Hi

I am writing a script which requires plotting a graph..
my code is like this: #my @count = join('\s', $clone_count);
         #my @count_window = join('\s', $count_window);
         #print "@count";

         #my @data = (\@count, \@count_window);

         #my $graph = GD::Graph::bars->new(600, 600);
         #$graph->set(
              # x_label => 'Hit density',
              # y_label => 'Frequency',
              # title => 'Hits per window',
              # y_max_value => 500,
              # y_label_skip => 50,
             
              # ) or warn $graph->error;
       
        # my $graph_image = $graph ->plot(\@data) or die "cannot plot the graph\n";
         #open (GRAPH, ">graph.png") or die "cannot open the GRAPH file";  
         #binmode GRAPH;
         #print GRAPH $graph_image->png
I am not getting any errors instead, when i open the file it says its not a png file as saved instead a text file. and even if opened as a text file it hasn't got anything!! jus a empty file.
                   

hmmm... all the lines are commented out. Is that the way you run the code?

no

these lines don't make sense to me:

my @count = join('\s', $clone_count);
my @count_window = join('\s', $count_window);

the join() function returns a string from a list, not a list from a string like you have it above. Did you mean to use split() instead of join()?

my @count = split(/\s/, $clone_count);
my @count_window = split(/\s/, $count_window);

#!/usr/bin/perl -w
use DBI;
use strict;
use Bio::SeqIO;
use Bio:erl;
use GD::Graph::bars;
#The program used to get the hits that corresponds to the wild type Arabidopsis.


my $connect;
my $database = 'Cloned_RNA_2_dev';
my $user ='root';
my $pass = '';
my $host = 'localhost';
my %sequences;
my $total_length;
my $length;
#open(RESULT, ">result.csv") or die "cannot open the RESULT file";
#print "sequence, Count, Countwindow\n";
#print RESULT "Sequences, Clonecount, Windowcount\n";  

# On connecting to the database the query is prepared once and they are executed more than once until it gets al the required information from the database.
my $dsn = qq(DBI:mysql:database=$database; host=$host);
$connect = DBI-> connect($dsn, $user, $pass,{printError =>1}) or die $DBI::errstr;
my $query = (qq(select c.Rna_sequence_sequence, c.clone_name, h.hit_start, h.hit_end, h.query_strand, h.hit_strand, h.frac_identical, h.accession from Cloned_rna c, Hsp h where c.Rna_sequence_sequence=h.Rna_sequence_sequence and h.frac_identical=1 and h.Sequence_db_idSequence_db =1133 and h.hit_start>=? && h.hit_end <=? and h.accession =?  ));
my $sql = $connect->prepare($query);


my $genome = Bio::SeqIO->new(-file=>'/home/shared-projects/sequence-dbs/TAIR7/TAIR7_nuclear_genome.fna', -format=>'fasta');
while (my $seq = $genome->next_seq()){
   $length = $seq->length();
   my $gseq =$seq->seq();
   my $id =$seq->id();
   #print RESULT  "Chromosome: $id\n";
   my $window_size = 500;
   my $step_size = 500;
   for(my $i=1;$i<=($length-$window_size); $i+=$step_size){
     my $window_start = $i;
     my $window_end = $i+$window_size;
     my $sucess=($sql->execute($window_start, $window_end, $id));
     die "query failed!\n $query \n" unless $sucess;
     while (my( $Rna_sequence_sequence, $clone_name,  $query_strand, $hit_strand, $frac_identical, $accession,$hit_start, $hit_end)= $sql->fetchrow_array()){
        # print "$Rna_sequence_sequence, $clone_name,  $query_strand, $hit_strand, $frac_identical, $accession,$hit_start, $hit_end\n";
         $sequences{$Rna_sequence_sequence}{"$clone_name,  $query_strand, $hit_strand, $frac_identical, $accession,$hit_start, $hit_end"}=1;
         
     }
     my @clone_count;
     my @count_window;;
     foreach my $sequence(keys %sequences){
         #print "$sequence\n";
         my $clone_count = keys % {$sequences{$sequence}};
         my $count_window = int($window_start/$window_size)+1;
        # print RESULT  "$sequence, $clone_count, $count_window\n";
         @clone_count = sort $clone_count;
         @count_window = split (/\s/, $count_window);
         #print "@count_window\n";
         
     }
     
                 
     my @data = (\@clone_count, \@count_window);
          my $graph = GD::Graph::bars->new(600, 600);
         $graph->set(
               x_label => 'Hit density',
               y_label => 'Frequency',
                  title => 'Hits per window',
               y_max_value => 500,
               y_label_skip => 50,
             
               ) or warn $graph->error;
       
         my $graph_image = $graph ->plot(\@data) or die "cannot plot the graph\n";
         open (GRAPH, ">graph.png") or die "cannot open the GRAPH file";  
         binmode GRAPH;
         print GRAPH $graph_image->png
                   
         

           
   }
}
           
I have got two datas
1. clone_count and
2.count_window.

I have to plot the graoh for this is there any thing else that i have to do before starting with the GD::grph??

thanks


Sorry, I have no experience with GD::grph (or any of the GD modules).

one thing that does pop out:

foreach my $sequence(keys %sequences){
    #print "$sequence\n";
    my $clone_count = keys % {$sequences{$sequence}};
    my $count_window = int($window_start/$window_size)+1;
   # print RESULT  "$sequence, $clone_count, $count_window\n";
    @clone_count = sort $clone_count;
    @count_window = split (/\s/, $count_window);
    #print "@count_window\n";
   
}

@clone_count is just going to be one number, that number will be how many keys there are in the last hash (% {$sequences{$sequence}}) as you loop through %sequence. That is probably not what you want to do, but I don't know what it is you want to do. Likewise, @count_window may not be what you need to accomplish the task, for similar reasons.

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