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STORIstats.pl
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STORIstats.pl
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#use lib '/nv/hp10/jstern7/perl5reinstall/lib';
#use lib '/nv/hp10/jstern7/perl5reinstall/lib/perl5';
use strict; use warnings;
use Fcntl ':flock';
use Data::Dumper;
use List::MoreUtils qw / uniq /;
use Statistics::Descriptive;
my %indexedNames_reverse=();
my $STORIdir = "/home/ec2-user/STORI/";
my $arrayFile = $STORIdir . "job_data_STORI.txt";
my $blastdbcmdPath = "/home/ec2-user/STORI/blastdbcmd";
my $blastdbDir="/home/ec2-user/STORI/universal20150110/blast";
my $clustalw_loc="/home/ec2-user/clustalw21/clustalw2";
my $clustalo_loc="/home/ec2-user/clustalo/clustalo";
my %converged=();
my %unconverged=();
my %paused=();
my %fin_=();
my %bact_fin_=();
my %arch_fin_=();
my %euk_fin_=();
my $repeat=1;
my %index_master=();
my %groups=();
LoadGroups();
#print "here is the converged hash after LoadGroups\n";
#print Dumper \%converged;
#print "here is groups after LoadGroups\n";
#print Dumper \%groups;
my %runHash = %{LoadRunData($arrayFile)};
#print "\n\n\nhere is the converged hash after LoadRunData\n";
#print Dumper \%converged;
#print "here is groups after LoadRunData\n";
#print Dumper \%groups;
my %run_params = %{LoadParams($arrayFile)};
my %clipboard_reverse_hash=();
my %clipboard_hash=();
my %clipboard=();
ShowMenu();
print "\n\n";
%index_master = %{ShowRuns()};
while ($repeat==1) {
my $input="";
$SIG{"ALRM"} = sub {die "TimeOut"}; #keep looping even without input
eval {alarm 300; print "STORI> "; $input = <>; alarm 0};
if ($@) {print "\n";}
else {
#print "You entered $input";
#print "\n";
}
if ($input =~ m/show\s(.+)/) {
if ($1 =~ m/groups/) {
print "showing the groups\n";
print Dumper \%groups;
#print Dumper \%converged;
}
elsif ($1 =~ m/runs/) {
print "showing the runs\n";
%index_master = %{ShowRuns()};
#Print2Darr(\@runArr);
#print Dumper \%runHash;
#print Dumper \%run_params;
}
elsif ($1 =~ m/clipboard\s?(.*)/) {
my $index=$1;
print "index\= $index\n";
if($index =~ m/^\d+$/) {
ShowClipboard($index); }
elsif ($index =~ m/^\-all\s?(.*)/) { #allows output of the clipboard contents so that sequences are matched
# with their parent taxon id, name and phylip abbreviation
my $orgFile = $1;
print "orgFile\= $orgFile\n";
if ($orgFile =~ m/(\S+)\s\-f\s(.+)/) { #this is a special case where the user did retrievals using subsampled
#taxa lists, and wishes to only output a table containing those subsampled taxa,
# and did not make separate 'subsample.txt' files, and instead prefers to
#filter the main taxa list (eg 'archaea.txt') through the 'taxa-master[subsample].txt' file,
# which contains only taxids but no nomenclature
# e.g., see figure 2 of Stern & Gaucher, 2013
my $org2 = $1;
my $filter = $2;
$filter = "taxa-master\[" . $filter . "\].txt";
print "filtering orgFile\= $org2 through $filter\n";
ShowOrganizedFilteredClipboard($org2, $filter);
}
else {
print "showing entire clipboard using org file $orgFile\n";
ShowOrganizedClipboard($orgFile);
}
}
elsif ($index =~ m/\-fulltaxa\s(.+)/) {
my $orgFile = $1;
print "showing clipboard taxa for which all families are present, using org file $orgFile\n";
ShowFullClipboard($orgFile);
}
else {
ShowClipboard();
}
}
else {
my $name = $1;
if (exists $groups{$name}) {
ShowTheseRuns($groups{$name});
}
elsif (exists $runHash{$name}) {
ShowRunResult($name);
}
elsif ($name =~ m/(.+)\s\-c/) {
ShowRunResultConcise($1);
}
elsif ($name =~ m/(.+)\s\-org\s(.+)/) {
ShowRunResultOrganized($1, $2);
}
}
}
elsif ($input =~ m/^group\s(\S+)\s\-f\s(\S+)\sthru\s(.+)/) {
my $newName = $1;
my $groupToFilter = $2;
my $expr = $3;
print "filter option.\n newName\= $newName\n groupToFilter\= $groupToFilter\n expr\= $expr\n";
MakeFilteredGroup($newName, $groupToFilter, $expr);
}
elsif ($input =~ m/^group\s(.+)/) {
my @input=split / /, $1;
my $groupName=shift(@input);
print "grouping groupName=$groupName groups=" . join(" ", @input) . "\n";
Group($groupName,\@input);
}
elsif ($input =~ m/annotate\s(.+)/) {
if (exists $clipboard_hash{$1}) {
my $ref = $clipboard{$clipboard_hash{$1}};
GetAnnotation($ref);
}
}
elsif ($input =~ m/^name\s(.+)/) {
my $ref = $clipboard{$clipboard_hash{$1}};
DoWordCensus($ref);
}
elsif ($input =~ m/Name\s(.+)/) {
AssignNames($1);
}
elsif ($input =~ m/rename\s(\d+)\s(\S+)/) {
if (exists $clipboard_hash{$1}) {
my $ref = $clipboard{$clipboard_hash{$1}};
my $oldName = $clipboard_hash{$1};
my $newName = $2;
$clipboard_hash{$1} = $newName;
$clipboard_reverse_hash{$newName} = $1;
delete $clipboard_reverse_hash{$oldName};
Rename($ref, $oldName, $newName);
}
else {
print "Sorry, index not found.\n";
}
}
elsif ($input =~ m/stats\s(.+)/) {
my $name=$1;
print "showing stats for run/group $name\n";
if (exists $groups{$name}) {
GroupStats($name);
}
else {
my $score = GetRunScore($name);
my $time = GetRunTime($name);
my $count = GetNumFamilies($name);
my @scoreTrend = @{GetAllRunScores($name)};
my @scoreTrend_r = @{Round(@scoreTrend)};
my @famTrend = @{GetNumFamsTrend($name)};
my @famTrend_r = @{Round(@famTrend)};
print "score: " . $score . "\ntime: " . $time . "\nnumFamilies: " . $count . "\n";
print join(" \| ", @scoreTrend_r) . "\n";
print join(" \| ", @famTrend_r) . "\n";
}
}
elsif ($input =~ m/ungroup\s(.+)/) {
my $groupName=$1;
print "ungrouping $groupName\n";
delete $groups{$groupName};
}
elsif ($input =~ m/clear\s(.+)/) {
my $indices=$1;
my @forClearing = @{IndexParser($indices)};
Clear(\@forClearing);
}
elsif ($input =~ m/detail\s(.+)/) {
my $name=$1;
print "details $name\n";
my $ref = $runHash{$name};
print Dumper $ref;
}
elsif ($input =~ m/compare\s(.+)\s(.+)/) {
my $run1=$1;
my $run2=$2;
PairwiseRunCompare($run1,$run2);
}
elsif ($input =~ m/getid\s(.+)/) {
my $name = $1;
if (exists $groups{$name}) {
GetID($name);
}
}
elsif ($input =~ m/parse\s(.+)/) {
IndexParser($1);
}
elsif ($input =~ m/summarize\s(.+)/) {
my $s_in = $1;
my $orgFile = -1; my $run=-1;
if ($s_in =~ m/(.+)\s\-org\s(.+)/) {
$run = $1;
$orgFile = $STORIdir . $2;
SummarizeFiltered($run, $orgFile);
}
else {
$run = $s_in;
if ($run =~ m/(\s|\.\.|\-)/) {
my @indices = @{IndexParser($run)};
foreach my $index (@indices) {
my $name = $index_master{$index};
Summarize($name);
}
}
elsif (exists $groups{$run}) {
my @runList = @{$groups{$run}};
foreach my $name (@runList) {
Summarize($name);
}
}
else {
Summarize($run);
}
}
}
elsif ($input =~ m/distance\s(identity|bitscore|length|sd)\s(.+)/) {
my $measure = $1;
my $indices = $2;
PrintDistanceMatrix($measure, $indices);
#distance <identity \|\| bitscore> <clipboard indices>
}
elsif ($input =~ m/menu/) {
ShowMenu(); }
elsif ($input =~ m/overlap/) {
FindOverlappingFamilies();
}
elsif ($input =~ m/export\sclipboard\s(\S+)\s(\S+)\s(\S+)/) {
my $famSuffix = $1;
my $fileName = $2;
my $orgFile = $3;
PrintToFileOrganizedClipboard($famSuffix, $fileName, $orgFile);
}
elsif ($input =~ m/exit/) {
$repeat=0;
}
SaveGroups();
LoadGroups();
}
print "bye!\n";
sub ShowMenu {
print "Welcome to STORI Stats!
\nMulti-node STORI ©2012 JG Stern & EA Gaucher
Single-node STORI ©2015 JG Stern
\n\t\tCommands:
\t\tshow <\'runs\' \|\| \'groups\' \|\| \'clipboard\' \[index \|\| \-all <org_file> \|\| \-fulltaxa <org_file>\] \|\| run-name [-c \|\| -org <file>]>
\t\tsummarize <run-name | indices | group> \[\-org <org_file> \(iff summarizing a single run\)\]
\t\tclear <clipboard indices>
\t\tdetail <run-name>
\t\tstats <run-name \|\| group-name>
\t\tannotate <clipboard index>
\t\tName <cutoff> (automatically renames families in clipboard\; moderately accurate)
\t\tmenu
\t\texit
\tExperimental commands:
\t\tgroup <new-group-name> \(<1 or more run-names> \|\| \-f <existing_group> thru <regexp>\)
\t\tungroup <group-name>
\t\tgetid <group>
\t\tdistance <identity \|\| bitscore \|\| sd> <clipboard indices>
\t\tscramble <clipboard indices>
\t\trename <clipboard index> <new_name>
\t\toverlap (identifies overlaps between families on the clipboard)
\t\texport clipboard <family-suffix> <file_name \(no path\)> <org_file \(no path\)>\n";
}
sub Rename {
#$ref, $oldName, $newName
my $ref = shift(@_);
my $oldName = shift(@_);
my $newName = shift(@_);
my %txgi = %{$ref};
delete $clipboard{$oldName};
$clipboard{$newName} = {%txgi};
}
sub PrintDistanceMatrix {
my $measure = shift(@_);
my $indices = shift(@_);
my @indexArr = @{IndexParser($indices)};
print "measure=$measure\n";
print "indices= " . join(" ", @indexArr) . "\n";
my %numberedFams=();
my @famArr=();
my $counter=0;
foreach my $index (@indexArr) {
if (exists $clipboard_hash{$index}) {
my $fam = $clipboard_hash{$index};
$numberedFams{$counter} = $fam;
push @famArr, $fam;
$counter++;
}
}
my %allpairs_lo=(); my %allpairs_mean=(); my %allpairs_hi=();
foreach my $numA (keys %numberedFams) {
foreach my $numB (keys %numberedFams) {
#if ($numA != $numB) {
my @temp = ($numA, $numB);
my @temp_s = sort { $a <=> $b } @temp; #sort ascending
my $famA = $numberedFams{$temp_s[0]};
my $famB = $numberedFams{$temp_s[1]};
my $famA_ref = $clipboard{$famA};
my $famB_ref = $clipboard{$famB};
if (!(exists $allpairs_lo{$famA}{$famB})) {
print "getting dist of $famA vs $famB\n";
my $ref = Distance($famA_ref, $famB_ref, $measure);
$allpairs_lo{$famA}{$famB} = $ref->[0];
$allpairs_mean{$famA}{$famB} = $ref->[1];
$allpairs_hi{$famA}{$famB} = $ref->[2];
}
#}
}
}
#print the lo matrix
print "-2stdev\n";
foreach my $famA (@famArr) {
foreach my $famB (@famArr) {
if (exists $allpairs_lo{$famA}{$famB}) {
print $allpairs_lo{$famA}{$famB} . " "; }
else {
print "- ";
}
}
print "\n";
}
#print the mean matrix
print "mean\n ";
foreach my $fam (@famArr) {
print $fam . " "; }
print "\n";
foreach my $famA (@famArr) {
print $famA . " ";
foreach my $famB (@famArr) {
if (exists $allpairs_mean{$famA}{$famB}) {
print $allpairs_mean{$famA}{$famB} . " "; }
else {
print "- ";
}
}
print "\n";
}
#print the hi matrix
print "+2stdev\n";
foreach my $famA (@famArr) {
foreach my $famB (@famArr) {
if (exists $allpairs_hi{$famA}{$famB}) {
print $allpairs_hi{$famA}{$famB} . " "; }
else {
print "- ";
}
}
print "\n";
}
}
sub Distance {
my $famA_ref = shift(@_);
my $famB_ref = shift(@_);
my $measure = shift(@_);
my @ans=(-1,-1,-1);
#print "finding distance between\n";
#print Dumper $famA_ref;
#print Dumper $famB_ref;
my $output;
if ($measure =~ m/sd/) {
my $locA = $STORIdir . "tempA.fasta";
MakeCleanFasta($famA_ref, $famB_ref, $locA); #make a fasta with acc format gi_A or gi_B
my $belvuIn = $STORIdir . "tempA.belvuIn";
AlignForBelvu($locA, $belvuIn); #align the fasta using clustalw and format the output for belvu
$output = RunScoredist($belvuIn); #run the scoredist algorithm in Belvu and compute the mean fam dist ± 2 SEM
print $output . "\n";
}
else {
my $locA = $STORIdir . "tempA.fasta";
my $locB = $STORIdir . "tempB.fasta";
MakeFasta($famA_ref, $locA);
MakeFasta($famB_ref, $locB);
my $cmd = "perl $STORIdir" . "smith-waterman-scripts/familyPairDistanceSW-2.pl " . $locA . " " . $locB;
$output = qx($cmd);
print $output . "\n";
}
if ($measure =~ m/identity/) {
#report distance as %identity
if ($output =~ m/identity\s(\S+)\s(\S+)\s(\S+)\n/) {
my $lo = $1; my $mean = $2; my $hi = $3;
$ans[0] = $lo;
$ans[1] = $mean;
$ans[2] = $hi;
}
}
elsif ($measure =~ m/bitscore/) {
#report distance as bitscore
if ($output =~ m/bitscore\s(\S+)\s(\S+)\s(\S+)\n/) {
my $lo = $1; my $mean = $2; my $hi = $3;
$ans[0] = $lo;
$ans[1] = $mean;
$ans[2] = $hi;
}
}
elsif ($measure =~ m/length/) {
#report alignment length
if ($output =~ m/length\s(\S+)\s(\S+)\s(\S+)\n/) {
my $lo = $1; my $mean = $2; my $hi = $3;
$ans[0] = $lo;
$ans[1] = $mean;
$ans[2] = $hi;
}
}
elsif ($measure =~ m/sd/) {
#report alignment length
if ($output =~ m/scoredist\s(\S+)\s(\S+)\s(\S+)\n/) {
my $lo = $1; my $mean = $2; my $hi = $3;
$ans[0] = $lo;
$ans[1] = $mean;
$ans[2] = $hi;
}
}
return \@ans;
}
sub RunScoredist {
my $belvuIn = shift(@_);
my $matrixFile = $STORIdir . "matrix.out";
my $cmd = $STORIdir . "belvu.LIN_64bit -T b -T p $belvuIn -o tree > $matrixFile";
print "cmd is $cmd\n";
system($cmd);
open MATRIX, "$matrixFile";
my %distances=();
my @seqNames=();
my $row=-1;
while (<MATRIX>) {
my $line=$_;
chomp($line);
my @lineArr = split /\t/, $line;
#pop(@lineArr);
my $col=0;
if ($lineArr[0] =~ m/\//) {
my $index=0;
foreach my $elt (@lineArr) {
$lineArr[$index] =~ s/(.+)\/.+/$1/;
$index++;
}
@seqNames = @lineArr;
#print join("\n", @seqNames);
}
elsif ($line =~ m/\d+/) {
foreach my $dist (@lineArr) {
$dist =~ m/\s*(\S+\.\S+)/;
$dist = $1;
#print "$row $col $dist\n";
$distances{$seqNames[$row]}{$seqNames[$col]}=$dist;
$col++;
}
}
$row++;
}
close MATRIX;
#print Dumper \%distances;
my @AvsB=(); my @BvsA=();
foreach my $gi1 (keys %distances) {
my %temp = %{$distances{$gi1}};
#print "$gi1\n";
#print Dumper \%temp;
foreach my $gi2 (keys %temp) {
#print "$gi1 $gi2\n";
if (($gi1 =~ m/A*/) && ($gi2 =~ m/B*/)) {
push(@AvsB, $temp{$gi2});
}
elsif (($gi1 =~ m/B*/) && ($gi2 =~ m/A*/)) {
push(@BvsA, $temp{$gi2});
}
}
}
#print Dumper \@AvsB;
#print Dumper \@BvsA;
my @alldist = (@AvsB, @BvsA);
my @ans = @{DoStats(\@alldist)};
my $final = "scoredist $ans[0] $ans[1] $ans[2]\n";
return $final;
}
sub DoStats {
my $arr_ref = shift(@_);
my @temp = @{$arr_ref};
my $n = $#temp;
my $sqrtn = sqrt($n);
my $mean = Mean(\@temp);
my $sd = Sd(\@temp);
my $stderr = ($sd/$sqrtn);
my $loBar = RoundScalar(($mean - (2*$stderr)));
my $hiBar = RoundScalar(($mean + (2*$stderr)));
$mean = RoundScalar($mean);
#print "doStats $loBar $mean $hiBar\n";
my @ans = ($loBar, $mean, $hiBar);
return \@ans;
}
sub AlignForBelvu {
#($locA, $belvuIn)
my $locA = shift(@_);
my $belvuIn = shift(@_);
my $temp = $STORIdir . "temp.aln";
my $cmd = "$clustalw_loc -INFILE=$locA -ALIGN -TYPE=PROTEIN -OUTFILE=$temp -OUTPUT=CLUSTAL -OUTORDER=ALIGNED -MATRIX=GONNET -GAPOPEN=8 -TYPE=PROTEIN -QUIET";
print "cmd is $cmd\n";
system($cmd);
$cmd = "$clustalo_loc -i $temp -o $belvuIn --outfmt=selex --force";
print "cmd is $cmd\n";
system($cmd);
}
sub MakeCleanFasta {
#($famA_ref, $famB_ref, $locA)
my $famA_ref = shift(@_);
my %txgiA = %{$famA_ref};
my $famB_ref = shift(@_);
my %txgiB = %{$famB_ref};
my $filepath = shift(@_);
my $cmd = "touch $filepath";
system($cmd);
$cmd = "rm $filepath";
system($cmd);
my %lookupA=(); my %lookupB=();
foreach my $taxon (keys %txgiA) {
if ($txgiA{$taxon} > -1) {
$lookupA{$txgiA{$taxon}} = $taxon;
}
}
foreach my $taxon (keys %txgiB) {
if ($txgiB{$taxon} > -1) {
$lookupB{$txgiB{$taxon}} = $taxon;
}
}
open (fastaFile, ">>$filepath");
foreach my $gi (keys %lookupA) {
my $taxon = $lookupA{$gi};
if ($gi > 0) {
my $cmd="$blastdbcmdPath -entry $gi -db " . $blastdbDir . "/$taxon -outfmt \"\%f\"";
#print out "cmd is: " . $cmd . "\n";
my $seq = qx($cmd);
#print out $seq;
my $replacementAcc = "\>A\_" . $gi . "\n";
$seq =~ s/\>.+\n/$replacementAcc/;
print fastaFile $seq;
}
}
foreach my $gi (keys %lookupB) {
my $taxon = $lookupB{$gi};
if ($gi > 0) {
my $cmd="$blastdbcmdPath -entry $gi -db " . $blastdbDir . "/$taxon -outfmt \"\%f\"";
#print out "cmd is: " . $cmd . "\n";
my $seq = qx($cmd);
#print out $seq;
my $replacementAcc = "\>B\_" . $gi . "\n";
$seq =~ s/\>.+\n/$replacementAcc/;
print fastaFile $seq;
}
}
close fastaFile;
}
sub MakeFasta {
my $fam_ref = shift(@_);
my %txgi = %{$fam_ref};
#print out "(begin MakeFasta) here is txgi\:\n";
#print out Dumper \%txgi;
my $filepath = shift(@_);
my $cmd = "touch $filepath";
system($cmd);
$cmd = "rm $filepath";
system($cmd);
my %lookup=();
foreach my $taxon (keys %txgi) {
if ($txgi{$taxon} > -1) {
$lookup{$txgi{$taxon}} = $taxon;
}
}
open (fastaFile, ">>$filepath");
foreach my $gi (keys %lookup) {
my $taxon = $lookup{$gi};
if ($gi > 0) {
my $cmd="$blastdbcmdPath -entry $gi -db " . $blastdbDir . "/$taxon -outfmt \"\%f\"";
#print out "cmd is: " . $cmd . "\n";
my $seq = qx($cmd);
#print out $seq;
print fastaFile $seq;
}
}
close fastaFile;
#print out "(MakeFasta)\n";
}
sub Clear {
my $arr_ref = shift(@_);
my @indices = @{$arr_ref};
print "Clearing from clipboard\: " . join(" ", @indices) . "\n";
foreach my $index (@indices) {
delete $clipboard{$clipboard_hash{$index}};
delete $clipboard_hash{$index};
}
}
sub FindOverlappingFamilies {
#Identify families on the clipboard that share members
my @pairScores=();
my %fortest=();
foreach my $famA (keys %clipboard) {
foreach my $famB (keys %clipboard) {
if (!($famA eq $famB)) {
my @temp = ($famA, $famB);
my @temp_s = sort {$a cmp $b} @temp;
my $concat = $temp_s[0] . $temp_s[1];
$fortest{$concat} = [@temp_s];
}
}
}
foreach my $arr_ref (values %fortest) {
my $famA = $arr_ref->[0];
my $famB = $arr_ref->[1];
my $agreementScore = GetAgreementScore($clipboard{$famA},$clipboard{$famB});
my $sizeA = GetFamSize($clipboard{$famA});
my $sizeB = GetFamSize($clipboard{$famB});
my @temp = ($famA, $famB, $agreementScore, $sizeA, $sizeB);
push @pairScores, [@temp];
}
my @pairScores_sorted = sort { $b->[2] <=> $a->[2] } @pairScores; #sort descending
#print Dumper \%clipboard_reverse_hash;
my @forClearing = ();
foreach my $line_ref (@pairScores_sorted) {
if ($line_ref->[2] > 0.5) {
my $famA = $line_ref->[0];
my $famB = $line_ref->[1];
my $sizeA = $line_ref->[3];
my $sizeB = $line_ref->[4];
my $famAid = $clipboard_reverse_hash{$famA};
my $famBid = $clipboard_reverse_hash{$famB};
print "$famA \(i\=$famAid\ | s\=$sizeA) $famB \(i\=$famBid\ | s\=$sizeB) $line_ref->[2]\n";
if ($sizeA > $sizeB) {
push @forClearing, $famBid; }
if ($sizeB > $sizeA) {
push @forClearing, $famAid; }
}
}
Clear(\@forClearing);
}
sub GetAgreementScore { #returns the #agreements normalized to the #taxa with a member in both famimlies
my %fam1 = %{shift(@_)};
my %fam2 = %{shift(@_)};
my $score=0;
my $size=0;
my @temp = keys %fam1;
my $size1=($#temp + 1);
@temp = keys %fam2;
my $size2=($#temp + 1);
if ($size1 < $size2) {
$size=$size1;}
else {
$size=$size2;}
foreach my $taxon (keys %fam1) {
if (exists $fam2{$taxon}) {
$fam1{$taxon} =~ m/\{*(\d+)\}*/;
my $gi1 = $1;
$fam2{$taxon} =~ m/\{*(\d+)\}*/;
my $gi2 = $1;
if ($gi1 eq $gi2) {
$score++;
}
}
}
my $final=0;
if ($size>0) {
$final=($score/$size);
}
return $final;
}
sub PrintToFileOrganizedClipboard {
my $suffix = shift(@_);
my $outFile = shift(@_);
my $orgFile = shift(@_);
$orgFile = $STORIdir . $orgFile;
my $filePath = $STORIdir . $outFile;
open clipFile, ">$filePath";
#print Dumper \%clipboard_hash;
#my $choice = shift(@_);
my @famNames=();
my @indices = keys %clipboard_hash;
my @indices_s = sort { $a <=> $b } @indices; #sort ascending
foreach my $index (@indices_s) {
push @famNames, $clipboard_hash{$index};
}
#print "\n";
print clipFile "taxID name phylum ";
foreach my $family (@famNames) {
print clipFile $family . $suffix . " ";
}
print clipFile "\n";
print "orgFile\= $orgFile\n";
if (!($orgFile eq "-1")) {
open Org, $orgFile;
}
my @taxids_ordered=();
my @names_ordered=();
my @phyla_ordered=();
while (<Org>) {
my $line = $_;
chomp($line);
if ($line =~ m/(\d+)\t(.+)\t(.+)/) {
push @taxids_ordered, $1;
push @names_ordered, $2;
push @phyla_ordered, $3;
#print "file\: $1 $2 $3\n";
}
}
close Org;
my $r=0;
foreach my $taxon (@taxids_ordered) {
print clipFile $taxon . " " . $names_ordered[$r] . " " . $phyla_ordered[$r] . " ";
foreach my $family (@famNames) {
if (exists $clipboard{$family}{$taxon}) {
print clipFile $clipboard{$family}{$taxon} . " ";
}
else {
print clipFile "-1 ";
}
}
print clipFile "\n";
$r++;
}
#print "\n\n";
close clipFile;
}
sub ShowOrganizedFilteredClipboard {
my $orgFile = shift(@_);
my $filter = shift(@_);
$orgFile = $STORIdir . "/" . $orgFile;
$filter = $STORIdir . "/" . $filter;
#print Dumper \%clipboard_hash;
#my $choice = shift(@_);
my @famNames=();
my @indices = keys %clipboard_hash;
my @indices_s = sort { $a <=> $b } @indices; #sort ascending
foreach my $index (@indices_s) {
push @famNames, $clipboard_hash{$index};
}
print "\n";
print "taxID name phylum ";
foreach my $family (@famNames) {
print $clipboard{$family}{"score"} . " ";
}
print "\n";
print "\n";
print "taxID name phylum ";
foreach my $family (@famNames) {
print $family . " ";
}
print "\n";
#print "orgFile\= $orgFile\n";
if (!($orgFile eq "-1")) {
open Org, $orgFile;
}
my @taxids_ordered=();
#my @names_ordered=();
#my @phyla_ordered=();
my %taxaNomenclature=();
while (<Org>) {
my $line = $_;
chomp($line);
if ($line =~ m/(\d+)\t(.+)\t(.+)/) {
#push @taxids_ordered, $1;
#push @names_ordered, $2;
#push @phyla_ordered, $3;
$taxaNomenclature{$1}{"name"} = $2;
$taxaNomenclature{$1}{"phylum"} = $3;
#print "file\: $1 $2 $3\n";
}
}
close Org;
if (!($filter eq "-1")) {
open Filter, $filter;
}
while (<Filter>) {
my $line = $_;
chomp($line);
if ($line =~ m/(\d+)/) {
push @taxids_ordered, $1;
}
}
close Filter;
my $r=0;
foreach my $taxon (@taxids_ordered) {
#print $taxon . " " . $names_ordered[$r] . " " . $phyla_ordered[$r] . " ";
print $taxon . " " . $taxaNomenclature{$taxon}{"name"} . " " . $taxaNomenclature{$taxon}{"phylum"} . " ";
foreach my $family (@famNames) {
if (exists $clipboard{$family}{$taxon}) {
print $clipboard{$family}{$taxon} . " ";
}
else {
print "-1 ";
}
}
print "\n";
$r++;
}
print "\n\n";
}
sub ShowOrganizedClipboard {
my $orgFile = shift(@_);
$orgFile = $STORIdir . "/" . $orgFile;
#print Dumper \%clipboard_hash;
#my $choice = shift(@_);
my @famNames=();
my @indices = keys %clipboard_hash;
my @indices_s = sort { $a <=> $b } @indices; #sort ascending
foreach my $index (@indices_s) {
push @famNames, $clipboard_hash{$index};
}
print "\n";
print "taxID name phylum ";
foreach my $family (@famNames) {
print $clipboard{$family}{"score"} . " ";
}
print "\n";
print "\n";
print "taxID name phylum ";
foreach my $family (@famNames) {
print $family . " ";
}
print "\n";
#print "orgFile\= $orgFile\n";
if (!($orgFile eq "-1")) {
open Org, $orgFile;
}
my @taxids_ordered=();
my @names_ordered=();
my @phyla_ordered=();
while (<Org>) {
my $line = $_;
chomp($line);
if ($line =~ m/(\d+)\t(.+)\t(.+)/) {
push @taxids_ordered, $1;
push @names_ordered, $2;
push @phyla_ordered, $3;
#print "file\: $1 $2 $3\n";
}
}
close Org;
my $r=0;
foreach my $taxon (@taxids_ordered) {
print $taxon . " " . $names_ordered[$r] . " " . $phyla_ordered[$r] . " ";
foreach my $family (@famNames) {
if (exists $clipboard{$family}{$taxon}) {
print $clipboard{$family}{$taxon} . " ";
}
else {
print "-1 ";
}
}
print "\n";
$r++;
}
print "\n\n";
}
sub ShowFullClipboard {
my $orgFile = shift(@_);
$orgFile = $STORIdir . "/" . $orgFile;
#print Dumper \%clipboard_hash;
#my $choice = shift(@_);