
-#READ ALL HASH CONTENTS INTO 2D ARRAY FOR EASY SORTING AND PRINTING TO OUT FILE
-my @unsorted;
-
-foreach my $entry (keys %all) {
-    my @info=@{$all{$entry}};
-    my @temp;
-    push (@temp,@info);
-    push (@unsorted,\@temp);
-}
-
-#SORT GENES BY PVALUE OR FITNESS DEPENDING ON WHICH FLAG WAS USED IN COMMANDLINE
-
-$sortkey=15; #default: sort by difference of means
-
-my @sorted = sort { $a->[$sortkey] <=> $b->[$sortkey] } @unsorted;
-
-#ADD NEW FIELDS TO HEADER (COLUMN NAMES)
-my $field="Mean".$labels[0].'.'.$labels[1];
-push (@header,$field,"DOF","TDIST","PVALUE");
-
-#PRINT TO OUT FILE
-open OUT, '>',"$outfile";
-print OUT (join(',',@header),"\n");
-foreach (@sorted){
-    my @woo=@{$_};
-    print OUT join(',',@woo),"\n";
-    }
-close OUT;
-
-
--- a/compGenes.xml	Wed Mar 29 14:54:07 2017 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,53 +0,0 @@
-<tool id="compGenes" name="Compare Genes" version="0.1.0">
-    
-    <!-- Margaret Antonio  17.01.08 -->
-
-    <description> compare gene aggregate fitness from two different experiments</description>
-    
-    <requirements>
-        <requirement type="package" version="5.18.1">perl</requirement>
-        <requirement type="package" version="2.45">perl_getopt_long</requirement>
-        <requirement type="package" version="1.02">perl_statistics_distributions</requiremnt>
-    </requirements>
-    
-    <command interpreter="perl">
-        compGenes.pl
-        -input1 $input1
-        -input2 $input2
-        -l1 $l1
-        -l2 $l2
-        -o $outfile
-    </command>
-   
-    <inputs>
-        <param name="input1" type="data" label="csv gene aggregate fitness file #1"/>
-        <param name="input2" type="data" label="csv gene aggregate fitness file #2"/>
-        <param name="l1" type="text" value ="input1" label="Label for input #1"/>
-        <param name="l2" type="text" value ="input2" label="Label for input #2"/>
-        
-
-    </inputs>
-   
-    <outputs>
-        <data format="csv" name="outfile"  />
-    </outputs>
-    
-    <help>
-        **What it does**
-        
-        This tool compares genes for an organism under different conditions. It takes two geneAgregate outputs and compares them calculating the difference in mean fitness for each gene. Example usage: compare organism in presence of control vs antibiotic. For different strains/genomes, where gene ids are not the same, use compStrains.pl;
-
-        
-        **The options explained**
-        
-        Input 1 and 2: These are the csv (comma separated values) files containing the gene fitness values. Since they should have been produced by the "Aggregate Fitness" tool, each line besides the header should represent the following information for a gene: Locus, Fitness, NumberofInsertions, StandardDev of insertion fitness, Standard Error of insertion fitness, and Marking
-        
-        Label 1 and 2: Labels for the column headers for files in the comparison
-        
-        
-        The name of your output file: self-explanatory. Remember to have it end in ".csv".
-        
-        
-    </help>
-    
-</tool>
--- a/tool_dependencies.xml	Wed Mar 29 14:54:07 2017 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,12 +0,0 @@
-<?xml version="1.0"?>
-<tool_dependency>
-    <package name="perl" version="5.18.1">
-         <repository changeset_revision="35f117d7396b" name="package_perl_5_18" owner="iuc" prior_installation_required="True" toolshed="https://toolshed.g2.bx.psu.edu" />
-    </package>
-    <package name="perl_statistics_distributions" version="1.02">
-        <repository changeset_revision="87b28bffa033" name="package_perl_statistics_distributions" owner="antmarge" toolshed="https://toolshed.g2.bx.psu.edu" />
-    </package>
-    <package name="perl_getopt_long" version="2.45">
-	<repository changeset_revision="6d8f9d1ee8d5" name="package_perl_getoptlong" owner="antmarge" toolshed="https://toolshed.g2.bx.psu.edu" />
-    </package>
-</tool_dependency>