| Subject: | showpage bug |
#!c:\Perl\bin\Perl.exe
# Hi
# Had a problem using Postscript::Simple 0.06p1
# see what I had to do in line 117 of my script below
# manually adding the showpage command
# I could not get any printout without this
# no biggy, but could be helpful to others.
# I've included a test input file for the script.
# Otherwise great mod!
# ::: Robin S. Matlib ::: Doctoral Candidate ::: Molecular Genetics :::
# :::::: Division of Biology and Biomedical Sciences ::::::
# ::::::::: Washington University in Saint Louis :::::::::
#
#!c:\Perl\bin\Perl.exe
# Robin S. Matlib 3/8/2004 12:33:02 PM
# ps_wconsensus.pl
# A script for graphically displaying iutput from WConsensus
# Stormo and Hartzell (1989, PNAS, 86:1183-1187)
# and Hertz et al. (1990, CABIOS, 6:81-92)
open (WCONSENSUS,$ARGV[0])||die "Couldn't open $ARGV[0]:$!\n";
while (<WCONSENSUS>) {
if (/COMMAND LINE\: (.*)/) {$title=$1;}
if (/(sequence (\d+)\: .*)/) {$seq=$2;push (@seqs,$1);}
if (/fragments\: \d+\-(\d+)/) {$seqhash{$seq}{"L"}=$1;}
if (/([ACGTN] [\.\d]+)/) {push (@obs,$1);}
if (/([ACGTN]) prior frequency = ([\.\d]+)/) {$prior{$1}=$2;}
if (/^INFORMATION CONTENT/) {last;}
}
while (<WCONSENSUS>) {
last if (/FINAL CYCLE/);
}
while (<WCONSENSUS>) {
if (/MATRIX (\d+)/) {$mtx=$1;push (@matrices,$1);}
if (/number of sequences = (\d+)/) {$mhash{$mtx}{"nos"}=$1;}
if (/width = (\d+)/) {$mhash{$mtx}{"w"}=$1;}
if (/crude information = ([\.\d]+)/) {$mhash{$mtx}{"crude"}=$1;}
if (/unadjusted information = ([\.\d]+)/) {$mhash{$mtx}{"unadjusted"}=$1;}
if (/size adjusted information = ([\.\d]+)/) {$mhash{$mtx}{"adjusted"}=$1;}
if (/ln\(p-value\) = ([\.\d\-]+)/) {$mhash{$mtx}{"lnp"}=$1;}
if (/p-value = ([\d\.E\-]+)/) {$mhash{$mtx}{"p"}=$1;}
if (/ln\(expected frequency\) = ([\.\d\-]+)/) {$mhash{$mtx}{"lne"}=$1;}
if (/expected frequency = ([\.\d]+)/) {$mhash{$mtx}{"e"}=$1;}
if (/(^[ACGTN])\s\|\s{2,3}([\d\s]+)/) {
#print STDERR;
$base=$1;$freqs=$2;
#print STDERR "base $base freqs $freqs\n";
@freqs=split(/\s+/,$freqs);
foreach $freq (@freqs) {
#print STDERR "freq $freq $base $prior{$base}\n";
#$freq/=$prior{$base};
#$freq = int (5*eval{log $freq;});
$freq=1 if ($freq<1);
#$freq++ if ($freq % 2);
}
@{$mhash{$mtx}{$base}}=@freqs;
}
if (/(\d+)\/(\d+)\s+(\w+)/) {$mhash{$mtx}{"seqhash"}{$1}{"begin"}=$2;$mhash{$mtx}{"sequence"}{$1}=$3}
}
use PostScript::Simple;
# create a new PostScript object
foreach $mtx (@matrices) {
$p = new PostScript::Simple(papersize => "Letter",colour => 1,
units => "in",landscape => 1);
# create a new page
##$p->newpage;
# add title in red
$p->setcolour("red");
$p->setfont("Times-Roman", 20);
$p->text(5.5,7.75,$title,'centre');
#add subtitle
$p->setfont("Times-Roman", 12);
$p->text(5.5,7.5,"MATRIX $mtx",'centre');
$p->setfont("Times-Roman", 9);
$p->text(5.5,7.25,"INFO crude: ".$mhash{$mtx}{"crude"}
." unadj: ".$mhash{$mtx}{"unadjusted"}
." adj: ".$mhash{$mtx}{"adjusted"}."\n"
." ln P: ".$mhash{$mtx}{"lnp"}
." p: ".$mhash{$mtx}{"p"}
." ln e: ".$mhash{$mtx}{"lne"}
." e: ".$mhash{$mtx}{"e"},'centre');
#A
$p->setcolour("brightgreen");
for ($i=1;$i<=$mhash{$mtx}{"w"};$i++) {
#print STDERR "$i ".${$mhash{$mtx}{"A"}}[$i-1],"\n";
$p->setfont("Times-Roman",${$mhash{$mtx}{"A"}}[$i-1]);
$p->text(1.5+$i*0.125,7.00,"A",'centre');
}
#T
$p->setcolour("red");
for ($i=1;$i<=$mhash{$mtx}{"w"};$i++) {
$p->setfont("Times-Roman",${$mhash{$mtx}{"T"}}[$i-1]);
$p->text(1.5+$i*0.125,6.875,"T",'centre');
}
#G
$p->setcolour(255,153,0);
for ($i=1;$i<=$mhash{$mtx}{"w"};$i++) {
$p->setfont("Times-Roman",${$mhash{$mtx}{"G"}}[$i-1]);
$p->text(1.5+$i*0.125,6.750,"G",'centre');
}
#C
$p->setcolour("blue");
for ($i=1;$i<=$mhash{$mtx}{"w"};$i++) {
$p->setfont("Times-Roman",${$mhash{$mtx}{"C"}}[$i-1]);
$p->text(1.5+$i*0.125,6.625,"C",'centre');
}
$i=0;
@sortedseqs = sort {$a <=> $b} keys %{$mhash{$mtx}{"seqhash"}};
foreach $seq (@sortedseqs) {
#print STDERR "$mtx: $seq ",$mhash{$mtx}{"nos"}," ",$mhash{$mtx}{"seqhash"}{$seq}{"begin"}," ",$mhash{$mtx}{"w"}," ",$seqhash{$seq}{"L"},"\n";
$i++;
$p->setcolour("black");
$p->line(1.5,0.8*$i*8/$mhash{$mtx}{"nos"}, 10.5,0.8*$i*(8/$mhash{$mtx}{"nos"}));
$p->setfont("Times-Roman", 7);
$p->text(0.25,0.8*$i*8/$mhash{$mtx}{"nos"}+0.0625,$seqs[$seq-1],'left');
$x1=1.5+9*$mhash{$mtx}{"seqhash"}{$seq}{"begin"}/$seqhash{$seq}{"L"};
$y1=0.8*$i*8/$mhash{$mtx}{"nos"};
$x2=$x1+9*$mhash{$mtx}{"w"}/$seqhash{$seq}{"L"};
$y2=$y1+0.150;
$p->setcolour("green");
$p->box($x1,$y1 , $x2,$y2, filled=>1);
$p->setcolour("black");
$p->setfont("Courier", 22);
$p->text($x1,$y1,$mhash{$mtx}{"sequence"}{$seq});
}
$p->{pspages} .= "\nshowpage\n";
# write the output to a file
$p->output("$ARGV[0].$mtx.ps");
}#matrix
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