Bio::Tools::Alignment::Trim - A kludge to do specialized trimming of sequence based on quality. use Bio::Tools::Alignment::Trim; $o_trim = new Bio::Tools::Alignment::Trim; $o_trim->set_reverse_designator("R"); $o_trim->set_forward_designator("F"); 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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Reporting Bugs
Report bugs to the Bioperl bug tracking system to help us keep track the bugs and their resolution. Bug reports can be submitted via email or the web: bioperl-bugs@bio.perl.org http://bugzilla.bioperl.org/ Email bioinformatics@dieselwurks.com 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!