Bio::Tools::Alignment Trim
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Inherit
Bio::Root::Root
Synopsis
  use Bio::Tools::Alignment::Trim;
$o_trim = Bio::Tools::Alignment::Trim->new();
$o_trim->set_reverse_designator("R");
$o_trim->set_forward_designator("F");
Description
This is a specialized module designed by Chad for Chad to trim sequences
based on a highly specialized list of requirements. In other words, write
something that will trim sequences 'just like the people in the lab would
do manually'.
I settled on a sliding-window-average style of search which is ugly and
slow but does _exactly_ what I want it to do.
Mental note: rewrite this.
It is very important to keep in mind the context in which this module was
written: strictly to support the projects for which Consed.pm was
designed.
Methods
BEGIN Code
newDescriptionCode
set_designatorsDescriptionCode
set_forward_designatorDescriptionCode
set_reverse_designatorDescriptionCode
get_designatorsDescriptionCode
trim_leading_polysDescriptionCode
dump_hashDescriptionCode
trim_singletDescriptionCode
trim_doubletDescriptionCode
chop_sequenceDescriptionCode
_get_startDescriptionCode
_get_endDescriptionCode
count_doublet_trailing_zerosDescriptionCode
_sliding_windowDescriptionCode
_print_formatted_qualitiesDescriptionCode
_get_end_oldDescriptionCode
Methods description
new()code    nextTop
 Title   : new()
Usage : $o_trim = Bio::Tools::Alignment::Trim->new();
Function: Construct the Bio::Tools::Alignment::Trim object. No parameters
are required to create this object. It is strictly a bundle of
functions, as far as I am concerned.
Returns : A reference to a Bio::Tools::Alignment::Trim object.
Args : (optional)
-windowsize (default 10)
-phreds (default 20)
set_designators($forward_designator,$reverse_designator)codeprevnextTop
 Title   : set_designators(<forward>,<reverse>)
Usage : $o_trim->set_designators("F","R")
Function: Set the string by which the system determines whether a given
sequence represents a forward or a reverse read.
Returns : Nothing.
Args : two scalars: one representing the forward designator and one
representing the reverse designator
set_forward_designator($designator)codeprevnextTop
 Title   : set_forward_designator($designator)
Usage : $o_trim->set_forward_designator("F")
Function: Set the string by which the system determines if a given
sequence is a forward read.
Returns : Nothing.
Args : A string representing the forward designator of this project.
set_reverse_designator($reverse_designator)codeprevnextTop
 Title   : set_reverse_designator($reverse_designator)
Function: Set the string by which the system determines if a given
sequence is a reverse read.
Usage : $o_trim->set_reverse_designator("R")
Returns : Nothing.
Args : A string representing the forward designator of this project.
get_designators()codeprevnextTop
 Title   : get_designators()
Usage : $o_trim->get_designators()
Returns : A string describing the current designators.
Args : None
Notes : Really for informational purposes only. Duh.
trim_leading_polys()codeprevnextTop
 Title   : trim_leading_polys()
Usage : $o_trim->trim_leading_polys()
Function: Not implemented. Does nothing.
Returns : Nothing.
Args : None.
Notes : This function is not implemented. Part of something I wanted to
do but never got around to doing.
dump_hash()codeprevnextTop
 Title   : dump_hash()
Usage : $o_trim->dump_hash()
Function: Unimplemented.
Returns : Nothing.
Args : None.
Notes : Does nothing.
trim_singlet($sequence,$quality,$name,$class)codeprevnextTop
 Title   : trim_singlet($sequence,$quality,$name,$class)
Usage : ($r_trim_points,$trimmed_sequence) =
@{$o_trim->trim_singlet($sequence,$quality,$name,$class)};
Function: Trim a singlet based on its quality.
Returns : a reference to an array containing the forward and reverse
trim points and the trimmed sequence.
Args : $sequence : A sequence (SCALAR, please)
$quality : A _scalar_ of space-delimited quality values.
$name : the name of the sequence
$class : The class of the sequence. One of qw(singlet
singleton doublet pair multiplet)
Notes : At the time this was written the bioperl objects SeqWithQuality
and PrimaryQual did not exist. This is what is with the clumsy
passing of references and so on. I will rewrite this next time I
have to work with it. I also wasn't sure whether this function
should return just the trim points or the points and the sequence.
I decided that I always wanted both so that's how I implemented
it.
- Note that the size of the sliding windows is set during construction of
the Bio::Tools::Alignment::Trim object.
trim_doublet($sequence,$quality,$name,$class)codeprevnextTop
 Title   : trim_doublet($sequence,$quality,$name,$class) 
Usage : ($r_trim_points,$trimmed_sequence) =
@{$o_trim->trim_singlet($sequence,$quality,$name,$class)};
Function: Trim a singlet based on its quality.
Returns : a reference to an array containing the forward and reverse
Args : $sequence : A sequence
$quality : A _scalar_ of space-delimited quality values.
$name : the name of the sequence
$class : The class of the sequence. One of qw(singlet
singleton doublet pair multiplet)
Notes : At the time this was written the bioperl objects SeqWithQuality
and PrimaryQual did not exist. This is what is with the clumsy
passing of references and so on. I will rewrite this next time I
have to work with it. I also wasn't sure whether this function
should return just the trim points or the points and the sequence.
I decided that I always wanted both so that's how I implemented
it.
chop_sequence($name,$class,$sequence,@points)codeprevnextTop
 Title   : chop_sequence($name,$class,$sequence,@points)
Usage : ($start_point,$end_point,$chopped_sequence) =
$o_trim->chop_sequence($name,$class,$sequence,@points);
Function: Chop a sequence based on its name, class, and sequence.
Returns : an array containing three scalars:
1- the start trim point
2- the end trim point
3- the chopped sequence
Args :
$name : the name of the sequence
$class : The class of the sequence. One of qw(singlet
singleton doublet pair multiplet)
$sequence : A sequence
@points : An array containing two elements- the first contains
the start trim point and the second conatines the end trim
point.
_get_start($r_quals,$windowsize,$phreds,$offset)codeprevnextTop
 Title   : _get_start($r_quals,$windowsize,$phreds,$offset)
Usage : $start_base = $self->_get_start($r_windows,5,20);
Function: Provide the start trim point for this sequence.
Returns : a scalar representing the start of the sequence
Args :
$r_quals : A reference to an array containing quality values. In
context, this array of values has been smoothed by then
sliding window-look ahead algorithm.
$windowsize : The size of the window used when the sliding window
look-ahead average was calculated.
$phreds : <fill in what this does here>
$offset : <fill in what this does here>
_get_end($r_qual,$windowsize,$phreds,$count)codeprevnextTop
 Title   : _get_end($r_qual,$windowsize,$phreds,$count)
Usage : my $end_base = &_get_end($r_windows,20,20,$start_base);
Function: Get the end trim point for this sequence.
Returns : A scalar representing the end trim point for this sequence.
Args :
$r_qual : A reference to an array containing quality values. In
context, this array of values has been smoothed by then
sliding window-look ahead algorithm.
$windowsize : The size of the window used when the sliding window
look-ahead average was calculated.
$phreds : <fill in what this does here>
$count : Start looking for the end of the sequence here.
count_doublet_trailing_zeros($r_qual)codeprevnextTop
 Title   : count_doublet_trailing_zeros($r_qual)
Usage : my $start_of_trailing_zeros = &count_doublet_trailing_zeros(\@qual);
Function: Find out when the trailing zero qualities start.
Returns : A scalar representing where the zeros start.
Args : A reference to an array of quality values.
Notes : Again, this should be rewritten to use PrimaryQual objects.
A more detailed explanation of why phrap puts these zeros here should
be written and placed here. Please email and hassle the author.
_sliding_window($r_quals,$windowsize)codeprevnextTop
 Title   : _sliding_window($r_quals,$windowsize)
Usage : my $r_windows = &_sliding_window(\@qual,$windowsize);
Function: Create a sliding window, look-forward-average on an array
of quality values. Used to smooth out differences in qualities.
Returns : A reference to an array containing the smoothed values.
Args : $r_quals: A reference to an array containing quality values.
$windowsize : The size of the sliding window.
Notes : This was written before PrimaryQual objects existed. They
should use that object but I haven't rewritten this yet.
_print_formatted_qualitiescodeprevnextTop
 Title   : _print_formatted_qualities(\@quals)
Usage : &_print_formatted_qualities(\@quals);
Returns : Nothing. Prints.
Args : A reference to an array containing quality values.
Notes : An internal procedure used in debugging. Prints out an array nicely.
_get_end_old($r_qual,$windowsize,$phreds,$count)codeprevnextTop
 Title   : _get_end_old($r_qual,$windowsize,$phreds,$count)
Usage : Deprecated. Don't use this!
Returns : Deprecated. Don't use this!
Args : Deprecated. Don't use this!
Methods code
BEGINTop
BEGIN {
    %DEFAULTS = ( 'f_designator' => 'f',
		  'r_designator' => 'r',
                  'windowsize' => '10',
                  'phreds' => '20');
}
newdescriptionprevnextTop
sub new {
    my ($class,@args) = @_;    
    my $self = $class->SUPER::new(@args);
    my($windowsize,$phreds) =
        $self->_rearrange([qw(
                    WINDOWSIZE
                    PHREDS
                              )],
                          @args);
    $self->{windowsize} = $windowsize || $DEFAULTS{'windowsize'};
    $self->{phreds} = $phreds || $DEFAULTS{'phreds'};
          # print("Constructor set phreds to ".$self->{phreds}."\n") if $self->verbose > 0;
$self->set_designators($DEFAULTS{'f_designator'}, $DEFAULTS{'r_designator'}); return $self;
}
set_designatorsdescriptionprevnextTop
sub set_designators {
    my $self = shift;
    ($self->{'f_designator'},$self->{'r_designator'}) = @_;
}
set_forward_designatordescriptionprevnextTop
sub set_forward_designator {
    my ($self,$desig) = @_;
    $self->{'f_designator'} = $desig;
}
set_reverse_designatordescriptionprevnextTop
sub set_reverse_designator {
    my ($self,$desig) = @_;
    $self->{'r_designator'} = $desig;
}
get_designatorsdescriptionprevnextTop
sub get_designators {
    my $self = shift;
    return("forward: ".$self->{'f_designator'}." reverse: ".$self->{'r_designator'});
}
trim_leading_polysdescriptionprevnextTop
sub trim_leading_polys {
	my ($self, $sequence) = @_;
}
dump_hashdescriptionprevnextTop
sub dump_hash {
	my $self = shift;
	my %hash = %{$self->{'qualities'}};
} # end dump_hash
}
trim_singletdescriptionprevnextTop
sub trim_singlet {
    my ($self,$sequence,$quality,$name,$class) = @_;
    # this split is done because I normally store quality values in a
# space-delimited scalar rather then in an array.
# I do this because serialization of the arrays is tough.
my @qual = split(' ',$quality); my @points; my $sequence_length = length($sequence); my ($returnstring,$processed_sequence); # smooth out the qualities
my $r_windows = &_sliding_window(\@qual,$self->{windowsize}); # find out the leading and trailing trimpoints
my $start_base = $self->_get_start($r_windows,$self->{windowsize},$self->{phreds}); my (@new_points,$trimmed_sequence); # do you think that any sequence shorter then 100 should be
# discarded? I don't think that this should be the decision of this
# module.
# removed, 020926
$points[0] = $start_base; # whew! now for the end base
# required parameters: reference_to_windows,windowsize,$phredvalue,start_base
my $end_base = &_get_end($r_windows,$self->{windowsize}, $self->{phreds},$start_base); $points[1] = $end_base; # now do the actual trimming
# CHAD : I don't think that it is a good idea to call chop_sequence here
# because chop_sequence also removes X's and N's and things
# and that is not always what is wanted
return\@ points;
}
trim_doubletdescriptionprevnextTop
sub trim_doublet {
    my ($self,$sequence,$quality,$name,$class) = @_;
    my @qual = split(' ',$quality);
    my @points;
    my $sequence_length = length($sequence);
    my ($returnstring,$processed_sequence);
          # smooth out the qualities
my $r_windows = &_sliding_window(\@qual,$self->{windowsize}); # determine where the consensus sequence starts
my $offset = 0; for (my $current = 0; $current<$sequence_length;$current++) { if ($qual[$current] != 0) { $offset = $current; last; } } # start_base required: r_quality,$windowsize,$phredvalue
my $start_base = $self->_get_start($r_windows,$self->{windowsize},$self->{phreds},$offset); if ($start_base > ($sequence_length - 100)) { $points[0] = ("FAILED"); $points[1] = ("FAILED"); return @points; } $points[0] = $start_base; #
# whew! now for the end base
#
# required parameters: reference_to_windows,windowsize,$phredvalue,start_base
# |
# 010420 NOTE: We will no longer get the end base to avoid the Q/--\___/-- syndrome
my $end_base = $sequence_length; my $start_of_trailing_zeros = &count_doublet_trailing_zeros(\@qual); $points[1] = $end_base; # CHAD : I don't think that it is a good idea to call chop_sequence here
# because chop_sequence also removes X's and N's and things
# and that is not always what is wanted
return @points; } # end trim_doublet
}
chop_sequencedescriptionprevnextTop
sub chop_sequence {
    my ($self,$name,$class,$sequence,@points) = @_;
     print("Coming into chop_sequence,\@ points are @points\n");
    my $fdesig = $self->{'f_designator'};
    my $rdesig = $self->{'r_designator'};
    if (!$points[0] && !$points[1]) {
	$sequence = "junk";
	return $sequence;
    }
    if ($class eq "singlet" && $name =~ /$fdesig$/) {
	$sequence = substr($sequence,$points[0],$points[1]-$points[0]);
    }
    elsif ($class eq "singlet" && $name =~ /$rdesig$/) {
	$sequence = substr($sequence,$points[0],$points[1]-$points[0]);
    }		
    elsif ($class eq "singleton" && $name =~ /$fdesig$/) {
	$sequence = substr($sequence,$points[0],$points[1]-$points[0]);
    }
    elsif ($class eq "singleton" && $name =~ /$rdesig$/) {
	$sequence = substr($sequence,$points[0],$points[1]-$points[0]);
    }
    elsif ($class eq "doublet") {
	$sequence = substr($sequence,$points[0],$points[1]-$points[0]);
    }
    # this is a _terrible_ to do this! i couldn't seem to find a better way
# i thought something like s/(^.*[Xx]{5,})//g; might work, but no go
# no time to find a fix!
my $length_before_trimming = length($sequence); my $subs_Xs = $sequence =~ s/^.*[Xx]{5,}//g; if ($subs_Xs) { my $length_after_trimming = length($sequence); my $number_Xs_trimmed = $length_before_trimming - $length_after_trimming; $points[0] += $number_Xs_trimmed; } $length_before_trimming = length($sequence); my $subs_Ns = $sequence =~ s/[Nn]{1,}$//g; if ($subs_Ns) { my $length_after_trimming = length($sequence); my $number_Ns_trimmed = $length_before_trimming - $length_after_trimming; $points[1] -= $number_Ns_trimmed; $points[1] -= 1; } push @points,$sequence; print("chop_sequence\@ points are @points\n"); return @points;
}
_get_startdescriptionprevnextTop
sub _get_start {
    my ($self,$r_quals,$windowsize,$phreds,$offset) = @_;
     print("Using $phreds phreds\n")  if $self->verbose > 0;
          # this is to help determine whether the sequence is good at all
my @quals = @$r_quals; my ($count,$count2,$qualsum); if ($offset) { $count = $offset; } else { $count = 0; } # search along the length of the sequence
for (; ($count+$windowsize) <= scalar(@quals); $count++) { # sum all of the quality values in this window.
my $cumulative=0; for($count2 = $count; $count2 < $count+$windowsize; $count2++) { if (!$quals[$count2]) { # print("Quals don't exist here!\n");
} else { $qualsum += $quals[$count2]; # print("Incremented qualsum to ($qualsum)\n");
} $cumulative++; } # print("The sum of this window (starting at $count) is $qualsum. I counted $cumulative bases.\n");
# if the total of windowsize * phreds is
if ($qualsum && $qualsum >= $windowsize*$phreds) { return $count; } $qualsum = 0; } # if ($count > scalar(@quals)-$windowsize) { return; }
return $count;
}
_get_enddescriptionprevnextTop
sub _get_end {
    my ($r_qual,$windowsize,$phreds,$count) = @_;
    my @quals = @$r_qual;
    my $total_bases = scalar(@quals);
    my ($count2,$qualsum,$end_of_quals,$bases_counted);
    if (!$count) { $count=0; }
  BASE: for (; $count < $total_bases; $count++) {
      $bases_counted = 0;
      $qualsum = 0;
    POSITION: for($count2 = $count; $count2 < $total_bases; $count2++) {
	$bases_counted++;

	if ($count2 == $total_bases-1) {
	    $qualsum += $quals[$count2];
	    $bases_counted++;
	    last BASE;
	}
	elsif ($bases_counted == $windowsize) {
	    $qualsum += $quals[$count2];
	    if ($qualsum < $bases_counted*$phreds) {
		return $count+$bases_counted+$windowsize;
	    }
	    next BASE;
	}
	else {
	    $qualsum += $quals[$count2];
	}
    }
      if ($qualsum < $bases_counted*$phreds) {
	  return $count+$bases_counted+$windowsize;
      }
      else { }
      $qualsum = 0;
  }				# end for
if ($end_of_quals) { my $bases_for_average = $total_bases-$count2; return $count2; } else { } if ($qualsum) { } # print ("$qualsum\n");
return $total_bases; } # end get_end
}
count_doublet_trailing_zerosdescriptionprevnextTop
sub count_doublet_trailing_zeros {
	my ($r_qual) = shift;
	my $number_of_trailing_zeros = 0;
	my @qualities = @$r_qual;
	for (my $current=scalar(@qualities);$current>0;$current--) {
		if ($qualities[$current] && $qualities[$current] != 0) {
			$number_of_trailing_zeros = scalar(@qualities)-$current;
			return $current+1;
		}
	}
	return scalar(@qualities);
} # end count_doublet_trailing_zeros
}
_sliding_windowdescriptionprevnextTop
sub _sliding_window {
    my ($r_quals,$windowsize) = @_;
    my (@window,@quals,$qualsum,$count,$count2,$average,@averages,$bases_counted);
    @quals = @$r_quals;    
    my $size_of_quality = scalar(@quals);
          # do this loop for all of the qualities
for ($count=0; $count <= $size_of_quality; $count++) { $bases_counted = 0; BASE: for($count2 = $count; $count2 < $size_of_quality; $count2++) { $bases_counted++; # if the search hits the end of the averages, stop
# this is for the case near the end where bases remaining < windowsize
if ($count2 == $size_of_quality) { $qualsum += $quals[$count2]; last BASE; } # if the search hits the size of the window
elsif ($bases_counted == $windowsize) { $qualsum += $quals[$count2]; last BASE; } # otherwise add the quality value
unless (!$quals[$count2]) { $qualsum += $quals[$count2]; } } unless (!$qualsum || !$windowsize) { $average = $qualsum / $bases_counted;
if (!$average) { $average = "0"; } push @averages,$average; } $qualsum = 0; } # 02101 Yes, I repaired the mismatching numbers between averages and windows.
# print("There are ".scalar(@$r_quals)." quality values. They are @$r_quals\n");
# print("There are ".scalar(@averages)." average values. They are @averages\n");
return\@ averages;
}
_print_formatted_qualitiesdescriptionprevnextTop
sub _print_formatted_qualities {
    my $rquals = shift;
    my @qual = @$rquals;
    for (my $count=0; $count<scalar(@qual) ; $count++) {
	if (($count%10)==0) { print("\n$count\t"); }
	if ($qual[$count]) { print ("$qual[$count]\t");}
	else { print("0\t"); }
    }
    print("\n");
}
_get_end_olddescriptionprevnextTop
sub _get_end_old {
    my ($r_qual,$windowsize,$phreds,$count) = @_;
    warn("Do Not Use this function (_get_end_old)");
    my $target = $windowsize*$phreds;
    my @quals = @$r_qual;
    my $total_bases = scalar(@quals);
    my ($count2,$qualsum,$end_of_quals);
    if (!$count) { $count=0; }
  BASE: for (; $count < $total_bases; $count++) {
      for($count2 = $count; $count2 < $count+$windowsize; $count2++) {
	  if ($count2 == scalar(@quals)-1) {
	      $qualsum += $quals[$count2];
	      $end_of_quals = 1;
	      last BASE;

	  }
	  $qualsum += $quals[$count2];
      }
      if ($qualsum < $windowsize*$phreds) {
	  return $count+$windowsize;
      }
      $qualsum = 0;
  }				# end for
} # end get_end_old
# Autoload methods go after =cut, and are processed by the autosplit program.
1; __END__
}
General documentation
NAME Top
Bio::Tools::Alignment::Trim - A kludge to do specialized trimming of
sequence based on quality.
FEEDBACKTop
Mailing ListsTop
User feedback is an integral part of the evolution of this and other
Bioperl modules. Send your comments and suggestions preferably to one
of the Bioperl mailing lists. Your participation is much appreciated.
  bioperl-l@bioperl.org                  - General discussion
http://bioperl.org/wiki/Mailing_lists - About the mailing
lists
Support Top
Please direct usage questions or support issues to the mailing list:
bioperl-l@bioperl.org
rather than to the module maintainer directly. Many experienced and
reponsive experts will be able look at the problem and quickly
address it. Please include a thorough description of the problem
with code and data examples if at all possible.
Reporting BugsTop
Report bugs to the Bioperl bug tracking system to help us keep track
the bugs and their resolution. Bug reports can be submitted via the
web:
  https://redmine.open-bio.org/projects/bioperl/
AUTHOR - Chad MatsallaTop
Email bioinformatics-at-dieselwurks.com
APPENDIXTop
The rest of the documentation details each of the object methods.
Internal methods are usually preceded with a _