[Bioperl-l] chromatogram

Malay mbasu at mail.nih.gov
Wed Nov 14 15:47:20 EST 2007


I guess you need chromatogram from SCF. I can't help in that. ABI.pm is 
not in Bioperl distribution. But to make the record straight, you can 
use one step chromatogram drawing in SVG from ABI file using my BioSVG
module, available at:

http://www.bioinformatics.org/~malay/biosvg/

Malay




Smithies, Russell wrote:
> Here's my trace viewer.
> Please excuse my dodgy Perl and debugging code as it's still under
> development  :-)
> 
> 
> Russell Smithies
> 
> Bioinformatics Software Developer
> T +64 3 489 9085
> E  russell.smithies at agresearch.co.nz
> 
> Invermay  Research Centre
> Puddle Alley, 
> Mosgiel, 
> New Zealand
> T  +64 3 489 3809   
> F  +64 3 489 9174  
> www.agresearch.co.nz
> 
> 
> ------------------------------------------------------------------------
> ------------------
> 
> #!perl -w
> use ABI;
> 
> use GD::Graph::lines;
> use GD::Graph::colour;
> use GD::Graph::Data;
> 
> use Data::Dumper;
> 
> 
> use Getopt::Long;
> 
> use constant HEIGHT => 300;
> 
> GetOptions ('h|height=i' => \$HEIGHT,
>             'f|file=s' => \$FILE,
>             'o|out=s' => \$OUTFILE,
>             'l|left=s' => \$LEFT_SEQ,
>             'r|right=s' => \$RIGHT_SEQ,
>             's|size=i' => \$SIZE,
>             ) || die <<USAGE;
> Usage: perl $0 -h 400 -f 1188_13_14728111_16654_48544_080.ab1 -o
> test2.png -l actacgtacgta -r atgatcgtacgtac
> or perl $0 --height 400 --file 1188_13_14728111_16654_48544_080.ab1
> --out test2.png --left actacgtacgta --right atgatcgtacgtac
> 
> Options:
> --height <pixels> Set height of image (${\HEIGHT} pixels default)
> --file <trace file-name> Filename for the ABI trace file
> --out <output file-name> Filename for the generated .png image
> --left <left end sequence>
> --right <right end sequence>
> --size <size of clipped fasta sequence>
> 
> Parse an ABI trace file and render a PNG image.
> See http://search.cpan.org/dist/ABI/ABI.pm
>     or
>     http://search.cpan.org/~bwarfield/GDGraph-1.44/Graph.pm
> USAGE
> 
> my $height = $HEIGHT || HEIGHT;
> my $file = $FILE;
> my $outfile = $OUTFILE;
> 
> my $abi = ABI->new(-file=> $file);
> 
> my @trace_a = $abi->get_trace("A"); # Get the raw traces for "A"
> my @trace_c = $abi->get_trace("C"); # Get the raw traces for "C"
> my @trace_g = $abi->get_trace("G"); # Get the raw traces for "G"
> my @trace_t = $abi->get_trace("T"); # Get the raw traces for "T"
> 
> my @base_calls = $abi->get_base_calls(); # Get the base calls
> my $sequence =$abi->get_sequence();
> @bp = split(//, $sequence);
> 
> 
> 
> # iterate over array
> $size = $abi->get_trace_length();
> for ($i=0,$count = 0; $i<$size; $i++) {
>      if(grep(/\b$i\b/, @base_calls)){
>        $bases[$i] = $bp[$count];
>        $count++;
>      }else{
>        $bases[$i] = ' ';
>      }
> }
> 
> # create the data. see GD::Graph::Data for details of the format
> my @data = (\@bases, \@trace_a, \@trace_c, \@trace_g, \@trace_t, );
> 
> my $graph = new GD::Graph::lines($abi->get_trace_length(),$height);
>    $graph->set(
>    title => $abi->get_sample_name(),
> #	y_max_value => $abi->get_max_trace() + 50,
> 	x_max_value => $abi->get_trace_length(),
> 	t_margin => 5,
>     b_margin => 5,
>     l_margin => 5,
>     r_margin => 5,
>     x_ticks => 0,
>     text_space => 0,
> 	line_width 	=> 1,
> 	transparent	=> 0,
> 	b_margin => 30,
> 	t_margin => 35,
> 	x_plot_values => 0,
> 	interlaced => 1,
> );
> 
> # allocate some colors for drawing the bases
> #use colors same as Chromas
> $graph->set( dclrs => [ qw( green blue black red pink) ] );
> 
> #plot the data
> my $gd = $graph->plot(\@data);
> 
> $black = $gd->colorAllocate(0,0,0);       # A
> $blue = $gd->colorAllocate(0,0,255);      # C
> $red = $gd->colorAllocate(255,0,0);       # G
> $green = $gd->colorAllocate(0,255,0);     # T
> $magenta =$gd->colorAllocate(255,0,255);  # N
> $white = $gd->colorAllocate(255,255,255);  # undefined aren't drawn
> $gray = $gd->colorAllocate(210,210,210);
> %colors = ("A", $green, "C", $blue, "G",$black, "T", $red, "N",
> $magenta, " ",$white);
> 
> #$start_base = index(lc($sequence),lc($LEFT_SEQ));
> $start_base = find_match($sequence,$LEFT_SEQ);
> 
> #if($end_base = rindex(lc($sequence),lc($RIGHT_SEQ)) > 0){
> $end_base = find_match($sequence,$RIGHT_SEQ, 1);
> if($end_base){
>  $end_base += length($RIGHT_SEQ);
> }
> 
> 
> # get the coords of the features on the image
> @coords = $graph->get_hotspot(1);
> $size = @coords;
> $printed_num = 1;
> $basecount = 0;
> $numstoprint = $basecount - $start_base;
> 
> # draw the colored bases and scale at top and bottom of image
> for ($i=0,$count = 0; $i<$size; $i++) {
>   $c = $coords[$i];
>   (undef, $xs, undef, undef, undef, undef) = @$c;
>   $base = $bases[$i];
>   if($base =~ /[ACGTN]/){
>    if($start_base - 1 == $basecount){$start_base_coord = $xs;}
>    if($end_base - 1 == $basecount){$end_base_coord = $xs;}
>    if(defined($SIZE) && $start_base+$SIZE -2 ==
> $basecount){$end_base_coord_by_size = $xs;}
>    $basecount++;
>    $numstoprint++;
>    $printed_num = 0;
>   }
>   # print the bases top and bottom
>   $gd->string(GD::Font->Small(),$xs,20,$base,$colors{$base});
>   $gd->string(GD::Font->Small(),$xs,$height - 30,$base,$colors{$base});
> 
>   # print scale
>   if($basecount > 0 && $numstoprint % 10 == 0 && $printed_num == 0){
>     if($LEFT_SEQ){
>       $gd->string(GD::Font->Small(),$xs,5,$numstoprint,$black);
>       $gd->string(GD::Font->Small(),$xs,$height -
> 15,$numstoprint,$black);
>       $printed_num = 1;
>     }else{
>       $gd->string(GD::Font->Small(),$xs,5,$numstoprint,$black);
>       $gd->string(GD::Font->Small(),$xs,$height -
> 15,$numstoprint,$black);
>       $printed_num = 1;
>     }
>   }
>   $top_right_corner = $xs;
> }
> 
> 
> 
> # only draw the clipped region if the calculated size is + or - 6bp
> #if(($end_base - $start_base) - $SIZE <= 6 && ($end_base - $start_base)
> - $SIZE >= -6 ){
> # draw the clipped regions as gray
>   #if LEFT_SEQ supplied and a match found
>   if($LEFT_SEQ && $start_base > 0){
>      $gd->filledRectangle(38,35,$start_base_coord - 1,$height -
> 33,$red);
>      $clipped = 1;
>   }
>  #if RIGHT_SEQ supplied and a match found
>  if($RIGHT_SEQ && $end_base > 0){
>    print join("\t", ($end_base)),"\n";
>    $gd->filledRectangle($end_base_coord,35,$top_right_corner,$height -
> 33,$gray);
>    $clipped = 1;
>  }
>  #if no RIGHT_SEQ supplied or no match found, use left match + seq
> length
>  if(!$RIGHT_SEQ || $end_base < 0){
>  
> $gd->filledRectangle($end_base_coord_by_size,35,$top_right_corner,$heigh
> t - 33,$blue);
>   $clipped = 1;
>  }
>  
> 
> 
> # set height based on max trace within clipped region
>    $graph->set(	y_max_value => 3000);#$abi->get_max_trace() + 50);
> 
>   # need to re-plot the data over the grayed out area
>   $graph->plot(\@data) if $clipped;
>   $gd->filledRectangle(0,0,$top_right_corner,33,$white);
> 
> #}
> 
> #print the graph
> open(OUT, ">$outfile") or die "can't open output file: $outfile\n";
> binmode OUT;
> print OUT $gd->png;
> close OUT;
> 
> 
> sub find_match{
>   my ($sequence,$query,$last) = @_;
>   return -1 if length($query) < 6;
>   my($odds, $evens, $ones, $twos, $threes, $match_pos);
>     # try exact match
>     $match_pos = do_regex($query, $sequence,$last); return $match_pos if
> $match_pos > 0;
> 
>     # try matching every second base starting from the second base e.g.
> it will be .C.T.C.G.etc
>     map {m/(\w)(\w)/g;  $odds.="$1."; $evens.=".$2"}
> ($query=~m/(\w\w)/g);
>     $match_pos = do_regex($odds, $sequence,$last);   return $match_pos
> if $match_pos > 0;
>     $match_pos = do_regex($evens, $sequence,$last);  return $match_pos
> if $match_pos > 0;
> 
>     # try matching every third base starting from the first base e.g. it
> will be C..T..G..T etc
>     map {m/(\w)(\w)(\w)/g; $ones.="$1.."; $twos.=".$2.";
> $threes.="..$3"} ($query =~m/(\w\w\w)/g);
>     $match_pos = do_regex($ones, $sequence,$last);   return $match_pos
> if $match_pos > 0;
>     $match_pos = do_regex($twos, $sequence,$last);   return $match_pos
> if $match_pos > 0;
>     $match_pos = do_regex($threes, $sequence,$last); return $match_pos
> if $match_pos > 0;
> 
>      # not found
>      return -1;
> }
> 
> sub do_regex(){
> 	my ($query,$sequence,$last)= @_;
>     #print "trying $query \n";
>     my $result = -1;
>       $result = pos($sequence)-length($query)+1 if $last && ($sequence
> =~ m/.*($query)/ig);
>       $result = pos($sequence)-length($query)+1 if($sequence =~
> m/.*?($query)/ig);
>     return $result;
> }
> 
> ------------------------------------------------------------------------
> ------------------
> 
>> -----Original Message-----
>> From: bioperl-l-bounces at lists.open-bio.org
> [mailto:bioperl-l-bounces at lists.open-
>> bio.org] On Behalf Of Lee Katz
>> Sent: Wednesday, 14 November 2007 2:28 p.m.
>> To: bioperl-l at lists.open-bio.org
>> Subject: [Bioperl-l] chromatogram
>>
>> Hi,
>> I would like to know how to draw a chromatogram file.  Does anyone
>> have any sample code where you read in an scf file and create a jpeg
>> or other image file?
>> For that matter, I want to be able to customize these images with base
>> calls if possible.  I really appreciate the help, so thanks!
>>
>> --
>> Lee Katz
>> _______________________________________________
>> Bioperl-l mailing list
>> Bioperl-l at lists.open-bio.org
>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
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-- 
Malay K Basu
www.malaybasu.net



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