File: ext.in

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loki 2.4.7.4-10
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#!+PERLPROG+
#
# Script to extract columns from loki.out
#
# Should work with output from all versions of Loki (up to loki_2.3)
#
# Simon Heath - September 2000
#
use Getopt::Std;
use IO::File;
use POSIX qw(tmpnam);
use strict;
my($i,$j,$k,%opt,$file,$hi,$lo,$flag,$out_type,$version,$link_fg,$start,$stop);
my($lg,%chrom,@map_start,@map_end,@map_length,$sex_map,$model);
my(@mkchrom,@mkpos,@mkname,$nmk,@col,$n_cov,$max_col,$ngroup);
my($it_col,$tv_col,$resvar_col,$mean_col,$addvar_col);
my($mean_set,$mean,$resvar_set,$resvar,$max_col1,$tau_col,$tau_beta,$tau,$tau_mode);
my($nc,$nqtl,$nqtl1,$line,$iter,$tv,$tv1,$sz,$nrand,@rand_col,@rand_fg,$tmp);
my(@no_output,$out_col_flag,$adj);
my($x1,$x2);
# Chromsome extracted defaults to the first one
$opt{c}=1;
getopts('xc:CDf:r:o:i:',\%opt);
# -r option sets a range of positions on the chromosome to look at
if($opt{r}) {
  $tmp=$opt{r};
  if($tmp=~/^([+-]?(?:(?:[0-9]*\.[0-9]+)|(?:[0-9]+))(?:[eE][-+]?[0-9]+)?)(.*)/) {
    $lo=$1;
	 $tmp=$2;
  }
  if($tmp=~/^[,-:](.*)/) {
    $tmp=$1;
	 if($tmp=~/^([+-]?(?:(?:[0-9]*\.[0-9]+)|(?:[0-9]+))(?:[eE][-+]?[0-9]+)?)/) {
	   $hi=$1;
	 }
  }
  die "Bad -r option\n" if(!defined($hi) && !defined($lo));
  if(defined($lo) && defined($hi) && $lo>$hi) {
    $tmp=$lo;
	 $lo=$hi;
	 $hi=$tmp;
  }
}
# -i option sets a range of iterations to consider
if($opt{i}) {
  $tmp=$opt{i};
  if($tmp=~/^([1-9][0-9]*)(.*)/) {
    $start=$1;
	 $tmp=$2;
  }
  if($tmp=~/^[,-:](.*)/) {
    $tmp=$1;
	 if($tmp=~/^([1-9][0-9]*)/) {
	   $stop=$1;
	 }
  }
  die "Bad -i option\n" if(!defined($start) && !defined($stop));
  if(defined($start) && defined($stop) && $start>$stop) {
    $tmp=$start;
	 $start=$stop;
	 $stop=$tmp;
  }
  $start=1 if(!defined($start));
}

# Set default number of genetic groups
$ngroup=1;
# Used to store columns where to find interesting quantitities
# -1 means not known
$it_col=-1; # Iteration count
$tv_col=-1; # Total genetic variance
$resvar_col=-1; # Residual variance
$mean_col=-1; # Grand mean
$max_col=-1; # No. fixed output columns
$n_cov=-1; # No. covariate columns
$ngroup=1; # No. genetic groups
$tau_col=-1;
$tau_mode=-1;
$out_type=-1; # Output type
# Open output file if specified, otherwise we use STDOUT
if($opt{o}) {
  open OFILE,">".$opt{o} or die "Couldn't open output file ",$opt{o},"\n";
} else {
  open OFILE,">&STDOUT" or die "Couldn't dup STDOUT\n";
}
$sex_map=0;
$i=$opt{x}+$opt{C}+$opt{D};
die "Can not specify more that 1 of the options C,D,x at once.\n" if($i>1);
$opt{x}=1 unless $i;
$file=$opt{f}?$opt{f}:"loki.out";
open FILE,$file or die "Could not open file '$file'\n";
# Go though file
while(<FILE>) {
  $line++;
  if($flag) { # Parse the data portion of the file
    split;
	 # Iteration number
	 $iter=$_[0];
	 if($opt{i}) {
	   next if($iter<$start);
		last if(defined($stop) && $iter>$stop);
	 }
	 $nc=@_;
	 next if($nc<$max_col);
	 if($version==-1) {
	   $i=$max_col+$_[6];
		last if($nc<$max_col);
		$ngroup=$_[7];
	 } else {$i=$max_col;}
	 $max_col1=$i;
	 if($opt{C}) {
	   for($i=0;$i<$max_col1;$i++) {print OFILE " $_[$i]";}
		print OFILE "\n";
		next;
	 }
	 # Total variance
	 $tv1=0; #first get non-genetic variance
	 for($j=0;$j<$nrand;$j++) {
	   if($rand_fg[$j]==2) {
		  $sz=$_[$rand_col[$j]];
		  $tv1+=$sz;
	   }
	 }
	 # Now get genetic variance
	 if($tv_col>=0) {$tv=$_[$tv_col];}
	 else { # Not specified, must calculate
	   $tv=0;
		for($j=0;$j<$nrand;$j++) {
		  $sz=$_[$rand_col[$j]];
		  $sz*=$sz if($rand_fg[$j]==1);
		  if($rand_fg[$j]!=2) {$tv+=$sz;}
		}
	 }
	 # Count QTL's
	 $nqtl=0;
	 $nqtl1=0;
	 while($i<$nc) {
	   $lg=$_[$i];
		die "Illegal linkage group $lg at line $line column ",$i+1,"\n" if($lg && !$chrom{$lg});
		$i+=1+$sex_map if($lg || !$out_type);
		$i+=4+$ngroup;
		if($tv_col<0) {
		  $sz=$_[$i-1];
		  $tv+=$sz*$sz;
		}
		$nqtl++;
		if($lg) {
		  $nqtl1++;
		}
	 }
	 # If QTL numbers are given, check against what we found
	 if($out_type<2) {
	   die "Mismatch in QTL numbers ($nqtl,$_[1]) at line $line\n" if($nqtl!=$_[1]);
	   die "Mismatch in linked QTL numbers ($nqtl1,$_[2]) at line $line\n" if($nqtl1!=$_[2]);
	 }
	 # Get residual variance
	 if(!$resvar_set) {
	   # Do we know where it is ?
		if($resvar_col>=0) {$resvar=$_[$resvar_col];}
		# if not, guess
		elsif($out_type<2) {$resvar=$_[4];}
		else {$resvar=$_[2];}
	 }
	 # Total non-genetic variance
	 $tv1+=$resvar;
	 # Print out a 'standard' (across output types) set of columns
	 if($opt{D}) {
		# Get Mean
		if(!$mean_set) {
		  if($mean_col>=0) {$mean=$_[$mean_col];}
		  elsif($out_type<2) {$mean=$_[3];}
		  else {$mean=$_[1];}
	   }
		# get Tau
		if($tau_col>=0) {$tau=$_[$tau_col];}
		elsif($tau_mode>=0) {
		  if($tau_mode==2) {$tau=$resvar*$tau_beta;}
		  else {$tau=$tau_beta;}
		} else {
		  # Must be a very early version, assume that we know where tau is...
		  $tau=$_[5];
		}
		print OFILE "$iter $nqtl $nqtl1 $mean $resvar $tau ";
		printf OFILE "%g",$tv;
		# Are we on a recent version with all column info?
		if($out_col_flag) {
		  for($i=1;$i<$max_col1;$i++) {
		    print OFILE " $_[$i]" if(!$no_output[$i]);
		  }
		# This is more complicated
		} else {
		  if(!$out_type) {$i=8;}
		  elsif($out_type<2) {$i=6;}
		  else {$i=3};
		  for(;$i<$max_col1;$i++) {
		    print OFILE " $_[$i]";
		  }
		}
		print OFILE "\n";
		# Extract information about linked QTL's
	 } elsif($opt{x} && $nqtl) {
	   # Go through QTL's
		$i=$max_col1;
		while($i<$nc) {
	     $lg=$_[$i];
		  if($lg eq $opt{c}) {
			 $j=$i+1;
		    if($lg) {
		      $x1=$_[$j++];
			   $x2=$_[$j++] if($sex_map);
			 }
			 # Select QTL based on linkage group and range
			 if(!$lg || !$opt{r} || ((!defined($lo) || $x1>=$lo) && (!defined($hi) || $x1<=$hi))) {
		      print OFILE $iter;
			   # Print position if linked
			   if($lg) {
				  print OFILE " $x1";
				  print OFILE " $x2" if($sex_map);
				}
				for($k=0;$k<2+$ngroup;$k++) {print OFILE " ",$_[$j++];}
				$sz=$_[$j];
				print OFILE " $sz";
				$sz*=$sz;
				if($tv>0.0) {printf OFILE " %g",$sz/$tv;}
				else {print OFILE " 0.0";}
				if(($tv1+$tv)>0.0) {printf OFILE " %g\n",$sz/($tv+$tv1)}
				else {print OFILE " 0.0\n";}
			 }
		  }
		  $i+=1+$sex_map if($lg || !$out_type);
		  $i+=4+$ngroup;
		}
    }
  # We've reached the end of the header
  } elsif(/^--*/) {
    $flag=1;
	 # $max_col will not be set if working with an earlier version
	 if($max_col<0) {
	   # but $n_cov should be set unless ...
	   if($n_cov>=0) {
		  if($out_type<0) {$out_type=1;}
	     $max_col=3+$n_cov;
		  $version=1;
		  if(!$out_type) {$max_col+=5;}
		  elsif($out_type==1) {$max_col+=3;}
		} else { # ... we are working with a genuine v2.0 copy
		  $out_type=0;
	     $max_col=8;
		  $version=-1;
	   }
	 }
  } elsif(!$flag) { # First parse the header
    if(/^Output format: (\d+)/) {
	   $out_type=$1;
		next;
	 }
	 if(/^Created by loki (\d+).(\d+).(\d+).*:/) {
		$version=2 if($1>2 || ($1==2 && $2>=3));
		next;
	 }
	 # Pull out linkage group information if it is there
	 if(/^Linkage groups:$/) {
      $link_fg=1;
	   next;
    }
	 if($link_fg==1) {
      # Check for linkage group names and map lengths
      if(/(\d+): (.*)$/) {
	     $lg=$1;
		  if($2=~/^(.*) Map range: (.*)/) {
		    $chrom{$lg}=$1;
		    if($2=~/\((-?[0-9.]+)cM to (-?[0-9.]+)cM\)(.*)/) {
		      $map_start[$lg][0]=$1;
		      $map_end[$lg][0]=$1;
			   if($3=~/\((-?[0-9.]+)cM to (-?[0-9.]+)cM\)/) {
		        $map_start[$lg][1]=$1;
		        $map_end[$lg][1]=$1;
				  $sex_map=1;
			   }
		    } else { die "Error reading linkage group map range\n"; }
		  } else {$chrom{$lg}=$1;}
		} elsif(/^\s+(.+) - ([\d\.]+)\s*([\d\.]*)/) {
		  if(!$opt{c} || $lg eq $opt{c}) {
	       $mkchrom[$nmk]=$lg;
			 $mkpos[$nmk][0]=$2;
			 $mkpos[$nmk][1]=$3;
			 $mkname[$nmk++]=$1;
		  }
	   } else {
	     # Check for total map length
        if(/^Total Map Length: (.*)$/) {
		    if($1=~/(\d\d*\.?\d*)cM(.*)/) {
		      $map_length[0]=$1;
			   if($2=~/(\d\d*\.?\d*)cM$/) {
			     $map_length[1]=$1;
			     $sex_map=1;
			   }
		    } else { die "Error reading map lengths\n"; }
		    $link_fg=2;
	       next;
	     }
	   }
	 }
	 $model=$1 if(/^Model: (.+)/);
	 if($link_fg<3) {
	   if(/^Output columns:$/) {
		  $link_fg=3;
		  $out_col_flag=1;
		  next;
		} elsif(/Output covariate data:$/) {
		  $link_fg=4;
		}
	 } elsif($link_fg>2) {
	   if(/(\d+): (.*)/) {
		  $col[$1]=$2;
		  $tmp=$1-1;
		  if($link_fg==4) {
		    $link_fg=3;
			 if(!$tmp) {$adj=6;}
		  }
		  $tmp+=$adj;
		  if($2 eq "Total genetic variance") {
		    $tv_col=$tmp;
			 $no_output[$tmp]=1;
		  } elsif($2 eq "Additive variance") {
		    $rand_fg[$nrand]=0;
			 $rand_col[$nrand++]=$tmp;
		  } elsif($2=~/^Additional random variance for/) {
		    $rand_fg[$nrand]=2;
			 $rand_col[$nrand++]=$tmp;
		  } elsif($2=~/\S+ size$/) {
		    $rand_fg[$nrand]=1;
			 $rand_col[$nrand++]=$tmp;
		  } elsif($2 eq "Residual variance") {
		    $resvar_col=$tmp;
			 $no_output[$tmp]=1;
		  } elsif($2 eq "Grand mean") {
		    $mean_col=$tmp;
			 $no_output[$tmp]=1;
		  } elsif($2 eq "Tau") {
		    $tau_col=$tmp;
			 $no_output[$tmp]=1;
		  } elsif($2 eq "No. QTL's in model") {
		    $no_output[$tmp]=1;
		  } elsif($2 eq "No. linked QTL's") {
		    $no_output[$tmp]=1;
		  } elsif($2 eq "No. covariate columns") {
		    $no_output[$tmp]=1;
		  } elsif($2 eq "No. genetic groups") {
		    $no_output[$tmp]=1;
		  }
		} elsif(/No. covariate columns: (\d+)/) {
		  $n_cov=$1;
		} elsif(/No. fixed output columns: (\d+)/) {
		  $max_col=$1;
		} elsif(/No. genetic groups: (\d+)/) {
		  $ngroup=$1;
		} elsif(/^Sex specific map$/) {
		  $sex_map=1;
		} elsif(/^Residual variance: ([0-9-.]+)/) {
		  $resvar_set=1;
		  $resvar=$1;
		} elsif(/^Grand mean: ([0-9-.]+)/) {
		  $mean_set=1;
		  $mean=$1;
		} elsif(/^Tau Mode: ([0-9]+)/) {
		  $tau_mode=$1;
		} elsif(/^Tau Beta: ([0-9.]+)/) {
		  $tau_beta=$1;
		}
	 }
  }
}