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cnv_ltrfinder2gff.pl
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cnv_ltrfinder2gff.pl
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#!/usr/bin/perl -w
#-----------------------------------------------------------+
# |
# cnv_ltrfinder2gff.pl - Converts ltr_finder to gff |
# |
#-----------------------------------------------------------+
# |
# AUTHOR: James C. Estill |
# CONTACT: JamesEstill_@_gmail.com |
# STARTED: 09/14/2007 |
# UPDATED: 01/23/2012 |
# |
# DESCRIPTION: |
# Converts the LTR_FINDER results to gff format. |
# |
# VERSION: $Rev$ |
# |
# LICENSE: |
# GNU General Public License, Version 3 |
# http://www.gnu.org/licenses/gpl.html |
# |
#-----------------------------------------------------------+
package DAWGPAWS;
#-----------------------------+
# INCLUDES |
#-----------------------------+
use strict;
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 Cwd; # Get the current working directory
use File::Copy; # Copy files
#-----------------------------+
# PROGRAM VARIABLES |
#-----------------------------+
my ($VERSION) = q$Rev$ =~ /(\d+)/;
# Get GFF version from environment, GFF2 is DEFAULT
my $gff_ver = uc($ENV{DP_GFF}) || "GFF2";
#-----------------------------+
# VARIABLE SCOPE |
#-----------------------------+
my $infile; # Infile. textfile result from LTR_FINDER
my $outfile; # Outfile.
# Booleans
my $quiet = 0;
my $verbose = 0;
my $show_help = 0;
my $show_usage = 0;
my $show_man = 0;
my $show_version = 0;
my $append = 0; # Append gff output to existing file
my $param; # Suffix appended to the end of the gff
my $seqname; #
my $program = "ltr_finder"; # The source program
my $delim = "_"; # Delimit character between program and paramter name
#-----------------------------+
# COMMAND LINE OPTIONS |
#-----------------------------+
my $ok = GetOptions(# REQUIRED OPTIONS
"i|infile=s" => \$infile,
"o|outfile=s" => \$outfile,
# ADDITIONAL OPTIONS
"gff-ver=s" => \$gff_ver,
"delim=s" => \$delim,
"p|param=s" => \$param,
"program=s" => \$program,
"s|seqname=s" => \$seqname,
"append" => \$append,
"q|quiet" => \$quiet,
"verbose" => \$verbose,
# ADDITIONAL INFORMATION
"usage" => \$show_usage,
"version" => \$show_version,
"man" => \$show_man,
"h|help" => \$show_help,);
#-----------------------------+
# SHOW REQUESTED HELP |
#-----------------------------+
if ( ($show_usage) ) {
# print_help ("usage", File::Spec->rel2abs($0) );
print_help ("usage", $0 );
}
if ( ($show_help) || (!$ok) ) {
# print_help ("help", File::Spec->rel2abs($0) );
print_help ("help", $0 );
}
if ($show_man) {
# User perldoc to generate the man documentation.
system ("perldoc $0");
exit($ok ? 0 : 2);
}
if ($show_version) {
print "\ncnv_ltrfinder2gff.pl:\n".
"Version: $VERSION\n\n";
exit;
}
#-----------------------------+
# STANDARDIZE GFF VERSION |
#-----------------------------+
unless ($gff_ver =~ "GFF3" ||
$gff_ver =~ "GFF2") {
# Attempt to standardize GFF format names
if ($gff_ver =~ "3") {
$gff_ver = "GFF3";
}
elsif ($gff_ver =~ "2") {
$gff_ver = "GFF2";
}
else {
print "\a";
die "The gff-version \'$gff_ver\' is not recognized\n".
"The options GFF2 or GFF3 are supported\n";
}
}
#-----------------------------------------------------------+
# MAIN PROGRAM BODY |
#-----------------------------------------------------------+
ltrfinder2gff ($program, $seqname, $infile, $outfile, $append, $param, $delim);
exit 0;
#-----------------------------------------------------------+
# SUBFUNCTIONS |
#-----------------------------------------------------------+
sub print_help {
my ($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;
}
sub ltrfinder2gff {
# seq_id could be extracted from the ltrfinder result
# but passing it to the subfunction directly allows for cases
# where the id assigned by ltr_struc differs from the way
# the user is referring to the assembly
# MAY WANT TO ALLOW FOR USING THE $ls_seq_id
# $d is the delim character
my ($gff_src, $seq_id, $lf_infile, $gffout, $do_append, $gff_suffix, $d) = @_;
#////////////////////////////////////////
#////////////////////////////////////////
#////////////////////////////////////////
# ltr finder results as an array
# new 01/28/2010
my @ltr_results;
# Starting i at -1 so that increments start at 0
my $i = -1;
my $j = -1;
#////////////////////////////////////////
#////////////////////////////////////////
#////////////////////////////////////////
# The gff src id
#my $gff_src = "ltr_finder";
if ($gff_suffix) {
# d is the delim character and is a varaible to allow for
# using : as apollo likes or _ as GBrowse likes
$gff_src = $gff_src.$d.$gff_suffix;
}
my $print_gff_out = 0; # Boolean to print out gff data
my $gff_str_out; # A single out string line of gff out
# LTF FINDER COUTNERS/INDICES
my $lf_id_num = 0; # Incremented for every predicted model
# LTR_FINDER BOOLEANS
my $in_emp_details = 0; # Exact match pairs details
my $in_ltr_align = 0; # Details of the LTR alignment
my $in_pbs_align = 0;
my $in_ppt;
my $lf_prog_name; # LTR Finder program name
my $lf_seq_id; # Seq id
my $lf_seq_len; # Sequence length
my $lf_version; # Version of LTR finder being parsed
my $lf_trna_db; # tRNA database used
# Status strings
my $has_5ltr_tg; # TG in 5' END of 5' LTR
my $has_5ltr_ca; # CA in 3' END of 5' LTR
my $has_3ltr_tg; # TG in 5' END of 3' LTR
my $has_3ltr_ca; # CA in 3' END of 3' LTR
my $has_tsr; # Has Target Site Replication
my $has_pbs; # Has Primer Binding Site
my $has_ppt; # Has Poly Purine Tract
my $has_rt; # Has Reverse Transcriptase
my $has_in_core; # Has Integrase Core
my $has_in_cterm; # Has Integrase C-term
my $has_rh; # Has RNAseH
#-----------------------------+
# OPEN GFF OUTFILE |
#-----------------------------+
# Default to STDOUT if no argument given
if ($gffout) {
if ($do_append) {
open (GFFOUT, ">>$gffout") ||
die "ERROR: Can not open gff outfile:\n $gffout\n";
}
else {
open (GFFOUT,">$gffout") ||
die "ERROR: Can not open gff outfile:\n $gffout\n";
}
}
else {
open (GFFOUT, ">&STDOUT") ||
die "Can not print to STDOUT\n";
}
if ($gff_ver =~ "GFF3") {
print GFFOUT "##gff-version 3\n";
}
#-----------------------------+
# OPEN INPUT FILE |
#-----------------------------+
if ($lf_infile) {
open (INFILE, "<$lf_infile") ||
die "ERROR: Can not open LTR_FINDER result file\n $lf_infile\n";
}
else {
print STDERR "Expecting input from STDIN\n";
open (INFILE, "<&STDIN") ||
die "Can not accept input from standard input.\n";
}
while (<INFILE>) {
chomp;
#
if (m/Nothing Header(.*)/) {
}
# IN NEW REC, GET ID
elsif (m/^\[(.*)\]/) {
#-----------------------------+
# PRINT STORED GFF OUTPUT |
# IF VALUES ARE PRESENT |
#-----------------------------+
# Increment $I and initialize j for protein domains
$i++;
$j = -1;
# override seq id if one passed
if ($seqname) {
$lf_seq_id = $seqname;
}
# # FULL SPAN
# if ($lf_span_start) {
# $gff_str_out = "$lf_seq_id\t". # Seq ID
# "$gff_src\t". # Source
# "LTR_retrotransposon\t". # Data type
# "$lf_span_start\t". # Start
# "$lf_span_end\t". # End
# "$lf_score\t". # Score
# "$lf_strand\t". # Strand
# ".\t". # Frame
# "ltr_finder_$lf_ltr_id\n"; # Retro ID
# print GFFOUT $gff_str_out;
# }
#
# if ($lf_5ltr_start) {
# $gff_str_out = "$lf_seq_id\t". # Seq ID
# "$gff_src\t". # Source
# "five_prime_LTR\t". # Data type
# "$lf_5ltr_start\t". # Start
# "$lf_5ltr_end\t". # End
# "$lf_score\t". # Score
# "$lf_strand\t". # Strand
# ".\t". # Frame
# "ltr_finder_$lf_ltr_id\n"; # Retro ID
# print GFFOUT $gff_str_out;
# }
#
# if ($lf_3ltr_start) {
# $gff_str_out = "$lf_seq_id\t". # Seq ID
# "$gff_src\t". # Source
# "three_prime_LTR\t". # Data type
# "$lf_3ltr_start\t". # Start
# "$lf_3ltr_end\t". # End
# "$lf_score\t". # Score
# "$lf_strand\t". # Strand
# ".\t". # Frame
# "ltr_finder_$lf_ltr_id\n"; # Retro ID
# print GFFOUT $gff_str_out;
# }
#
# if ($has_pbs) {
# $gff_str_out = "$lf_seq_id\t". # Seq ID
# "$gff_src\t". # Source
# "primer_binding_site\t". # Data type
# "$lf_pbs_start\t" . # Start
# "$lf_pbs_end\t". # End
# "$lf_score\t". # Score
# "$lf_strand\t". # Strand
# ".\t". # Frame
# "ltr_finder_$lf_ltr_id\n"; # Retro ID
# print GFFOUT $gff_str_out;
# }
#
#
# if ($has_ppt) {
# $gff_str_out = "$lf_seq_id\t". # Seq ID
# "$gff_src\t". # Source
# "RR_tract\t". # Data type
# "$lf_ppt_start\t". # Start
# "$lf_ppt_end\t". # End
# "$lf_score\t". # Score
# "$lf_strand\t". # Strand
# ".\t". # Frame
# "ltr_finder_$lf_ltr_id\n"; # Retro ID
# print GFFOUT $gff_str_out;
# }
#
#
# if ($has_tsr) {
#
# $gff_str_out = "$lf_seq_id\t". # Seq ID
# "$gff_src\t". # Source
# "target_site_duplication\t". # Data type
# "$lf_5tsr_start\t". # Start
# "$lf_5tsr_end\t". # End
# "$lf_score\t". # Score
# "$lf_strand\t". # Strand
# ".\t". # Frame
# "ltr_finder_$lf_ltr_id\n"; # Retro ID
# print GFFOUT $gff_str_out;
#
# $gff_str_out = "$lf_seq_id\t". # Seq ID
# "$gff_src\t". # Source
# "target_site_duplication\t". # Data type
# "$lf_3tsr_start\t". # Start
# "$lf_3tsr_end\t". # End
# "$lf_score\t". # Score
# "$lf_strand\t". # Strand
# ".\t". # Frame
# "ltr_finder_$lf_ltr_id\n"; # Retro ID
# print GFFOUT $gff_str_out;
#
# }
#
#
# # Integrase Core
# if ($has_in_core) {
# #/////////
# # NOT SONG
# #\\\\\\\\\
# $gff_str_out = "$lf_seq_id\t". # Seq ID
# "$gff_src\t". # Source
# "integrase_core_domain\t". # Data type
# "$lf_in_core_dom_start\t". # Start
# "$lf_in_core_dom_end\t". # End
# "$lf_score\t". # Score
# "$lf_strand\t". # Strand
# ".\t". # Frame
# "ltr_finder_$lf_ltr_id\n"; # Retro ID
# print GFFOUT $gff_str_out;
#
# #/////////
# # NOT SONG
# #\\\\\\\\\
# $gff_str_out = "$lf_seq_id\t". # Seq ID
# "$gff_src\t". # Source
# "integrase_core_orf\t". # Data type
# "$lf_in_core_orf_start\t". # Start
# "$lf_in_core_orf_end\t". # End
# "$lf_score\t". # Score
# "$lf_strand\t". # Strand
# ".\t". # Frame
# "ltr_finder_$lf_ltr_id\n"; # Retro ID
# print GFFOUT $gff_str_out;
#
# } # End of has in_core
#
#
# if ($has_in_cterm) {
#
# #/////////
# # NOT SONG
# #\\\\\\\\\
# $gff_str_out = "$lf_seq_id\t". # Seq ID
# "$gff_src\t". # Source
# "integrase_cterm_domain\t". # Data type
# "$lf_in_cterm_dom_start\t". # Start
# "$lf_in_cterm_dom_end\t". # End
# "$lf_score\t". # Score
# "$lf_strand\t". # Strand
# ".\t". # Frame
# "ltr_finder_$lf_ltr_id\n"; # Retro ID
# print GFFOUT $gff_str_out;
#
# $gff_str_out = "$lf_seq_id\t". # Seq ID
# "$gff_src\t". # Source
# "integrase_cterm_orf\t". # Data type
# "$lf_in_cterm_orf_start\t". # Start
# "$lf_in_cterm_orf_end\t". # End
# "$lf_score\t". # Score
# "$lf_strand\t". # Strand
# ".\t". # Frame
# "ltr_finder_$lf_ltr_id\n"; # Retro ID
# print GFFOUT $gff_str_out;
#
# } # End of has_in_cterm
#
# if ($has_rh) {
#
# #/////////
# # NOT SONG
# #\\\\\\\\\
# $gff_str_out = "$lf_seq_id\t". # Seq ID
# "$gff_src\t". # Source
# "rnaseh_domain\t". # Data type
# "$lf_rh_dom_start\t". # Start
# "$lf_rh_dom_end\t". # End
# "$lf_score\t". # Score
# "$lf_strand\t". # Strand
# ".\t". # Frame
# "ltr_finder_$lf_ltr_id\n"; # Retro ID
# print GFFOUT $gff_str_out;
#
# $gff_str_out = "$lf_seq_id\t". # Seq ID
# "$gff_src\t". # Source
# "rnaseh_orf\t". # Data type
# "$lf_rh_orf_start\t". # Start
# "$lf_rh_orf_end\t". # End
# "$lf_score\t". # Score
# "$lf_strand\t". # Strand
# ".\t". # Frame
# "ltr_finder_$lf_ltr_id\n"; # Retro ID
# print GFFOUT $gff_str_out;
#
# }
#
# if ($has_rt) {
#
# #/////////
# # NOT SONG
# #\\\\\\\\\
# $gff_str_out = "$lf_seq_id\t". # Seq ID
# "$gff_src\t". # Source
# "rt_domain\t". # Data type
# "$lf_rt_dom_start\t". # Start
# "$lf_rt_dom_end\t". # End
# "$lf_score\t". # Score
# "$lf_strand\t". # Strand
# ".\t". # Frame
# "ltr_finder_$lf_ltr_id\n"; # Retro ID
# print GFFOUT $gff_str_out;
#
# $gff_str_out = "$lf_seq_id\t". # Seq ID
# "$gff_src\t". # Source
# "rt_orf\t". # Data type
# "$lf_rt_orf_start\t". # Start
# "$lf_rt_orf_end\t". # End
# "$lf_score\t". # Score
# "$lf_strand\t". # Strand
# ".\t". # Frame
# "ltr_finder_$lf_ltr_id\n"; # Retro ID
# print GFFOUT $gff_str_out;
#
# } # End of has_reverse_transcriptase
#-----------------------------+
# LOAD ID VAR |
#-----------------------------+
# $lf_ltr_id = $1;
$ltr_results[$i]{lf_ltr_id} = $1;
}
# SEQ ID AND LENGTH
elsif (m/>Sequence: (.*) Len:(.*)/){
# Incrmenting here would be the number of contigs that are being processed
$lf_seq_id = $1;
$lf_seq_len = $2;
}
# SPAN LOCATION, LENGTH, AND STRAND
elsif (m/^Location : (\d*) - (\d*) Len: (\d*) Strand:(.)/){
# $lf_span_start = $1;
# $lf_span_end = $2;
# $lf_length = $3;
# $lf_strand = $4;
$ltr_results[$i]{lf_span_start} = $1;
$ltr_results[$i]{lf_span_end} = $2;
$ltr_results[$i]{lf_length} = $3;
$ltr_results[$i]{lf_strand} = $4;
$ltr_results[$i]{lf_seq_id} = $lf_seq_id;
}
# SCORE SIMILARITY
elsif (m/^Score : (.*) \[LTR region similarity:(.*)\]/){
$ltr_results[$i]{lf_score} = $1; # Score
$ltr_results[$i]{lf_ltr_similarity} = $2; # Similarity of LTRs
}
# STATUS SET
elsif (m/^Status : (\d)(\d)(\d)(\d)(\d)(\d)(\d)(\d)(\d)(\d)(\d)/){
# Since this is a binary string, it can be split as digits
# and used to load the $has_* booleans
$has_5ltr_tg = $1;
$has_5ltr_ca = $2;
$has_3ltr_tg = $3;
$has_3ltr_ca = $4;
$has_tsr = $5;
$has_pbs = $6;
$has_ppt = $7;
$has_rt = $8;
$has_in_core = $9;
$has_in_cterm = $10;
$has_rh = $11;
}
# 5' LTR
elsif (m/^5\'-LTR : (\d*) - (\d*) Len: (\d*)/){
$ltr_results[$i]{lf_5ltr_start} = $1;
$ltr_results[$i]{lf_5ltr_end} = $2;
$ltr_results[$i]{lf_5ltr_len} = $3;
}
# 3' LTR
elsif (m/^3\'-LTR : (\d*) - (\d*) Len: (\d*)/){
$ltr_results[$i]{lf_3ltr_start} = $1;
$ltr_results[$i]{lf_3ltr_end} = $2;
$ltr_results[$i]{lf_3ltr_len} = $3;
}
# TARGET SITE REPLICATION
elsif (m/TSR : (\d*) - (\d*) , (\d*) - (\d*) \[(.*)\]/){
$ltr_results[$i]{lf_5tsr_start} = $1;
$ltr_results[$i]{lf_5tsr_end} = $2;
$ltr_results[$i]{lf_3tsr_start} = $3;
$ltr_results[$i]{lf_3tsr_end} = $4;
$ltr_results[$i]{lf_tsr_string} = $5;
}
# SHARPNESS METRIC
elsif (m/^Sharpness: (.*),(.*)/){
$ltr_results[$i]{lf_sharp5} = $1;
$ltr_results[$i]{lf_sharp_3} = $2;
}
# PBS
elsif (m/PBS : \[(\d*)\/(\d*)\] (\d*) - (\d*) \((.*)\)/) {
$ltr_results[$i]{lf_pbs_num_match} = $1; # Number of matching bases
$ltr_results[$i]{lf_pbs_aln_len} = $2; # PBS alignment length
$ltr_results[$i]{lf_pbs_start} = $3; # Start of PBS signal
$ltr_results[$i]{lf_pbs_end} = $4; # End of PBS signal
$ltr_results[$i]{lf_pbs_trna} = $5; # PBS tRNA type and anti-codon
}
# PPT
elsif (m/PPT : \[(\d*)\/(\d*)\] (\d*) - (\d*)/) {
$ltr_results[$i]{lf_ppt_num_match} = $1;
$ltr_results[$i]{lf_ppt_aln_len} = $2;
$ltr_results[$i]{lf_ppt_start} = $3;
$ltr_results[$i]{lf_ppt_end} = $4;
}
# PROTEIN DOMAINS
# This will need to be modified and checked after another run
# using ps_scan to get the additional domains
#
#Domain: 56796 - 57326 [possible ORF:56259-59144, (IN (core))]
elsif (m/Domain: (\d*) - (\d*) \[possible ORF:(\d*)-(\d*), \((.*)\)\]/) {
my $lf_domain_name = $5;
#///////////////////////////
# PUSH ALL DOMAIN DATA TO HREF
#//////////////////////////
# Increment j for index of protein domains
$j++;
$ltr_results[$i]{lf_dom}[$j]{lf_dom_start} = $1;
$ltr_results[$i]{lf_dom}[$j]{lf_dom_end} = $2;
# 3 and 5 are potential ORFS
$ltr_results[$i]{lf_dom}[$j]{lf_dom_name} = $5;
#-----------------------------+
# NORMALIZE DOMAIN NAME |
#-----------------------------+
if ($lf_domain_name =~ 'IN \(core\)') {
$ltr_results[$i]{lf_dom}[$j]{lf_dom_name_norm} = "Integrase";
$ltr_results[$i]{lf_dom}[$j]{lf_dom_name_short} = "int";
}
elsif ($lf_domain_name =~ 'IN \(c-term\)') {
$ltr_results[$i]{lf_dom}[$j]{lf_dom_name_norm} = "C-terminal";
$ltr_results[$i]{lf_dom}[$j]{lf_dom_name_short} = "cterm";
}
elsif ($lf_domain_name =~ 'RH') {
$ltr_results[$i]{lf_dom}[$j]{lf_dom_name_norm} = "RnaseH";
$ltr_results[$i]{lf_dom}[$j]{lf_dom_name_short} = "rh";
}
elsif ($lf_domain_name =~ 'RT') {
$ltr_results[$i]{lf_dom}[$j]{lf_dom_name_norm} = "Reverse Transcriptase";
$ltr_results[$i]{lf_dom}[$j]{lf_dom_name_short} = "rvt";
}
else {
# print "\a";
# print STDERR "Unknown domain type: $lf_domain_name\n";
$ltr_results[$i]{lf_dom}[$j]{lf_dom_name_norm} = $lf_domain_name;
$ltr_results[$i]{lf_dom}[$j]{lf_dom_name_short} = $lf_domain_name;
}
} # End of elsif Domain
#-----------------------------+
# FILE HEADER INFORMATION |
#-----------------------------+
# PROGRAM NAME
elsif (m/^Program : (.*)/) {
$lf_prog_name = $1;
# $ltr_results[$i]{program} = $1;
}
# PROGRAM VERSION
elsif (m/^Version : (.*)/) {
$lf_version = $1;
# $ltr_results[$i]{lf_version} = $1;
}
# MOD HERE
if ($print_gff_out) {
}
}
close INFILE;
#-----------------------------------------------------------+
# PRINT OUTPUT FROM THE ARRAY OF HASHES |
#-----------------------------------------------------------+
for my $href ( @ltr_results ) {
# For GFF2 format attribute is same for all parts
my $attribute = "ltr_finder_".$href->{lf_ltr_id};
my $model_num = $href->{lf_ltr_id};
$model_num = sprintf("%04d", $model_num);
# parent id
my $parent_id;
# If GFF3 format encode seq_ids to follow specifications
if ($gff_ver =~ "GFF3") {
$href->{lf_seq_id} = seqid_encode( $href->{lf_seq_id} );
if ($param) {
$parent_id = $href->{lf_seq_id}."_".
"ltr_finder".
"_par".$param.
"_model".$model_num;
}
else {
$parent_id = $href->{lf_seq_id}."_".
"ltr_finder".
"_model".$model_num;
}
# Reset attribute to include the seq id to maintain
# unique IDs for large datasets
}
#-----------------------------+
# LTR retrotransposon span |
#-----------------------------+
if ($gff_ver =~ "GFF3") {
$attribute = "ID=".$parent_id;
}
$gff_str_out = $href->{lf_seq_id}."\t". # Seq ID
"$gff_src\t". # Source
"LTR_retrotransposon\t". # Data type
$href->{lf_span_start}."\t". # Start
$href->{lf_span_end}."\t". # End
$href->{lf_score}."\t". # Score
$href->{lf_strand}."\t". # Strand
".\t". # Frame
$attribute.
"\n";
print GFFOUT $gff_str_out;
#-----------------------------+
# 5 Prime LTR |
#-----------------------------+
if ($gff_ver =~ "GFF3") {
$attribute = "ID=".$parent_id."_five_prime_LTR".
";Name=Five Prime LTR".
";Parent=".$parent_id;
}
$gff_str_out = $href->{lf_seq_id}."\t". # Seq ID
"$gff_src\t". # Source
"five_prime_LTR\t". # Data type
$href->{lf_5ltr_start}."\t". # Start
$href->{lf_5ltr_end}."\t". # End
$href->{lf_score}."\t". # Score
$href->{lf_strand}."\t". # Strand
".\t". # Frame
$attribute.
"\n";
print GFFOUT $gff_str_out;
#-----------------------------+
# 3 Prime LTR |
#-----------------------------+
if ($gff_ver =~ "GFF3") {
$attribute = "ID=".$parent_id."_three_prime_LTR".
";Name=Three Prime LTR".
";Parent=".$parent_id;
}
$gff_str_out = $href->{lf_seq_id}."\t". # Seq ID
"$gff_src\t". # Source
"three_prime_LTR\t". # Data type
$href->{lf_3ltr_start}."\t". # Start
$href->{lf_3ltr_end}."\t". # End
$href->{lf_score}."\t". # Score
$href->{lf_strand}."\t". # Strand
".\t". # Frame
$attribute.
"\n";
print GFFOUT $gff_str_out;
#-----------------------------+
# PRIMER BINDING SITE |
#-----------------------------+
if ($gff_ver =~ "GFF3") {
$attribute = "ID=".$parent_id."_primer_binding_site".
";Name=PBS".
";Parent=".$parent_id;
}
# print only if a PBS has been annotated
if ( $href->{lf_pbs_start} ) {
$gff_str_out = $href->{lf_seq_id}."\t". # Seq ID
"$gff_src\t". # Source
"primer_binding_site\t". # Data type
$href->{lf_pbs_start}."\t". # Start
$href->{lf_pbs_end}."\t". # End
$href->{lf_score}."\t". # Score
$href->{lf_strand}."\t". # Strand
".\t". # Frame
$attribute.
"\n";
print GFFOUT $gff_str_out;
}
#-----------------------------+
# RR_tract |
#-----------------------------+
if ($gff_ver =~ "GFF3") {
$attribute = "ID=".$parent_id."_RR_tract".
";Name=PPT".
";Parent=".$parent_id;
}
# print only if RR_tract has been annotated
if ($href->{lf_ppt_start}) {
$gff_str_out = $href->{lf_seq_id}."\t". # Seq ID
"$gff_src\t". # Source
"RR_tract\t". # Data type
$href->{lf_ppt_start}."\t". # Start
$href->{lf_ppt_end}."\t". # End
$href->{lf_score}."\t". # Score
$href->{lf_strand}."\t". # Strand
".\t". # Frame
$attribute.
"\n";
print GFFOUT $gff_str_out;
}
#-----------------------------+
# 5' TSD |
#-----------------------------+
if ( $href->{lf_5tsr_start}) {
if ($gff_ver =~ "GFF3") {
$attribute = "ID=".$parent_id."_tsd5".
";Name=Target Site Duplication".
";Parent=".$parent_id;
}
$gff_str_out = $href->{lf_seq_id}."\t". # Seq ID
"$gff_src\t". # Source
"target_site_duplication\t". # Data type
$href->{lf_5tsr_start}."\t". # Start
$href->{lf_5tsr_end}."\t". # End
$href->{lf_score}."\t". # Score
$href->{lf_strand}."\t". # Strand
".\t". # Frame
$attribute.
"\n";
print GFFOUT $gff_str_out;
}
#-----------------------------+
# 3' TSD |
#-----------------------------+
if ( $href->{lf_3tsr_start}) {
if ($gff_ver =~ "GFF3") {
$attribute = "ID=".$parent_id."_tsd3".
";Name=Target Site Duplication".
";Parent=".$parent_id;
}
$gff_str_out = $href->{lf_seq_id}."\t". # Seq ID
"$gff_src\t". # Source
"target_site_duplication\t". # Data type
$href->{lf_3tsr_start}."\t". # Start
$href->{lf_3tsr_end}."\t". # End
$href->{lf_score}."\t". # Score
$href->{lf_strand}."\t". # Strand
".\t". # Frame
$attribute.
"\n";
print GFFOUT $gff_str_out;
}
#-----------------------------+
# PROTEIN DOMAINS |
#-----------------------------+
for my $dom ( @{ $href->{lf_dom} } ) {
# The following will just print the name
my $type = $dom->{lf_dom_name_norm};
if ($gff_ver =~ "GFF3") {
$attribute = "ID=".$parent_id.$dom->{lf_dom_name_short}.
";Name=".$dom->{lf_dom_name_norm}.
";Parent=".$parent_id;
#$type = "polypeptide_domain";
$type = "transposable_element_gene";
# It may be necessary to first define a "gene" and
# then set domains..
}
$gff_str_out = $href->{lf_seq_id}."\t". # Seq ID
"$gff_src\t". # Source
$type."\t".
$dom->{lf_dom_start}."\t". # Start
$dom->{lf_dom_end}."\t". # End
$href->{lf_score}."\t". # Score
$href->{lf_strand}."\t". # Strand
".\t". # Frame
$attribute.
"\n";
print GFFOUT $gff_str_out;
}
}
close GFFOUT;
} # End of ltrfinder2gff subfunction
sub seqid_encode {
# Following conventions for GFF3 v given at http://gmod.org/wiki/GFF3
# Modified from code for urlencode in the perl cookbook
# Ids must not contain unescaped white space, so spaces are not allowed
my ($value) = @_;
$value =~ s/([^[a-zA-Z0-9.:^*$@!+_?-|])/"%" . uc(sprintf "%lx" , unpack("C", $1))/eg;
return ($value);
}
sub gff3_encode {
# spaces are allowed in attribute, but tabs must be escaped
my ($value) = @_;
$value =~ s/([^[a-zA-Z0-9.:^*$@!+_?-| ])/"%" . uc(sprintf "%lx" , unpack("C", $1))/eg;
return ($value);
}
1;
__END__
=head1 NAME
cnv_ltrfinder2gff.pl - Converts LTR_Finder output to gff format
=head1 VERSION
This documentation refers to program version $Rev$
=head1 SYNOPSIS
=head2 Usage
cnv_ltrfinder2gff.pl -i lf_result.txt -o lf_result.gff
=head2 Required Arguments
--infile # Path to the input file
# Result from a single record fasta file
--outdir # Base output dir
=head1 DESCRIPTION
Convert the ltrfinder output to gff format. This assumes that the output
from ltr_finder correspons to a single BAC. A suffix can be passed with the
--suffix option to provide a suffix for the source column. For example
run default ltr_finder results with --suffix def to create