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comparison compStrains.pl @ 17:bc81db58983c draft

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author antmarge
date Wed, 29 Mar 2017 14:21:12 -0400
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16:4cea5e173134 17:bc81db58983c
1 #!/usr/bin/perl -w
2
3 #Margaret Antonio 16.01.13
4
5 #DESCRIPTION: Takes two aggregate.pl outputs and compares them using mean difference, pval for each
6 #gene. Can compare, for example, 19F in glucose and TIGR4 in glucose.
7 #DIFFERENT GENOMES (ie. diff. strains).
8 #Requires CONVERSION FILE
9
10 #USAGE: perl compStrains.pl -c <conversion.csv> <options>
11 #[<aggregateFile1.csv aggregateFile2.csv> OR -indir <indir/>]
12
13 use Data::Dumper;
14 use strict;
15 use Getopt::Long;
16 use warnings;
17 use File::Path;
18 use File::Basename;
19 use Statistics::Distributions;
20
21 #ASSIGN INPUTS TO VARIABLES USING FLAGS
22 our ($input1,$input2,$out,$sortkey,$round,$l1,$l2,$cfile);
23 GetOptions(
24 'o:s' =>\$out,
25 's:i' => \$sortkey,
26 'r:i'=> \$round,
27 'l1:s'=> \$l1,
28 'l2:s'=> \$l2,
29 'c:s'=> \$cfile,
30 'input1:s'=>\$input1,
31 'input2:s'=>\$input2
32 );
33
34 sub print_usage() {
35 print "\n";
36 print "\n##################################################################\n";
37 print "compStrains.pl: compare genes from a tn-seq experiment\n";
38 print "\tfor two DIFFERENT strains/genomes using aggregate files\n";
39
40 print "\nDESCRIPTION: Takes two aggregate.pl outputs and compares them by\n";
41 print "calculating the difference in mean fitness.\n";
42
43 print "Example: two strains tested under same condition.\n";
44 print "Note: For same strains (genomes), use compGenes.pl\n";
45
46 print "\nUSAGE:\n";
47 print "perl compStrains.pl -c conversion.csv -d inputs/\n";
48
49 print "\nREQUIRED:\n";
50 print " -d\tDirectory containing all input files (files from\n";
51 print " \taggregate fitness script)\n";
52 print " \tOR\n";
53 print " \tIn the command line (without a flag), input the name(s) of\n";
54 print " \ttwo files containing aggregate gene fitness values. \n\n";
55 print " -c\tConversion file: two columns with homologs for both organisms\n";
56
57 print "\nOPTIONAL:\n";
58 print " -h\tPrints usage and exits program\n";
59 print " -o\tOutput file for comparison data. Default: label1label2.csv\n";
60 print " -s\tSort output by this index of the file (indices begin at 0).\n";
61 print " \tDefault: by mean\n";
62 print " -r\tRound final output numbers to this number of decimals\n";
63 print " -l\tLabels for input files. Default: filenames\n";
64 print " \tTwo strings, comma separated (i.e. -l expt1,expt2).\n";
65 print " \tOrder should match file order.\n";
66 print " \n~~~~Always check that file paths are correctly specified~~~~\n";
67 print "\n##################################################################\n";
68 }
69
70 #THE @files ARRAY WILL CONTAIN INPUT FILE NAMES
71 my @files=($input1,$input2);
72
73 #GET LABELS:
74 my @labels = ($l1,$l2);
75
76
77 #CHECK IF REQ. VARIABLES WERE DEFINED USING FLAGS. IF NOT THEN USE DEFAULT VALUES
78
79 if (!$out) {$out="comp.".$labels[0].$labels[1].".csv"}
80 if (!$round){$round='%.4f'}
81
82 #OPEN INPUTTED AGGREGATE GENE FILES AND STORE THEIR CONTENTS INTO TWO HASHES
83 #FILE1 GOES INTO HASH %ONE AND FILE2 GOES INTO HASH %TWO.
84
85 #FILE1 OPENING ---> %one WHERE KEY:VALUE IS GENE_ID:(GENE_ID,INSERTIONS,MEAN,ETC.)
86 my @header;
87 my %one;
88
89 open (F1,'<',$files[0]);
90
91 #STORE COLUMN NAMES (FIRST LINE OF FILE1) FOR HEADER AND APPEND LABELS
92 my $head=<F1>; #the header in the file
93 my @cols=split(',',$head);
94 @cols=@cols[0,1,2,3,4,5,6]; #get rid of blank columns
95 for (my $j=0;$j<scalar @cols;$j++){
96 $cols[$j]=$cols[$j].'-'.$labels[0]; #mark each column name with file it comes from
97 }
98 push (@header,@cols);
99
100 while (my $line=<F1>){
101 chomp $line;
102 my @info=split(",",$line);
103 #Only keep the first 7 columns (Ones about blanks aren't needed for comparisons)
104 @info=@info[0,1,2,3,4,5,6];
105 #Sometimes genes that don't have a gene name can't be blank, so fill with NA
106 if (!$info[5]){
107 $info[5]="NA";
108 }
109 #If there are no insertions in the column "total", then make it =0 rather than blank
110 if (!$info[6]){
111 $info[6]=0;
112 }
113 $one{$info[0]}=\@info;
114 }
115 close F1;
116
117 #FILE2 OPENING ---> %two WHERE KEY:VALUE IS GENE_ID:(GENE_ID,INSERTIONS,MEAN,ETC.)
118
119 my %two;
120 open (F2,'<',$files[1]);
121
122 #STORE COLUMN NAMES (FIRST LINE OF FILE2) FOR HEADER AND APPEND LABELS
123 $head=<F2>; #the header in the file
124 @cols=split(',',$head);
125 @cols=@cols[0,1,2,3,4,5,6]; #get rid of blank columns
126 for (my $j=0;$j<scalar @cols;$j++){
127 $cols[$j]=$cols[$j].'-'.$labels[1]; #mark each column name with file it comes from
128 }
129 push (@header,@cols);
130
131 while (my $line=<F2>){
132 chomp $line;
133 my @info=split(",",$line);
134 @info=@info[0,1,2,3,4,5,6];
135 if (!$info[5]){
136 $info[5]="NA";
137 }
138 if (!$info[6]){
139 $info[6]=0;
140 }
141 $two{$info[0]}=\@info;
142 }
143 close F2;
144
145
146 #READ CONVERSION FILE INTO ARRAY.
147 #Conversion file must have strain 1 for file 1 in column 1 (index 0) and
148 #strain 2 for file 2 in column 2 (index 1)
149 #conversion file must be tab delimited with no NA fields
150 #If homologs (exist then take info from hashes (%one and %two) by referring to gene_id in KEY
151
152 my @all; #store all homologs in this hash
153 open (CONV,'<',$cfile);
154 while (my $line=<CONV>){
155 chomp $line;
156 my @genes=split("\t",$line); #Array @genes will contain two genes (SP_0000,SPT_0000)
157 if (scalar @genes==2 and $genes[0] ne "" and $genes[1] ne ""){
158 my @info;
159 my @oneArray=@{$one{$genes[0]}};
160 my @twoArray=@{$two{$genes[1]}};
161 push (@info,@oneArray,@twoArray);
162 my $diff=sprintf("$round",($info[1]-$info[8]));
163 my $total1=$info[6];
164 my $total2=$info[13];
165 my $sd1=$info[3];
166 my $se1=$info[4];
167 my $sd2=$info[10];
168 my $se2=$info[11];
169 my $df=$total1+$total2-2;
170 my $tdist;
171 my $pval;
172 #TDIST, PVAL calculations with fail if standard dev, error, or counts are not real numbers
173 #or if 0 ends up in denominator
174 if ($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 $sd2==0){
175 ($tdist,$pval)=("NA","NA");
176 }
177 else{
178 $tdist=sqrt((($diff)/(sqrt((($sd1**2)/$total1)+(($sd2**2)/$total2))))**2);
179 $pval=Statistics::Distributions::tprob($df,$tdist);
180 }
181 push (@info,$diff,$df,$tdist,$pval);
182 push (@all,\@info);
183 }
184 }
185 close CONV;
186
187 #SORT THE HOMOLOGS BY THE SORTKEY OR BY DEFAULT DIFFERENCE IN MEAN FITNESSES
188 if (!$sortkey){
189 $sortkey=14; #for mean difference
190 }
191 my @sorted = sort { $b->[$sortkey] <=> $a->[$sortkey] } @all;
192
193 #FINISH THE HEADER BY ADDING COLUMN NAMES FOR MEAN-DIFF, DOF, TDIST, AND PVALUE
194 my $field="MeanDiff(".$labels[0].'.'.$labels[1].")";
195 push (@header,$field,"DOF","TDIST","PVALUE");
196
197 #PRINT MATCHED HOMOLOG INFORMATION INTO A SINGLE OUTPUT FILE
198 open OUT, '>',"$out";
199 print OUT (join(',',@header),"\n");
200 foreach (@sorted){
201 my @woo=@{$_};
202 print OUT join(',',@woo),"\n";
203 }
204
205 close OUT;
206
207