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.
FEEDBACK
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AUTHOR - Chad Matsalla
Email bioinformatics-at-dieselwurks.comAPPENDIX
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!