G::IO FastaI
Included librariesPackage variablesGeneral documentationMethods
Package variables
Privates (from "my" definitions)
$prev = ''
$infile = ''
Included modules
G
G::Messenger
Inherit
G::IO::GenBankO G::IO::Handler
Synopsis
No synopsis!
Description
No description!
Methods
close_gb
No description
Code
filepath
No description
Code
getnucs
No description
Code
goto_origin
No description
Code
new
No description
Code
next_locus
No description
Code
open_gb
No description
Code
read_features
No description
Code
read_header
No description
Code
read_locus
No description
Code
Methods description
None available.
Methods code
close_gbdescriptionprevnextTop
sub close_gb {
    my $this = shift;
    close(FASTA);
}
filepathdescriptionprevnextTop
sub filepath {
    my $this = shift;

    return $infile;
}
getnucsdescriptionprevnextTop
sub getnucs {
    my $this = shift;

    while(<FASTA>){
	$prev = $_;
	last if (/^\s*\n$/ || /^>/);
	s/[^A-Za-z]//g;
	$this->{"SEQ"} .= lc($_);
    }
}
goto_origindescriptionprevnextTop
sub goto_origin {
    my $this = shift;
}
newdescriptionprevnextTop
sub new {
    my $pkg = shift;
    my $filename = shift;
    my $option = shift;
    my $this = new G("blessed");

    bless $this;

    return $this;
}
next_locusdescriptionprevnextTop
sub next_locus {
    my $this = shift;
    my $msg = shift;
    undef %{$this};
    $this->read_locus();
    $this->getnucs();

    if (length($this->{SEQ}) > 0){
	$this->seq_info() unless($msg);
	return 1;
    }else{
	return 0;
    }
}
open_gbdescriptionprevnextTop
sub open_gb {
    my $this = shift;
    my $filename = shift;
    $infile = $filename;
    
    open(FASTA, $filename) || die("Error at G::IO::FastaI: $!\n");
    return *FASTA;
}
read_featuresdescriptionprevnextTop
sub read_features {
    my $this = shift;
}
read_headerdescriptionprevnextTop
sub read_header {
    my $this = shift;
}
read_locusdescriptionprevnextTop
sub read_locus {
    my $this = shift;
    local($_);

    if($prev =~ /^>(.*)$/){
	$this->{LOCUS}->{id} = $1;
	return;
    }

    while(<FASTA>){
	chomp;
	if (/^>(.*)$/){
	    $this->{LOCUS}->{id} = $1;
	    last;
	}
    }
}
General documentation
No general documentation available.