NAME

 PrimerView - generates graphical outputs that map the position and distribution of primers to the target sequence
 

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();  

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

FEEDBACK

 damienoh@gwu.edu

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.

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

cpanm PRIMERVIEW

perl -MCPAN -e shell
install PRIMERVIEW