comparison gomwu_a.pl @ 1:f7287f82602f draft

"planemo upload commit 486235d6560c9e95bd42152ad19bf7c3941cdc1b"

0:91261b42c07e

See README_GO_MWU.txt file for details.

Mikhail Matz, UT Austin; [e-mail]

";

print "@ARGV";

my $onto=$ARGV[0] or die $usage;
my $gen2go=$ARGV[1] or die $usage;

if ($div eq "BP") { $division="biological_process";}
elsif ($div eq "MF") { $division="molecular_function";}
elsif ($div eq "CC") { $division="cellular_component";}
else { die "unrecognized division: $div\n";}

my $inname2=$measure.".".$div.".tmp";
my $inname3=$div."_".$measure;
my $inname31="dissim0_".$div."_".$gen2go;
my $inname4="dissim_".$div."_".$measure."_".$gen2go;

my @donealready=();

open GO, $onto or die "cannot open ontology $onto\n";
open CORAL, $gen2go or die "cannot open genes2go table $gen2go\n";

	if (!$l){
		$l++;
		next;
	}
	chomp;
	($seq,$ns)=split(/,/, $_);
	if ($seq=~/SEQ/) { $seq.="_s";}
	$dnds{$seq}=$ns;
}

#reformatting

my %level={};
my %desc={};
my %value={};
my $des;
my $go; 
my $l;
my $gn;
my $val;
my @gos=();
my %genes={};
my @gcount=();
my %gci={};
my %goi={};

while (<TAB>){
	chomp;
	($des,$go,$l,$val,$gn)=split(/\t/,$_);
	$value{$gn}=$val;
	$desc{$go}=$des;
	push @{$genes{$go}},$gn;
	push @gcount, $gn unless ($gci{$gn}==1) ;
	$gci{$gn}=1;

				$overlap{$go2,$go}=min($shared/($#{$genes{$go}}+1),$shared/($#{$genes{$go2}}+1));			
			}
		}
	}

	open OUT, ">$inname31" or die "gomwu_b: cannot create output $inname31\n";
	
	print {OUT} join("\t",@gos),"\n";

	foreach $go (@gos) {
		$overlap{$go,$go}=1;

1:f7287f82602f

See README_GO_MWU.txt file for details.

Mikhail Matz, UT Austin; [e-mail]

";

use File::Basename;

print "@ARGV";

my $onto=$ARGV[0] or die $usage;
my $gen2go=$ARGV[1] or die $usage;

if ($div eq "BP") { $division="biological_process";}
elsif ($div eq "MF") { $division="molecular_function";}
elsif ($div eq "CC") { $division="cellular_component";}
else { die "unrecognized division: $div\n";}

($mname,$mdir,$mext) = fileparse($measure,'\..*');
($aname,$adir,$aext) = fileparse($gen2go,'\..*');
print "$mname - $mdir - $mext\n";
my $inname2=$mdir.$mname.".".$div.".tmp";
my $inname3=$mdir.$mname."_".$div.".tsv";
my $inname31=$mdir."dissim0_".$div."_".$aname.$aext;
my $inname4=$mdir."dissim_".$div."_".$mname."_".$aname.$aext;

my @donealready=();

open GO, $onto or die "cannot open ontology $onto\n";
open CORAL, $gen2go or die "cannot open genes2go table $gen2go\n";

	if (!$l){
		$l++;
		next;
	}
	chomp;
	($seq,$ns)=split(/\t/, $_);
	if ($seq=~/SEQ/) { $seq.="_s";}
	$dnds{$seq}=$ns;
}

#reformatting

my %level={};
my %desc={};
my %value={};
my $des;
my $go; 
my $ll;
my $gn;
my $val;
my @gos=();
my %genes={};
my @gcount=();
my %gci={};
my %goi={};

while (<TAB>){
	chomp;
	($des,$go,$ll,$val,$gn)=split(/\t/,$_);
	$value{$gn}=$val;
	$desc{$go}=$des;
	push @{$genes{$go}},$gn;
	push @gcount, $gn unless ($gci{$gn}==1) ;
	$gci{$gn}=1;

				$overlap{$go2,$go}=min($shared/($#{$genes{$go}}+1),$shared/($#{$genes{$go2}}+1));			
			}
		}
	}

	open OUT, ">$inname31" or die "gomwu_a: cannot create output $inname31\n";
	
	print {OUT} join("\t",@gos),"\n";

	foreach $go (@gos) {
		$overlap{$go,$go}=1;