G::Seq

Primitive

Summary Included libraries Package variables Synopsis Description General documentation Methods
Summary
G::Seq::Eliminate - Perl extension for blah blah blah
Package variables top
Globals (from use vars definitions)
@EXPORT
$VERSION
@EXPORT_OK
Privates (from my definitions)
%CodonTable = ( 'gac', 'D', 'caa', 'Q', 'gca', 'A', 'ctg', 'L', 'gat', 'D', 'cag', 'Q', 'gcc', 'A', 'ctt', 'L', 'gaa', 'E', 'agc', 'S', 'gcg', 'A', 'ata', 'I', 'gag', 'E', 'agt', 'S', 'gct', 'A', 'atc', 'I', 'aga', 'R', 'tca', 'S', 'gga', 'G', 'att', 'I', 'agg', 'R', 'tcc', 'S', 'ggc', 'G', 'cca', 'P', 'cga', 'R', 'tcg', 'S', 'ggg', 'G', 'ccc', 'P', 'cgc', 'R', 'tct', 'S', 'ggt', 'G', 'ccg', 'P', 'cgg', 'R', 'aca', 'T', 'gta', 'V', 'cct', 'P', 'cgt', 'R', 'acc', 'T', 'gtc', 'V', 'atg', 'M', 'aaa', 'K', 'acg', 'T', 'gtg', 'V', 'tgg', 'W', 'aag', 'K', 'act', 'T', 'gtt', 'V', 'tgc', 'C', 'cac', 'H', 'tac', 'Y', 'tta', 'L', 'tgt', 'C', 'cat', 'H', 'tat', 'Y', 'ttg', 'L', 'taa', '/', 'aac', 'N', 'ttc', 'F', 'cta', 'L', 'tag', '/', 'aat', 'N', 'ttt', 'F', 'ctc', 'L', 'tga', '/' )
Included modulestop
G::Messenger
SubOpt
strict
Inherit top
AutoLoader Exporter
Synopsistop
  use G::Seq::Primitive;
  blah blah blah
Descriptiontop
Stub documentation for G::Seq::Eliminate was created by h2xs. It looks like the
author of the extension was negligent enough to leave the stub
unedited.

Blah blah blah.
Methodstop
DESTROYNo descriptionCode
complementNo descriptionCode
newNo descriptionCode
translateNo descriptionCode

Methods description

Methods code

DESTROYdescriptiontopprevnext
sub DESTROY {
    my $self = shift;
}
complementdescriptiontopprevnext
sub complement {
    my $nuc = reverse(shift);
    
    $nuc =~ tr
	[acgturymkdhbvwsnACGTURYMKDHBVWSN]
	[tgcaayrkmhdvbwsnTGCAAYRKMHDVBWSN];
    return $nuc;
}
newdescriptiontopprevnext
sub new {
    my $pkg = shift;
    my $filename = shift;
    my $option = shift;
    my $this;

    return $this;
}
translatedescriptiontopprevnext
sub translate {
    my $seq = lc(shift);
    my $amino = '';

    while(3 <= length($seq)){
	my $codon = substr($seq, 0, 3);
	substr($seq, 0, 3) = '';
	if ($codon =~ /[^atgc]/){
	    $amino .= '?';
	}else{
	    $amino .= $CodonTable{$codon};
	}
    }
    if(length($seq)){
	msg_error("Translation: illegal length.\n");
    }

    return $amino;
}

General documentation

AUTHOR top
A. U. Thor, a.u.thor@a.galaxy.far.far.away
SEE ALSO top
perl(1).