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Commit message:
Deleted selected files |
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removed:
compStrains.pl |
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| diff -r 02d7230ec559 -r 873b49ef0e14 compStrains.pl --- a/compStrains.pl Tue Mar 28 22:17:39 2017 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
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| b'@@ -1,252 +0,0 @@\n-#!/usr/bin/perl -w\n-\n-#Margaret Antonio 16.01.13\n-\n-#DESCRIPTION: Takes two aggregate.pl outputs and compares them using mean difference, pval for each\n-#gene. Can compare, for example, 19F in glucose and TIGR4 in glucose.\n-#DIFFERENT GENOMES (ie. diff. strains).\n-#Requires CONVERSION FILE\n-\n-#USAGE: perl compStrains.pl -c <conversion.csv> <options>\n- #[<aggregateFile1.csv aggregateFile2.csv> OR -indir <indir/>]\n-\n-use Data::Dumper;\n-use strict;\n-use Getopt::Long;\n-use warnings;\n-use File::Path;\n-use File::Basename;\n-use Statistics::Distributions;\n-\n-#ASSIGN INPUTS TO VARIABLES USING FLAGS\n-our ($indir,$h,$out,$sortkey,$round,$l,$cfile);\n-GetOptions(\n-\'d:s\' => \\$indir,\n-\'h\' => \\$h,\n-\'o:s\' =>\\$out,\n-\'s:i\' => \\$sortkey,\n-\'r:i\'=> \\$round,\n-\'l1:s\'=> \\$l1,\n-\'l2:s\'=> \\$l2,\n-\'c:s\'=> \\$cfile,\n-);\n-\n-sub print_usage() {\n- print "\\n";\n- print "\\n##################################################################\\n";\n- print "compStrains.pl: compare genes from a tn-seq experiment\\n";\n- print "\\tfor two DIFFERENT strains/genomes using aggregate files\\n";\n- \n- print "\\nDESCRIPTION: Takes two aggregate.pl outputs and compares them by\\n";\n- print "calculating the difference in mean fitness.\\n";\n- \n- print "Example: two strains tested under same condition.\\n";\n- print "Note: For same strains (genomes), use compGenes.pl\\n";\n- \n- print "\\nUSAGE:\\n";\n- print "perl compStrains.pl -c conversion.csv -d inputs/\\n";\n- \n- print "\\nREQUIRED:\\n";\n- print " -d\\tDirectory containing all input files (files from\\n";\n- print " \\taggregate fitness script)\\n";\n- print " \\tOR\\n";\n- print " \\tIn the command line (without a flag), input the name(s) of\\n";\n- print " \\ttwo files containing aggregate gene fitness values. \\n\\n";\n- print " -c\\tConversion file: two columns with homologs for both organisms\\n";\n-\n- print "\\nOPTIONAL:\\n";\n- print " -h\\tPrints usage and exits program\\n";\n- print " -o\\tOutput file for comparison data. Default: label1label2.csv\\n";\n- print " -s\\tSort output by this index of the file (indices begin at 0).\\n";\n- print " \\tDefault: by mean\\n";\n- print " -r\\tRound final output numbers to this number of decimals\\n";\n- print " -l\\tLabels for input files. Default: filenames\\n";\n- print " \\tTwo strings, comma separated (i.e. -l expt1,expt2).\\n";\n- print " \\tOrder should match file order.\\n";\n-\tprint " \\n~~~~Always check that file paths are correctly specified~~~~\\n";\n- print "\\n##################################################################\\n";\n-}\n-if ($h){\n- print_usage();\n- exit;\n-}\n-if (!$indir and (scalar @ARGV==0)){\n-\tprint "\\nERROR: Please correctly specify input files or directory\\n";\n- print_usage();\n-\tprint "\\n";\n-\texit;\n-}\n-if (!$cfile){\n-\tprint "\\nERROR: Please correctly specify the required conversion file\\n";\n- print_usage();\n-\tprint "\\n";\n-\texit;\n-}\n-\n-#THE @files ARRAY WILL CONTAIN INPUT FILE NAMES, EXTRACTED FROM A DIRECTORY (-indir) OR ARGV\n-my @files;\n-if ($indir){\n- my $directory="$indir";\n- opendir(DIR, $directory) or (print "Couldn\'t open $directory: $!\\n" and print_usage() and exit);\n- my @direct= readdir DIR;\n- my $tail=".csv";\n- foreach (@direct){\n- if (index($_, $tail) != -1){\n- $_=$indir.$_;\n- push (@files,$_);\n- }\n- }\n- closedir DIR;\n-}\n-else{\n- @files=@ARGV;\n-}\n-\n-#GET LABELS: USE (-l) OR USE FILNEAMES AS LABELS FOR COLUMNS IN OUTPUT FILE\n-\n-my @labels;\n-\n-my @labels = ($l1,$l2);\n-#if ($l){\n-# @labels=split(\',\',$l);\n-#}\n-#else{\n-# foreach (@files){\n-# my $filename=basename($_);\n-# my @temp=split(\'\\\\.\',$filename);\n-# my $colName=$temp[0];\n-# push (@labels,$colName);\n- }\n-}\n-\n-#CHECK IF REQ. VARIABLES WERE DEFINED USING FLAGS. IF NOT THEN USE DEFAULT VALUES\n-\n-if (!$out) {$out="comp.".$labels[0].$labels[1].".csv"}\n-if (!$round){$round=\'%.4f\'}\n-\n-#OPEN INPUTTED AGGREGATE GENE FILES AND ST'..b'SH %ONE AND FILE2 GOES INTO HASH %TWO.\n-\n-#FILE1 OPENING ---> %one WHERE KEY:VALUE IS GENE_ID:(GENE_ID,INSERTIONS,MEAN,ETC.)\n-my @header;\n-my %one;\n-\n-open (F1,\'<\',$files[0]);\n-\n-#STORE COLUMN NAMES (FIRST LINE OF FILE1) FOR HEADER AND APPEND LABELS\n-my $head=<F1>; #the header in the file\n-my @cols=split(\',\',$head);\n-@cols=@cols[0,1,2,3,4,5,6]; #get rid of blank columns\n-for (my $j=0;$j<scalar @cols;$j++){\n- $cols[$j]=$cols[$j].\'-\'.$labels[0]; #mark each column name with file it comes from\n-}\n-push (@header,@cols);\n-\n-while (my $line=<F1>){\n- chomp $line;\n- my @info=split(",",$line);\n- #Only keep the first 7 columns (Ones about blanks aren\'t needed for comparisons)\n- @info=@info[0,1,2,3,4,5,6];\n- #Sometimes genes that don\'t have a gene name can\'t be blank, so fill with NA\n- if (!$info[5]){\n- $info[5]="NA";\n- }\n- #If there are no insertions in the column "total", then make it =0 rather than blank\n- if (!$info[6]){\n- $info[6]=0;\n- }\n- $one{$info[0]}=\\@info;\n-}\n-close F1;\n-\n-#FILE2 OPENING ---> %two WHERE KEY:VALUE IS GENE_ID:(GENE_ID,INSERTIONS,MEAN,ETC.)\n-\n-my %two;\n-open (F2,\'<\',$files[1]);\n-\n-#STORE COLUMN NAMES (FIRST LINE OF FILE2) FOR HEADER AND APPEND LABELS\n-$head=<F2>; #the header in the file\n-@cols=split(\',\',$head);\n-@cols=@cols[0,1,2,3,4,5,6]; #get rid of blank columns\n-for (my $j=0;$j<scalar @cols;$j++){\n- $cols[$j]=$cols[$j].\'-\'.$labels[1]; #mark each column name with file it comes from\n-}\n-push (@header,@cols);\n-\n-while (my $line=<F2>){\n- chomp $line;\n- my @info=split(",",$line);\n- @info=@info[0,1,2,3,4,5,6];\n- if (!$info[5]){\n- $info[5]="NA";\n- }\n- if (!$info[6]){\n- $info[6]=0;\n- }\n- $two{$info[0]}=\\@info;\n-}\n-close F2;\n-\n-\n-#READ CONVERSION FILE INTO ARRAY.\n-#Conversion file must have strain 1 for file 1 in column 1 (index 0) and\n- #strain 2 for file 2 in column 2 (index 1)\n- #conversion file must be tab delimited with no NA fields\n-#If homologs (exist then take info from hashes (%one and %two) by referring to gene_id in KEY\n-\n-my @all; #store all homologs in this hash\n-open (CONV,\'<\',$cfile);\n-while (my $line=<CONV>){\n- chomp $line;\n- my @genes=split("\\t",$line); #Array @genes will contain two genes (SP_0000,SPT_0000)\n- if (scalar @genes==2 and $genes[0] ne "" and $genes[1] ne ""){\n- my @info;\n- my @oneArray=@{$one{$genes[0]}};\n- my @twoArray=@{$two{$genes[1]}};\n- push (@info,@oneArray,@twoArray);\n- my $diff=sprintf("$round",($info[1]-$info[8]));\n- my $total1=$info[6];\n- my $total2=$info[13];\n- my $sd1=$info[3];\n- my $se1=$info[4];\n- my $sd2=$info[10];\n- my $se2=$info[11];\n- my $df=$total1+$total2-2;\n- my $tdist;\n- my $pval;\n- #TDIST, PVAL calculations with fail if standard dev, error, or counts are not real numbers\n- #or if 0 ends up in denominator\n- if ($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 $sd2==0){\n- ($tdist,$pval)=("NA","NA");\n- }\n- else{\n- $tdist=sqrt((($diff)/(sqrt((($sd1**2)/$total1)+(($sd2**2)/$total2))))**2);\n- $pval=Statistics::Distributions::tprob($df,$tdist);\n- }\n- push (@info,$diff,$df,$tdist,$pval);\n- push (@all,\\@info);\n- }\n-}\n-close CONV;\n-\n-#SORT THE HOMOLOGS BY THE SORTKEY OR BY DEFAULT DIFFERENCE IN MEAN FITNESSES\n-if (!$sortkey){\n- $sortkey=14; #for mean difference\n-}\n-my @sorted = sort { $b->[$sortkey] <=> $a->[$sortkey] } @all;\n-\n-#FINISH THE HEADER BY ADDING COLUMN NAMES FOR MEAN-DIFF, DOF, TDIST, AND PVALUE\n-my $field="MeanDiff(".$labels[0].\'.\'.$labels[1].")";\n-push (@header,$field,"DOF","TDIST","PVALUE");\n-\n-#PRINT MATCHED HOMOLOG INFORMATION INTO A SINGLE OUTPUT FILE\n-open OUT, \'>\',"$out";\n-print OUT (join(\',\',@header),"\\n");\n-foreach (@sorted){\n- my @woo=@{$_};\n- print OUT join(\',\',@woo),"\\n";\n- }\n-\n-close OUT;\n-\n-\n' |