cnv_ltrstruc2fasta.pl

#!/usr/bin/perl -w
#-----------------------------------------------------------+
#                                                           |
# cnv_ltrstruc2fasta.pl - Convert ltrstruc rpt to fasta     |
#                                                           |
#-----------------------------------------------------------+
#                                                           |
#  AUTHOR: James C. Estill                                  |
# CONTACT: JamesEstill_@_gmail.com                          |
# STARTED: 07/22/2008                                       |
# UPDATED: 07/22/2008                                       |
#                                                           |
# DESCRIPTION:                                              |
#  Convert *rpt.txt output files from LTR_STRUC to          |
#  fasta files. These fasta files are placed in the         |
#  directory specified by the --outdir argument.            |
#  This is a quick and dirty modification of an existing    |
#  full annotation program.                                 |
#                                                           |
# EXAMPLE:                                                  |
#  cnv_ltrstruc2fasta.pl -i reports/                        |
#                        --outdir testoutdir/               |
#                        -test_out_summary.txt              |
#                                                           |
# VERSION: $Rev$                                            |
#                                                           |
# LICENSE:                                                  |
#  GNU General Public License, Version 3                    |
#  http://www.gnu.org/licenses/gpl.html                     |  
#                                                           |
#-----------------------------------------------------------+

package DAWGPAWS;

#-----------------------------+
# INCLUDES                    |
#-----------------------------+
use strict;
use File::Copy;
use Getopt::Long;
# The following needed for printing help
use Pod::Select;               # Print subsections of POD documentation
use Pod::Text;                 # Print POD doc as formatted text file
use IO::Scalar;                # For print_help subfunction
use IO::Pipe;                  # Pipe for STDIN, STDOUT for POD docs
use File::Spec;                # Convert a relative path to an abosolute path
use Bio::Seq;
use Bio::Tools::Run::StandAloneBlast;

#-----------------------------+
# PROGRAM VARIABLES           |
#-----------------------------+
my ($VERSION) = q$Rev$ =~ /(\d+)/;

#-----------------------------+
# VARIABLE SCOPE              |
#-----------------------------+
my $e_val = 0.00001;

# Required variables
#my $indir;
my $outfile;
my $gff_outfile;
my $repdir;
my $fs_outfile;               # Feature summary outfile
my $outdir;

# Booleans
my $quiet = 0;
my $verbose = 0;
my $show_help = 0;
my $show_usage = 0;
my $show_man = 0;
my $show_version = 0;
my $do_copy = 0;
my $do_seq_data = 1;          # Create files in outdir with sequence data

my $name_root;

#-----------------------------+
# COMMAND LINE OPTIONS        |
#-----------------------------+
my $ok = GetOptions(# REQUIRED OPTIONS
#		    "i|indir=s"     => \$indir,
                    "o|outfile=s"   => \$outfile, # fasta out file?
#		    "g|gff-out=s"   => \$gff_outfile,
#		    "f|feat-sum=s"  => \$fs_outfile,
		    "r|results=s"   => \$repdir,
		    # ADDITIONAL OPTIONS
		    "outdir=s"      => \$outdir,
#		    "e|e-val=s"     => \$e_val,
		    "c|copy"        => \$do_copy,
		    "q|quiet"       => \$quiet,
		    "s|seq-data"    => \$do_seq_data,
		    "verbose"       => \$verbose,
		    # ADDITIONAL INFORMATION
		    "usage"         => \$show_usage,
		    "version"       => \$show_version,
		    "man"           => \$show_man,
		    "h|help"        => \$show_help,);

#-----------------------------+
# SHOW REQUESTED HELP         |
#-----------------------------+
if ( ($show_usage) ) {
    print_help ("usage", $0 );
}

if ( ($show_help) || (!$ok) ) {
    print_help ("help",  $0 );
}

if ($show_version) {
    print "\n$0:\nVersion: $VERSION\n\n";
    exit;
}

if ($show_man) {
    # User perldoc to generate the man documentation.
    system("perldoc $0");
    exit($ok ? 0 : 2);
}

#-----------------------------+
# CHECK REQUIRED ARGS         |
#-----------------------------+
if ( (!$outfile) || (!$repdir)  ) {
#    print "ERROR: Featsummary file must be specified\n" if !$fs_outfile;
    print "ERROR: Output file must be specified\n" if !$outfile;
    print "ERROR: Reports directory must be specified\n" if !$repdir;
    print "\n";
#    print_help ("usage", $0 );
}

#-----------------------------------------------------------+
# MAIN PROGRAM BODY                                         |
#-----------------------------------------------------------+

#-----------------------------+
# CHECK FOR SLASH IN DIR      |
# VARIABLES                   |
#-----------------------------+
# If the indir does not end in a slash then append one
# TO DO: Allow for backslash

unless ($repdir =~ /\/$/ ) {
    $repdir = $repdir."/";
}

#-----------------------------+
# OPEN FILEHANDLE FOR FASTA   |
#-----------------------------+ 


#-----------------------------+
# Get the LTR_STRUC report    |
# files                       |
#-----------------------------+
opendir(REPDIR,$repdir) 
    || die "Can not open results direcotry:\n$repdir\n";
my @report_files = grep /rprt\.txt$/, readdir REPDIR;
@report_files = sort(@report_files);
closedir (REPDIR); 
# Sort the array of reports

my $num_report_files = @report_files;

if ($verbose) {
    print STDERR "\n-----------------------------------------------\n";
    print STDERR " Report files to process: $num_report_files\n";
    print STDERR "-----------------------------------------------\n\n";
}

my $ind_report_num=0;

for my $ind_report (@report_files) {
    
    
    # This is the id of the sequence the report is for
    #my $ind_report_id = substr ($ind_report,0,$name_root_len);    
    my $ind_report_id = $ind_report;
 
    print STDERR "\tReport: $ind_report\n" if $verbose;
    $ind_report_num++;
    print STDERR "\tProcessing report $ind_report_num".
	" of $num_report_files\n" unless $quiet;
    
    my $seq_id = $ind_report;
    my $gff_out_path = $gff_outfile;
    my $report_file_path = $repdir.$ind_report;


    ltrstruc2fasta ( $seq_id, $report_file_path,
		     1, $ind_report_num,
		     $do_seq_data, $gff_out_path);

} # End for for each individual report


exit 0;

#-----------------------------------------------------------+ 
# SUBFUNCTIONS                                              |
#-----------------------------------------------------------+


sub ltrstruc2fasta {
    # A GROSS MODIFICATION OF AN EXISTING SCRIPT
    
    # Not renaming the vars ... but gff_out and gff_append both
    # refer to the annotation file
    # VARS PASSED TO THE SUBFUNCTION


    my ($gff_seq_id, $report_in, $gff_append, $ls_id_num, 
	$print_seq_data, $gff_out) = @_;


    # FASTA RELATED VARS
    my $qry_seq;
    
    # Counters
    my $ltr5_blank_count = 0;

    # LTR STRUC VARS
    my $ls_score;        # Score assigned by LTR_STRUC
    my $ls_contig_len;   # Length of the source contig
    my $ls_orientation;  # Orientation 
    my $ls_retro_len;    # Overall length of the retrotransposon
    my $ls_longest_orf;  # Length of the longest ORF
    my $ls_rt_frame1;
    my $ls_rt_frame2;
    my $ls_rt_frame3;
    my $ls_5ltr_len;     # Length of the 5' LTR
    my $ls_3ltr_len;     # Length of the 3' LTR
    my $ls_ltr_homology; # Percent ID of LTRs
    my $ls_5dinuc;       # 5' dinucleotide sequence
    my $ls_3dinuc;       # 3' dinucleotide sequence
    my $ls_5tsr_seq;     # 5' Target site rep sequence
    my $ls_3tsr_seq;     # 3' Target site rep sequence
    my $ls_5flank_seq;   # 5' Flanking sequence
    my $ls_3flank_seq;   # 3' Flanking sequence
    my $ls_pbs_seq;      # Primer Binding Site Sequence
    my $ls_ppt_seq;      # Polypuring Tract sequence
    my $ls_5id_seq;
    my $ls_3id_seq;
    my $ls_5ltr_seq;     # Sequence of the 5' LTR
    my $ls_3ltr_seq;
    my $ls_full_retro_seq; 
    my $par_5ltr_len;      # Length of the 5' LTR as parsed
    my $par_3ltr_len;      # Length of the 3' LTR as parsed

    # BOOLEANS
    my $in_rt_frame_1 = 0;
    my $in_rt_frame_2 = 0;
    my $in_rt_frame_3 = 0;
    my $in_5id_seq = 0;
    my $in_3id_seq = 0;
    my $in_5ltr = 0;
    my $in_3ltr = 0;
    my $in_complete_seq = 0;
    my $in_aligned_ltrs = 0;

    # Coordinate values
    my $full_retro_start;
    my $full_retro_end;
    my $ltr5_start;
    my $ltr5_end;
    my $ltr3_start;
    my $ltr3_end;
    my $pbs_start;
    my $pbs_end;
    my $ppt_start;
    my $ppt_end;

    # GFF Coordinates values
    # These are from absolute start of the query sequence string
    # starting the index value at one
    my $gff_full_retro_start;
    my $gff_full_retro_end;
    my $gff_ltr5_start;
    my $gff_ltr5_end;
    my $gff_ltr3_start;
    my $gff_ltr3_end;
    my $gff_pbs_start;
    my $gff_pbs_end;
    my $gff_ppt_start;
    my $gff_ppt_end;
    my $gff_5tsr_start;
    my $gff_5tsr_end;
    my $gff_3tsr_start;
    my $gff_3tsr_end;

    # Coordinate substring tests
    my $ppt_from_full_retro;
    my $ppt_from_query_seq;
    my $pbs_from_full_retro;
    my $pbs_from_query_seq;
    my $tsd5_from_query_seq;
    my $tsd3_from_query_seq;

    
    #-----------------------------+
    # GET DATA FROM REPORT FILE   |
    #-----------------------------+
    open (REPIN, "<$report_in")
	|| die "ERROR: Can not open report file:\n$report_in\n";

    while (<REPIN>) {
	# Remove windows line endings
	# Since LTR_Struc work
	s/\r//g;
	chomp;
	if ($in_rt_frame_1) {

	}
	elsif (m/COMPLETE SEQUENCE OF PUTATIVE TRANSPOSON/) {
	    $in_3ltr = 0;
	    $in_complete_seq = 1;
	}
	elsif (m/^ALIGNED LTRS:/) {
	    $in_complete_seq = 0;
	    $in_aligned_ltrs = 1;
	}
	elsif ($in_rt_frame_2) {

	}
	elsif ($in_rt_frame_3) {

	}
	elsif ($in_5id_seq) {

	}
	elsif ($in_3id_seq) {

	}
	elsif ($in_complete_seq) {
	    $ls_full_retro_seq = $ls_full_retro_seq.$_;
	}
	elsif(/CUT-OFF SCORE:\s+(\d\.\d+)/){
	    $ls_score = $1;
	}
	elsif(m/TRANSPOSON IS IN (.*) ORIENTATION/) {
	    $ls_orientation = $1;
	    if ($ls_orientation =~ "NEGATIVE") {
		$ls_orientation = "-";
	    }
	    elsif ($ls_orientation =~ "POSITIVE") {
		$ls_orientation = "+";
	    }
	    else {
		# If return can not be parsed just use dot
		# this indicates unknown orientation if gff
		$ls_orientation = "."; 
	    }
	}
	#-----------------------------+
	# SEQUENCE DATA               |
	#-----------------------------+
	elsif ($in_5ltr) {
	    $ls_5ltr_seq = $ls_5ltr_seq.$_;
	    my $len_inline = length ($_);

	    # The following for debug
	    #print STDERR "\tLEN: $len_inline\n";

	    if ($len_inline == 0 ) {
		$ltr5_blank_count++;
		if ($ltr5_blank_count == 2) {
		    # Set in_5ltr boolean to false
		    $in_5ltr = 0;
		    $in_3ltr = 1;
		}
	    }

	}
	elsif ($in_3ltr) {
	    $ls_3ltr_seq = $ls_3ltr_seq.$_;

	    
	}
	elsif (m/DINUCLEOTIDES: (.*)\/(.*)/) {
	    $ls_5dinuc = $1;
	    $ls_3dinuc = $2;
	}
	elsif (m/DIRECT REPEATS: (.*)\/(.*)/) {
	    $ls_5tsr_seq = $1;
	    $ls_3tsr_seq = $2;
	}
	elsif (m/PBS: (.*)/) {
	    $ls_pbs_seq = $1;
	}
	elsif (m/POLYPURINE TRACT: (.*)/){
	    $ls_ppt_seq = $1;
	}
	elsif (m/5\' FLANK: (.*)/) {
	    $ls_5flank_seq = $1;
	}
	elsif (m/3\' FLANK: (.*)/) {
	    $ls_3flank_seq = $1;
	}
	#-----------------------------+
	# OTHER DATA                  |
	#-----------------------------+
	elsif(m/OVERALL LENGTH OF TRANSPOSON:\s+(\d+)/){
	    $ls_retro_len = $1;
	}
	elsif(m/LENGTH OF LONGEST ORF:\s+(\d+)/){
	    $ls_longest_orf = $1;
	}
	elsif(m/LENGTH OF PUTATIVE 3\' LTR:\s+(\d+)/){
	    $ls_3ltr_len = $1;
	}
	elsif(m/LENGTH OF PUTATIVE 5\' LTR:\s+(\d+)/){
	    $ls_5ltr_len = $1;
	}
	elsif(m/LTR PAIR HOMOLOGY:\s+(\S+)%/){
	    $ls_ltr_homology = $1;
	}
	#-----------------------------+
	# SET BOOLEAN FLAGS           |
	#-----------------------------+
	elsif (m/LTRS:/) {
	    $in_5ltr = 1;
	}
    }

    close (REPIN);


    #-----------------------------+
    # GET COORDINATES             |
    #-----------------------------+
    $par_5ltr_len = length($ls_5ltr_seq);
    $par_3ltr_len = length($ls_3ltr_seq);

    print STDERR "5 LTR Len: $par_5ltr_len\t" if $verbose;
    print STDERR "$ls_5ltr_len\n" if $verbose;
    print STDERR "3 LTR Len: $par_3ltr_len\t" if $verbose;
    print STDERR "$ls_3ltr_len\n" if $verbose;


#    $full_retro_start = index($qry_seq,$ls_full_retro_seq) + 1;
    # Changed the above to the following to make the full retro start at zero
    $full_retro_start = 0;
    $full_retro_end = $full_retro_start + $ls_retro_len;
    
    # The following will have a problem on 100% identical LTRs
    # however, telling the search to start at the end of the
    # 5' LTR will solve this problem since the index function
    # will accept an offset at the third argument
    $ltr5_start = index ($ls_full_retro_seq, $ls_5ltr_seq) + 1;
    $ltr5_end = $ltr5_start + $ls_5ltr_len;
    $ltr3_start = index ($ls_full_retro_seq, $ls_3ltr_seq) + 1;
    $ltr3_end = $ltr3_start + $ls_3ltr_len;
    $pbs_start = index ($ls_full_retro_seq, $ls_pbs_seq) + 1 ;
    $pbs_end = $pbs_start + length($ls_pbs_seq);
    $ppt_start = index ($ls_full_retro_seq, $ls_ppt_seq) + 1;
    $ppt_end = $ppt_start + length($ls_ppt_seq);

    #-----------------------------+
    # GET EXTRACTED SEQS          |
    #-----------------------------+
    # This is to test if the coordinates I am returning matches the
    # observations that LTR_STRUC is reporting
    $ppt_from_full_retro = substr ($ls_full_retro_seq, $ppt_start - 1,
				   length($ls_ppt_seq) );
    $pbs_from_full_retro = substr ($ls_full_retro_seq, $pbs_start - 1,
				   length($ls_pbs_seq) );

    #-----------------------------+
    # GFF COORDINATES             |
    #-----------------------------+
    # Full retro (not includings tsds)
    $gff_full_retro_start = $full_retro_start;                      # OK
    $gff_full_retro_end = $gff_full_retro_start + $ls_retro_len - 1;# OK
    # Subunits (including the putative tsds)
    $gff_pbs_start = $pbs_start - 1 + $full_retro_start;            # OK
    $gff_pbs_end = $gff_pbs_start + length($ls_pbs_seq) - 1;        # OK
    $gff_ppt_start = $ppt_start - 1 + $full_retro_start;            # OK
    $gff_ppt_end = $gff_ppt_start + length($ls_ppt_seq) - 1;        # OK
    # LTRs
    $gff_ltr5_start = $gff_full_retro_start;                        # OK
    $gff_ltr5_end = $gff_ltr5_start + $ls_5ltr_len - 1;             # OK
    $gff_ltr3_end = $gff_full_retro_end;                            # OK
    $gff_ltr3_start = $gff_ltr3_end - $ls_3ltr_len + 1;             # OK
    # TSRs - Currently returning correct on positive strand
    $gff_5tsr_start = $gff_full_retro_start - length($ls_5tsr_seq); # OK
    $gff_5tsr_end = $gff_5tsr_start + length($ls_5tsr_seq) - 1;     # OK
    $gff_3tsr_start = $gff_full_retro_start + $ls_retro_len;        # OK
    $gff_3tsr_end = $gff_3tsr_start + length($ls_3tsr_seq) - 1;     # OK

    # SEQID
    my $name_root = $gff_seq_id;

    # DINUCLEOTIDES
    my $ltr_5_dn_start = substr($ls_5ltr_seq, 0, 2);
    my $ltr_5_dn_end = substr($ls_5ltr_seq, 
			      length($ls_5ltr_seq) - 2 , 2);

    


    my $gff_result_id = "ltr_struc_".$ls_id_num;
    #-----------------------------+
    # PRINT SEQ DATA              |
    #-----------------------------+
    if ($print_seq_data) {
	
	# This uses the global $outdir variable

	#-----------------------------+
	# 5' LTR                      |
	#-----------------------------+
	my $ltr5_seq_path = $outdir."ltr5_ltr_struc.fasta";
	open (LTR5OUT, ">>$ltr5_seq_path") ||
	    die "Can not open 5\'LTR sequence output file:\n$ltr5_seq_path\n";
	print LTR5OUT ">".$name_root."_".$gff_result_id.
	    "|five_prime_ltr\n";
	print LTR5OUT "$ls_5ltr_seq\n";
	close (LTR5OUT);
	
	#-----------------------------+
	# 3' LTR                      |
	#-----------------------------+
	my $ltr3_seq_path = $outdir."ltr3_ltr_struc.fasta";
	open (LTR3OUT, ">>$ltr3_seq_path") ||
	    die "Can not open 3\'LTR sequence output file:\n$ltr3_seq_path\n";
	print LTR3OUT ">".$name_root."_".$gff_result_id.
	    "|three_prime_ltr\n";
	print LTR3OUT "$ls_3ltr_seq\n";
	close (LTR3OUT);

	#-----------------------------+
	# PBS                         |
	#-----------------------------+
	my $pbs_seq_path = $outdir."pbs_ltr_struc.fasta";
	open (PBSOUT, ">>$pbs_seq_path") ||
	    die "Can not open PBS sequence output file:\n$pbs_seq_path\n";
	print PBSOUT ">".$name_root."_".$gff_result_id.
	    "|primer_binding_site\n";
	print PBSOUT "$ls_pbs_seq\n";
	close (PBSOUT);

	#-----------------------------+
	# PPT                         |
	#-----------------------------+
	my $ppt_seq_path = $outdir."ppt_ltr_struc.fasta";
	open (PBSOUT, ">>$ppt_seq_path") ||
	    die "Can not open PPT sequence output file:\n$ppt_seq_path\n";
	print PBSOUT ">".$name_root."_".$gff_result_id.
	    "|RR_tract\n";
	print PBSOUT "$ls_pbs_seq\n";
	close (PBSOUT);
	
	#-----------------------------+
	# FULL RETRO MODEL            |
	#-----------------------------+ 
	# NOTE THIS INCLUDES NESTED LTR RETROS
	# LTR_retrotransposon
	my $ltr_seq_out = $outdir."full_ltr_retro.fasta";
	open (LTROUT, ">>$ltr_seq_out") ||
	    die "Can not open full ltr retro sequence outfile\n";
	print LTROUT ">".$name_root."_".$gff_result_id.
	    "|LTR_retrotransposon\n";
	print LTROUT "$ls_full_retro_seq\n";
	close (LTROUT);
	    

    }

}


sub seq_annotate {

    my $max_num_hits = 1;
    my @ans;              # Answer
    my $vals;             # Hash Reference to values
    my $feat_name;

    # annotate a seq from a datbase
    my ($seq_id, $seq_string, $blastdb, $max_e_val ) = @_;
    # dbh is the database handle where the data are to be store
    # seq_id is the id of the query sequence
    # seq_string is the
    # b should set the number of alignments returned
    my @bl_params = ('b'       => 1,
		     'e-value' => $max_e_val,
		     'program' => 'blastx', 
		     'database' => $blastdb);
    my $factory = Bio::Tools::Run::StandAloneBlast->new(@bl_params);
    
    my $qry_input = Bio::Seq->new(-id=> $seq_id,
				  -seq=>$seq_string );
    
    my $blast_report = $factory->blastall($qry_input);

    # This currently assumes a single query sequence was used
    my $hit_count = 0;
    
    while (my $blast_result = $blast_report->next_result()) {

	while (my $blast_hit = $blast_result->next_hit()) {
	    
	    while (my $blast_hsp = $blast_hit->next_hsp())
	    {

		if ($hit_count < $max_num_hits) {
		    my ($feat_start, $feat_end) = $blast_hsp->range('query');

		    # Print to STDERR IF VERBOSE
#		    print STDERR $feat_name."\n" if $verbose;    
#		    print $feat_start."\n" if $verbose;
#		    print $feat_end."\n" if $verbose;
#		    print STDERR
#			$blast_result->query_name."\n" if $verbose;
#		    print STDERR 
#			$blast_hsp->query_string."\n" if $verbose;
		    $hit_count++;
		    #my @range = $blast_hsp->range('query');

		    # Load values to the hash reference
		    #$vals->{'feat_name'} = $feat_name;
		    $vals->{'feat_name'} = $blast_result->database_name;
		    $vals->{'feat_start'} = $feat_start;
		    $vals->{'feat_end'} = $feat_end;
		    $vals->{'qry_id'} = $blast_result->query_name;
		    $vals->{'feat_seq'} = $blast_hsp->query_string;

		} # End of hit_count
	    }
	}
    } # End of while blast_result

    # Return the feature annotation
    if ($hit_count > 0) {
	return $vals;
    }
    else {
	return 0;
    }

}


sub print_help {
    my ($help_msg, $podfile) =  @_;
    # help_msg is the type of help msg to use (ie. help vs. usage)
    
    print "\n";
    
    #-----------------------------+
    # PIPE WITHIN PERL            |
    #-----------------------------+
    # This code made possible by:
    # http://www.perlmonks.org/index.pl?node_id=76409
    # Tie info developed on:
    # http://www.perlmonks.org/index.pl?node=perltie 
    #
    #my $podfile = $0;
    my $scalar = '';
    tie *STDOUT, 'IO::Scalar', \$scalar;
    
    if ($help_msg =~ "usage") {
	podselect({-sections => ["SYNOPSIS|MORE"]}, $0);
    }
    else {
	podselect({-sections => ["SYNOPSIS|ARGUMENTS|OPTIONS|MORE"]}, $0);
    }

    untie *STDOUT;
    # now $scalar contains the pod from $podfile you can see this below
    #print $scalar;

    my $pipe = IO::Pipe->new()
	or die "failed to create pipe: $!";
    
    my ($pid,$fd);

    if ( $pid = fork() ) { #parent
	open(TMPSTDIN, "<&STDIN")
	    or die "failed to dup stdin to tmp: $!";
	$pipe->reader();
	$fd = $pipe->fileno;
	open(STDIN, "<&=$fd")
	    or die "failed to dup \$fd to STDIN: $!";
	my $pod_txt = Pod::Text->new (sentence => 0, width => 78);
	$pod_txt->parse_from_filehandle;
	# END AT WORK HERE
	open(STDIN, "<&TMPSTDIN")
	    or die "failed to restore dup'ed stdin: $!";
    }
    else { #child
	$pipe->writer();
	$pipe->print($scalar);
	$pipe->close();	
	exit 0;
    }
    
    $pipe->close();
    close TMPSTDIN;

    print "\n";

    exit 0;
   
}


1;
__END__

# Old print_help
sub print_help {

    # Print requested help or exit.
    # Options are to just print the full 
    my ($opt) = @_;

    my $usage = "USAGE:\n". 
	"MyProg.pl -i InFile -o OutFile";
    my $args = "REQUIRED ARGUMENTS:\n".
	"  --infile       # Path to the input file\n".
	"  --outfile      # Path to the output file\n".
	"\n".
	"OPTIONS::\n".
	"  --version      # Show the program version\n".     
	"  --usage        # Show program usage\n".
	"  --help         # Show this help message\n".
	"  --man          # Open full program manual\n".
	"  --quiet        # Run program with minimal output\n";
	
    if ($opt =~ "full") {
	print "\n$usage\n\n";
	print "$args\n\n";
    }
    else {
	print "\n$usage\n\n";
    }
    
    exit;
}

=head1 NAME

cnv_ltrstruc2gff.pl - Convert LTR_STRUC report output files to gff

=head1 VERSION

This documentation refers to program version $Rev: 343 $

=head1 SYNOPSIS

=head2 Usage

    cnv_ltrstruc2gff.pl -i InDir -o OutDir -r LStrucOut

=head2 Required Arguments

    --indir         # Directory with the fasta files
    --outdir        # Directory for the base output dir
    --results       # Directory containing the LTR_STRUC results

=head1 DESCRIPTION

Given a directory containing the output from LTR_STRUC and a directory
containing the fasta files that the structural predictions were made
from,

=head1 REQUIRED ARGUMENTS

=over 2

=item -i,--indir

Path of the intput directory containing the fasta files that were
analyzed by LTR_STRUC.

=item -o,--outdir

Path of the output directory that will serve as the base for the
output from the conversion to gff.

=item -r,--results

Path of the directory containing the results from LTR_STRUC. It is 
expected that these file names will end with rprt.txt.

=back

=head1 OPTIONS

=over 2

=item --usage

Short overview of how to use program from command line.

=item --help

Show program usage with summary of options.

=item --version

Show program version.

=item --man

Show the full program manual. This uses the perldoc command to print the 
POD documentation for the program.

=item -q,--quiet

Run the program with minimal output.

=back

=head1 DIAGNOSTICS

Error messages generated by this program and possible solutions are listed
below.

=over 2

=item ERROR: No fasta files were found in the input directory

The input directory does not contain fasta files in the expected format.
This could happen because you gave an incorrect path or because your sequence 
files do not have the expected *.fasta extension in the file name.

=item ERROR: Could not create the output directory

The output directory could not be created at the path you specified. 
This could be do to the fact that the directory that you are trying
to place your base directory in does not exist, or because you do not
have write permission to the directory you want to place your file in.

=back

=head1 CONFIGURATION AND ENVIRONMENT

The program cnv_ltrstruc2gff.pl does not currently require an 
external configuration file or make use of variables defined in the
user's environment.

=head1 DEPENDENCIES

=head2 Required Software

=over

=item * LTR_Struc

This program is designed to work with output files generated by
the LTR_Struc
program. This program is available for download from:
http://www.genetics.uga.edu/retrolab/data/LTR_Struc.html

=back

=head2 Required Perl Modules

=over

=item * File::Copy

This module is required to copy the BLAST results.

=item * Getopt::Long

This module is required to accept options at the command line.

=back

=head1 BUGS AND LIMITATIONS

=head2 Bugs

=over 2

=item * No bugs currently known 

If you find a bug with this software, file a bug report on the DAWG-PAWS
Sourceforge website: http://sourceforge.net/tracker/?group_id=204962

=back

=head1 SEE ALSO

The cnv_ltrstruc2fasta.pl program is part of the DAWG-PAWS package of genome
annotation programs. See the DAWG-PAWS web page 
( http://dawgpaws.sourceforge.net/ )
or the Sourceforge project page 
( http://sourceforge.net/projects/dawgpaws ) 
for additional information about this package.

=head1 LICENSE

GNU GENERAL PUBLIC LICENSE, VERSION 3

http://www.gnu.org/licenses/gpl.html

=head1 AUTHOR

James C. Estill E<lt>JamesEstill at gmail.comE<gt>

=head1 HISTORY

STARTED: 07/22/2008

UPDATED: 07/22/2008

VERSION: $Rev:$

=cut

#-----------------------------------------------------------+
# HISTORY                                                   |
#-----------------------------------------------------------+
#
# 09/25/2007
# - Started from existing program, cnv_ltrstruc2ann.pl
# - This program does just a subset of the functions of
#   the larger cnv_ltrstruc2ann.pl program
#