Bio::Tools::Alignment::Trim - A kludge to do specialized trimming of sequence based on quality.

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

   new()
        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)
        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($designator)
        Title   : set_forward_designator($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($reverse_designator)
        Title   : set_reverse_designator($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()
        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()
        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()
        Title   : dump_hash()
        Usage   : $o_trim->dump_hash()
        Function: Unimplemented.
        Returns : Nothing.
        Args    : None.
        Notes   : Does nothing.

   trim_singlet($sequence,$quality,$name,$class)
        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)
        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,$sequence,@points)
        Title   : chop_sequence($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)
        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)
        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($r_qual)
        Title   : count_doublet_trailing_zeros($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)
        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_qualities
        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)
        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!

perl v5.32.1                                       2021-08-15                   Bio::Tools::Alignment::Trim(3pm)

       Email bioinformatics-at-dieselwurks.com

       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.

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       Bio::Tools::Alignment::Trim - A kludge to do specialized trimming of      sequence based on quality.

         use Bio::Tools::Alignment::Trim;
         $o_trim = Bio::Tools::Alignment::Trim->new();
         $o_trim->set_reverse_designator("R");
         $o_trim->set_forward_designator("F");