G::Seq

Eliminate

G::Seq::Eliminate - Perl extension for blah blah blah

  use G::Seq::Eliminate;
  blah blah blah

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.

Methods description

Methods code

    my $self = shift;

    &opt_default(upstream=>15,downstream=>15);
    my @args=opt_get(@_);

    my $gb=opt_as_gb(shift @args);
    my $upstream=int(opt_val("upstream")/3);
    my $downstream=int(opt_val("downstream")/3);
    my $start;
    my $i=1;
    my $j;
    my $switch;
    my @result;


    foreach($gb->cds()){
	$switch=0;
	if($gb->{"CDS$i"}->{direction} eq 'direct'){ 
	    $start=$gb->{"CDS$i"}->{start};
	    for($j = -$upstream * 3 + $start;$j <= $downstream * 3 + $start;$j += 3){
		if($j != $start && substr($gb->{SEQ},$j-1,3) eq 'atg'){
		    $switch=1;
		}
	    }
	}
	elsif($gb->{"CDS$i"}->{direction} eq 'complement'){
	    $start=$gb->{"CDS$i"}->{end};
	    for($j = $upstream * 3 + $start;$j >= -$downstream * 3 + $start;$j -= 3){
		if($j != $start && substr($gb->{SEQ},$j-1,3) eq 'cat'){
		    $switch=1;
		}
	    }
	} 
	$gb->{"CDS$i"}->{on}=0 if($switch==1);
	push(@result,"CDS$i") if($switch==0);
	$i++;
    }
    return\@ result;

    &opt_default(upstream=>30,downstream=>30);
    my @args=opt_get(@_);

    my $gb=opt_as_gb(shift @args);
    my $uppos=opt_val("upstream");
    my $downpos=opt_val("downstream");
    my $pat=shift;
    my $start;
    my $i=1;
    my $j;
    my $switch;
    my @result;


    foreach($gb->cds()){
	$switch=0;
	if($gb->{"CDS$i"}->{direction} eq 'direct'){ 
	    $start=$gb->{"CDS$i"}->{start};
	    for($j = -$uppos + $start;$j <= $downpos+ $start;$j ++){
		if($gb->getseq($j,$j+length($pat)-1) eq $pat){
		    $switch=1;
		}
	    }
	}
	elsif($gb->{"CDS$i"}->{direction} eq 'complement'){
	    $start=$gb->{"CDS$i"}->{end};
	    for($j = $uppos+ $start;$j >= -$downpos+ $start;$j --){
		if($gb->getseq($j-length($pat)+1,$j) eq _complement($pat)){ 
		    $switch=1;
		}
	    }
	} 
	$gb->{"CDS$i"}->{on}=0 if($switch==1);
	push(@result,"CDS$i") if($switch==0);
	$i++;
    }
    return\@ result;

    my $pkg = shift;
    my $filename = shift;
    my $option = shift;
    my $this;

    return $this;

    &opt_default(Max=>10000,Min=>20);
    my @args=opt_get(@_);

    my $gb=opt_as_gb(shift @args);
    my $max=opt_val("Max");
    my $min=opt_val("Min");
    my $start;
    my $end;
    my $num=1;
    my $tmp;
    my $switch;
    my @result;

    foreach($gb->cds()){
	$switch=0;
	$tmp=$num-1;
	if($gb->{"CDS$num"}->{direction} eq 'direct' && $gb->{"CDS"."$tmp"}->{direction} eq 'direct'){
	    $start = $gb->{"CDS$num"}->{start};
	    $end = $gb->{"CDS"."$tmp"}->{end};
	    $switch=1 if($start-$end > $max || $start-$end < $min);
	}
	elsif($gb->{"CDS$num"}->{direction} eq 'complement' && $gb->{"CDS"."$tmp"}->{direction} eq 'complement'){
	    $start = $gb->{"CDS$num"}->{start};
	    $end = $gb->{"CDS"."$tmp"}->{end};
	    $switch=1 if($start-$end > $max || $start-$end < $min);
	}
	$gb->{"CDS$num"}->{on}=0 if($switch==1);
	push(@result,"CDS$num") if($switch==0);
	$num++;
    }

    return\@ result;

General documentation

A. U. Thor, a.u.thor@a.galaxy.far.far.away

perl(1).