Modware::Search

Chromosome

   Modware::Search::Chromosome - collection of methods that return iterators of Modware::Feature::CHROMOSOME objects

   #USE CASE: print the sequence of all of the chromosomes to a file for a blast database
   open FILE, ">chromosomes.fa" or die "could not open file for writing\n";

   my @chromosomes = Modware::Search::Chromosome->Search_all_chromosomes();

   foreach my $chromosome (@chromosomes) {
      print FILE $chromosome->sequence( -format => 'fasta' );
   }

   Modules in the Modware::Search are all class methods.  These methods
   return iterators or arrays of objects (depending on the context)
   So Modware:::Search::Gene contains methods that return iterators or arrays of 
   Modware::Feature::CHROMOSOME objects.

Methods description

 Title    : Search_all_chromosomes
          :
 Function : returns array of all chromosomes
          :
 Usage    : my @features = Modware::Search::Chromosome->Search_all_chromosomes();
          :
 Returns  : Iterator or array of Modware::Features (depending on context)
 Args     : none

 Title    : Search_chromosome_by_name
          :
 Function : returns a chromosome with a name such as '1' or '2' or 'M'
          :
 Usage    : my $chromosome = Modware::Search::Chromosome->Search_chromosome_by_name();
          :
 Returns  : Iterator or array of Modware::Features (depending on context)
 Args     : STRING: chromosome name

 Title    : sth_to_iterator
          :
 Function : Given a statement handle pointing to feature_ids,
          : create an iterator of Modware::Features containing
          : the features identified by the feature_ids
          :
 Returns  : an iterator of Features
 Args     : an active statement handle pointing to feature_ids

Methods code

   my ($self, @args) = @_;

   my $dbh    = new Modware::DBH;
   my @results;

   my $sth = $dbh->prepare("
        SELECT FEATURE_ID FROM V_CHROMOSOME_FEATURES
   ");

   $sth->execute();

   while (  my $feature_id  = $sth->fetchrow() ) {
      my $feat = new Modware::Feature( -feature_id => $feature_id );
      push @results, $feat;
   }
   $sth->finish;

   return @results;

   my ($self, $chromosome_name ) = @_;

   my $dbh    = new Modware::DBH;
   my @results;

   my $sth = $dbh->prepare("
        SELECT FEATURE_ID FROM V_CHROMOSOME_FEATURES WHERE NAME = ?
   ");

   $sth->execute($chromosome_name);

   while (  my $feature_id  = $sth->fetchrow() ) {
      my $feat = new Modware::Feature( -feature_id => $feature_id );
      push @results, $feat;
   }
   $sth->finish;

   return @results;

    my ( $self, $sth ) = @_;

    my @data;
    while ( my $row = $sth->fetchrow() ) {
        my $args   = { -feature_id => $row };
        push( @data, $args );
    }

    my $itr = new Modware::Iterator(
        -CLASS => "Modware::Feature",
        -DATA  =>\@ data
    );

    return $itr;

General documentation

   Eric Just e-just@northwestern.edu

   The rest of the documentation details each of the object
   methods. Internal methods are usually preceded with a _

Copyright © 2006, Northwestern University All rights reserved.