NAME PrimerView - generates graphical outputs that map the position and distribution of primers to the target sequence =head1 SYNOPSIS use strict; use warnings; use PRIMERVIEW;

my $in_file = "test_seqs.fasta";

my $tmp = PRIMERVIEW->new();

$tmp->load_selections(  
   in_file        => $in_file, 
   single_view    => "1",   
   batch_view     => "1",      
   clean_up        => "1"   
);   

 $tmp->run_primerview();  
=head1 DESCRIPTION
designs forward and reverse primers from multi-sequence datasets, and generates graphical outputs that map the position and distribution of primers to the target sequence
=head1 FEEDBACK
damienoh@gwu.edu
=head2 Mailing Lists
User feedback is an integral part of the evolution of this module. Send your comments and suggestions preferably to one of the mailing lists.  Your participation is much appreciated.
 

Support Please direct usage questions or support issues to: <damienoh@gwu.edu> Please include a thorough description of the problem with code and data examples if at all possible. =head2 Reporting Bugs Report bugs to the GitHub bug tracking system to help keep track of the bugs and their resolution. Bug reports can be submitted via the GitHub page: https://github.com/dohalloran/PrimerView/issues

AUTHORS - Damien OHalloran Email: damienoh@gwu.edu =head1 APPENDIX The rest of the documentation details each of the object methods.

new() Title : new() Usage : my $tmp = PRIMERVIEW->new(); Function: constructor routine Returns : a blessed object Args : none

load_selections() Title : load_selections() Usage : $tmp->load_selections( in_file => $in_file, single_view => "1", batch_view => "1", clean_up => "1" ); Function: Populates the user data into $self hash Returns : nothing returned Args : -in_file, the name of the file containing the sequences in fasta format -single_view, return a single graphical file depicting the primer mapped to the sequence for every primer 1=Yes, 0=No -batch_view, return a single graphical file depicting all primers mapped to the sequence for each sequence 1=Yes, 0=No -cleanup, option to delete tmp file: 1=Yes, 0=No

run_primerview() Title : run_primerview() Usage : $tmp->run_primerview(); Function: parses input and executes commands based on %arg Returns : graphical files based on user selections Args : none provided

parser() Title : parser() Usage : parser($input_file); Function: parses the contents of the fasta file into ids and sequences Returns : send back a reference to the arrays containing seqs and ids Args : fasta file

_primerview() Title : _primerview() Usage : _primerview( $fasta, $temp_seq, $len_seq, $shift_id, $sequence, $id_uniq, $len_uniq ); Function: runs and parses the primer3 side of things Returns : primer feature files Args : $fasta, $temp_seq, $len_seq, $shift_id, $sequence, $id_uniq, $len_uniq

_align_muscle() Title : _align_muscle() Usage : _align_muscle(); Function: generates an alignment using MUSCLE of the primer and sequence Returns : alignment Args : none (globs the files)

_align_convert() Title : _align_convert() Usage : _align_convert(); Function: converts alignment from aln to clustalw Returns : clustalw alignment Args : none (globs the files)

_graphics() Title : _graphics() Usage : _graphics(); Function: converts each clustal alignment to a graphical output Returns : jpeg Args : none (globs the files)

_graphics_all_primers() Title : _graphics_all_primers() Usage : _graphics_all_primers(); Function: converts each feature file to a single graphical output Returns : png Args : none (globs the files)

_cleanup() Title : _cleanup() Usage : _cleanup(); Function: option to delete tmp files Returns : nothing Args : 1=yes, 0=no

LICENSE AND COPYRIGHT Copyright (C) 2017 Damien M. O'Halloran GNU GENERAL PUBLIC LICENSE Version 2, June 1991