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cnv_ltrstruc2ann.pl
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#!/usr/bin/perl -w
#-----------------------------------------------------------+
# |
# cnv_ltrstruc2ann.pl - Convert ltrstruc rpt to annotation |
# |
#-----------------------------------------------------------+
# |
# AUTHOR: James C. Estill |
# CONTACT: JamesEstill_@_gmail.com |
# STARTED: 04/14/2008 |
# UPDATED: 06/02/2009 |
# |
# DESCRIPTION: |
# Convert *rpt.txt output files from LTR_STRUC to |
# annotation coordinates mapped on the LTR Ret |
# |
# VERSION: $Rev$ |
# |
# LICENSE: |
# GNU General Public License, Version 3 |
# http://www.gnu.org/licenses/gpl.html |
# |
#-----------------------------------------------------------+
#
# TO DO: * Add percent divergence of the LTRs to the annotation
# * Decide of this should be append to an existing gff file or write
# a new gff for every sequence
# * Add support for GFF3 output
#
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 $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 = 0; # Create files in outdir with sequence data
my $name_root;
#-----------------------------+
# COMMAND LINE OPTIONS |
#-----------------------------+
my $ok = GetOptions(# REQUIRED OPTIONS
# "i|indir=s" => \$indir,
"o|outfile=s" => \$outfile,
"g|gff-out=s" => \$gff_outfile,
"f|feat-sum=s" => \$fs_outfile,
"r|results=s" => \$repdir,
# ADDITIONAL OPTIONS
"outdir=s" => \$outdir,
"e|e-val=s" => \$e_val,
"c|copy" => \$do_copy,
"q|quiet" => \$quiet,
"s|seq-data" => \$do_seq_data,
"verbose" => \$verbose,
# ADDITIONAL INFORMATION
"usage" => \$show_usage,
"version" => \$show_version,
"man" => \$show_man,
"h|help" => \$show_help,);
#-----------------------------+
# SHOW REQUESTED HELP |
#-----------------------------+
if ( ($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 = $repdir."/";
}
#-----------------------------+
# OPEN FEATURE SUMMARY OUTFILE|
# PRINT HEADER |
#-----------------------------+
open (FEATSUM, ">$fs_outfile") ||
die "Can not open the feature summary file\n";
print FEATSUM "#seq_id\t". # 1
"fl_rpn_start\t". # 2
"fl_rpn_end\t". # 3
"ltr_5_start\t". # 4
"ltr_5_end\t". # 5
"ltr_5_dn_start\t". # 6
"ltr_5_dn_end\t". # 7
"ltr_3_start\t". # 8
"ltr_3_end\t". # 9
"ltr_3_dn_start\t". # 10
"ltr_3_dn_end\t". # 11
"pbs_start\t". # 12
"pbs_end\t". # 13
"ppt_start\t". # 14
"ppt_end\t". # 15
"tsd_5_start\t". # 16
"tsd_5_end\t". # 17
"tsd_5_seq\t". # 18
"tsd_3_start\t". # 19
"tsd_3_end\t". # 20
"tsd_3_seq\t". # 21
"gag_s\tgag_e\t". # 22 GAG
"zf_s\tzf_e\t". # 24 Zinc finger, gag component
"rvp_s\trvp_e\t". # 26 Protease/AP
"rve_s\trve_e\t". # 28 INTEGRASE
"rvt_s\trvt_e\t". # 30 Reverse Transcriptase
"rh_s\trh_e\t". # 32 RnaseH
"chrom_s\tchrom_e\t". # 34 Chromodomain
"env_s\tenv_e\t". # 36Envelope
"flank_5_seq\t". # 38 5' Flanking Sequence
"flank_3_seq\t". # 39 3' Flanking Sequence
"strand". # 40 Strand as reported from ltr_struc
"\n";
#-----------------------------+
# 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;
if ($ind_report_num == 1) {
# Generall if first record start new gff file
# 04/14/2008
# Changed the following to append to existing gff file
ltrstruc2ann ( $seq_id, $report_file_path,
1, $ind_report_num,
$do_seq_data, $gff_out_path);
}
else {
ltrstruc2ann ( $seq_id, $report_file_path,
1, $ind_report_num,
$do_seq_data, $gff_out_path);
}
} # End for for each individual report
exit;
#-----------------------------------------------------------+
# SUBFUNCTIONS |
#-----------------------------------------------------------+
# Dropping fasta_in
sub ltrstruc2ann {
# Not renaming the vars ... but gff_out and gff_append both
# refer to the annotation file
# VARS PASSED TO THE SUBFUNCTION
# my ($report_in, $gff_out, $gff_append, $ls_id_num,
# $print_seq_data) = @_;
my ($gff_seq_id, $report_in, $gff_append, $ls_id_num,
$print_seq_data, $gff_out) = @_;
# Trying to make $gff_out an option
# my ($report_in, $gff_append, $ls_id_num,
# $print_seq_data) = @_;
# my ($gff_out) = shift;
# 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 $tsd3_from_query_seq;
#-----------------------------+
# OPEN GFF OUTPUT FILE |
#-----------------------------+
if ($gff_append) {
open (GFFOUT, ">>$gff_out") ||
die "ERROR: Could not open gff output file:\b$gff_out\n";
}
else
{
open (GFFOUT, ">$gff_out") ||
die "ERROR: Could not open gff output file:\n$gff_out\n";
}
#-----------------------------+
# 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) {
# Changed the above to the following
# .. this may cause some problems if single character for correct carriage
# returns
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
# Annotate the internal sequence features using local databases
my @blast_dbs = ("/db/jlblab/pfam/gag_poaceae",
"/db/jlblab/pfam/zf_cchc_poaceae",
"/db/jlblab/pfam/rvp_all_poa",
"/db/jlblab/pfam/rve_poaceae",
"/db/jlblab/pfam/rvt_poaceae", # both rvt_1 and rvt_2
"/db/jlblab/pfam/rh_poaceae",
"/db/jlblab/pfam/chromo_viridiplant",
"/db/jlblab/pfam/dros_env",
);
# SEQID
my $name_root = $gff_seq_id;
# PRINT GFF OUTPUT |
#-----------------------------+
# Data type follows SONG
# http://song.cvs.sourceforge.net/*checkout*/song/ontology/so.obo
# my $name_root = "ltr_retro_model";
my $gff_result_id = "ltr_struc_".$ls_id_num;
print GFFOUT "$name_root\t". # Seq ID
"ltr_struc\t". # Source
"LTR_retrotransposon\t". # Data type, has to be exon for APOLLO
"$gff_full_retro_start\t". # Start
"$gff_full_retro_end\t". # End
"$ls_score\t". # Score
"$ls_orientation\t". # Strand
".\t". # Frame
"$gff_result_id\n"; # Retro Id
print FEATSUM "$name_root\t";
print FEATSUM "$gff_full_retro_start\t";
print FEATSUM "$gff_full_retro_end\t";
print GFFOUT "$name_root\t". # Seq ID
"ltr_struc\t". # Source
"five_prime_LTR\t". # SO:0000425
"$gff_ltr5_start\t". # Start
"$gff_ltr5_end\t". # End
"$ls_score\t". # Score
"$ls_orientation\t". # Strand
".\t". # Frame
"$gff_result_id\n"; # Retro Id
print FEATSUM "$gff_ltr5_start\t";
print FEATSUM "$gff_ltr5_end\t";
# DINUCLEOTIDES
my $ltr_5_dn_start = substr($ls_5ltr_seq, 0, 2);
my $ltr_5_dn_end = substr($ls_5ltr_seq,
length($ls_5ltr_seq) - 2 , 2);
print FEATSUM "$ltr_5_dn_start\t";
print FEATSUM "$ltr_5_dn_end\t";
print GFFOUT "$name_root\t". # Seq ID
"ltr_struc\t". # Source
"three_prime_LTR\t". # SO:0000426
"$gff_ltr3_start\t". # Start
"$gff_ltr3_end\t". # End
"$ls_score\t". # Score
"$ls_orientation\t". # Strand
".\t". # Frame
"$gff_result_id\n"; # Retro Id
print FEATSUM "$gff_ltr3_start\t";
print FEATSUM "$gff_ltr3_end\t";
# SEQ HAS TG/CA
# #print "\t\t3\'LTR: $ls_3ltr_seq\n";
my $ltr_3_dn_start = substr($ls_3ltr_seq,0,2);
my $ltr_3_dn_end = substr($ls_3ltr_seq,
length($ls_3ltr_seq) - 2, 2);
print FEATSUM "$ltr_3_dn_start\t";
print FEATSUM "$ltr_3_dn_end\t";
print GFFOUT "$name_root\t". # Seq ID
"ltr_struc\t". # Source
"primer_binding_site\t". # SO:0005850
"$gff_pbs_start\t". # Start
"$gff_pbs_end\t". # End
"$ls_score\t". # Score
"$ls_orientation\t". # Strand
".\t". # Frame
"$gff_result_id\n"; # Retro Id
print FEATSUM "$gff_pbs_start\t";
print FEATSUM "$gff_pbs_end\t";
print GFFOUT "$name_root\t". # Seq ID
"ltr_struc\t". # Source
"RR_tract\t". # SO:0000435
"$gff_ppt_start\t". # Start
"$gff_ppt_end\t". # End
"$ls_score\t". # Score
"$ls_orientation\t". # Strand
".\t". # Frame
"$gff_result_id\n"; # Retro Id
print FEATSUM "$gff_ppt_start\t";
print FEATSUM "$gff_ppt_end\t";
print GFFOUT "$name_root\t". # Seq ID
"ltr_struc\t". # Source
"target_site_duplication\t". # SO:0000434
"$gff_5tsr_start\t". # Start
"$gff_5tsr_end\t". # End
"$ls_score\t". # Score
"$ls_orientation\t". # Strand
".\t". # Frame
"$gff_result_id\n"; # Retro Id
print FEATSUM "$gff_5tsr_start\t";
print FEATSUM "$gff_5tsr_end\t";
print FEATSUM "$ls_5tsr_seq\t";
print GFFOUT "$name_root\t". # Seq ID
"ltr_struc\t". # Source
"target_site_duplication\t". # SO:0000434
"$gff_3tsr_start\t". # Start
"$gff_3tsr_end\t". # End
"$ls_score\t". # Score
"$ls_orientation\t". # Strand
".\t". # Frame
"$gff_result_id\n"; # Retro Id
print FEATSUM "$gff_3tsr_start\t";
print FEATSUM "$gff_3tsr_end\t";
print FEATSUM "$ls_3tsr_seq\t";
# Extract BLAST OUTPUT
my $max_e_val = $e_val;
my $seq_id = $name_root;
my $seq_string = $ls_full_retro_seq;
#///////////////////////
foreach my $blastdb (@blast_dbs) {
my $annotated_rpn = seq_annotate ($seq_id, $seq_string,
$blastdb, $max_e_val );
if ($annotated_rpn) {
print GFFOUT "$name_root\t". # Seq ID
"blastx\t". # Source
$annotated_rpn->{ feat_name }."\t".
$annotated_rpn->{ feat_start }."\t".
$annotated_rpn->{ feat_end }."\t".
"$ls_score\t". # Score
"$ls_orientation\t". # Strand
".\t". # Frame
"$gff_result_id\n"; # Retro Id
print FEATSUM $annotated_rpn->{ feat_start }."\t";
print FEATSUM $annotated_rpn->{ feat_end }."\t";
if ($verbose) {
print STDERR "$name_root\t". # Seq ID
"blastx\t". # Source
$annotated_rpn->{ feat_name }."\t".
$annotated_rpn->{ feat_start }."\t".
$annotated_rpn->{ feat_end }."\t".
"$ls_score\t". # Score
"$ls_orientation\t". # Strand
".\t". # Frame
"$gff_result_id\n"; # Retro Id
}
}
else {
print FEATSUM "N\tN\t";
}
}
# PRINT FLANKING SEQUENCES
print FEATSUM "$ls_5flank_seq\t";
print FEATSUM "$ls_3flank_seq\t";
# PRINT ORIENTATION FROM LTR STRUC
print FEATSUM "$ls_orientation";
#my $ls_5flank_seq; # 5' Flanking sequence
#my $ls_3flank_seq; # 3' Flanking sequence
# END OF ALL FEATURES, PRINT NEWLINE TO FEATSUM
print FEATSUM "\n";
if ($verbose) {
print STDOUT "$name_root\t". # Seq ID
"ltr_struc\t". # Source
"LTR_retrotransposon\t". # Data type, has to be exon for APOLLO
"$gff_full_retro_start\t". # Start
"$gff_full_retro_end\t". # End
"$ls_score\t". # Score
"$ls_orientation\t". # Strand
".\t". # Frame
"$gff_result_id\n"; # Retro Id
print STDOUT "$name_root\t". # Seq ID
"ltr_struc\t". # Source
"primer_binding_site\t". # SO:0005850
"$gff_pbs_start\t". # Start
"$gff_pbs_end\t". # End
"$ls_score\t". # Score
"$ls_orientation\t". # Strand
".\t". # Frame
"$gff_result_id\n"; # Retro Id
print STDOUT "$name_root\t". # Seq ID
"ltr_struc\t". # Source
"RR_tract\t". # SO:0000435
"$gff_ppt_start\t". # Start
"$gff_ppt_end\t". # End
"$ls_score\t". # Score
"$ls_orientation\t". # Strand
".\t". # Frame
"$gff_result_id\n"; # Retro Id
print STDOUT "$name_root\t". # Seq ID
"ltr_struc\t". # Source
"five_prime_LTR\t". # SO:0000425
"$gff_ltr5_start\t". # Start
"$gff_ltr5_end\t". # End
"$ls_score\t". # Score
"$ls_orientation\t". # Strand
".\t". # Frame
"$gff_result_id\n"; # Retro Id
print STDOUT "$name_root\t". # Seq ID
"ltr_struc\t". # Source
"three_prime_LTR\t". # SO:0000426
"$gff_ltr3_start\t". # Start
"$gff_ltr3_end\t". # End
"$ls_score\t". # Score
"$ls_orientation\t". # Strand
".\t". # Frame
"$gff_result_id\n"; # Retro Id
print STDOUT "$name_root\t". # Seq ID
"ltr_struc\t". # Source
"target_site_duplication\t". # SO:0000434
"$gff_5tsr_start\t". # Start
"$gff_5tsr_end\t". # End
"$ls_score\t". # Score
"$ls_orientation\t". # Strand
".\t". # Frame
"$gff_result_id\n"; # Retro Id
print STDOUT "$name_root\t". # Seq ID
"ltr_struc\t". # Source
"target_site_duplication\t". # SO:0000434
"$gff_3tsr_start\t". # Start
"$gff_3tsr_end\t". # End
"$ls_score\t". # Score
"$ls_orientation\t". # Strand
".\t". # Frame
"$gff_result_id\n"; # Retro Id
}
#-----------------------------+
# PRINT SUMMARY OUTPUT |
#-----------------------------+
if ($verbose) {
print STDERR "\t\tScore: $ls_score\n";
print STDERR "\t\tOrientation: $ls_orientation\n";
print STDERR "\t\tRetro Len: $ls_retro_len\n";
print STDERR "\t\tLongest Orf: $ls_longest_orf\n";
print STDERR "\t\tPair Homology: $ls_ltr_homology\n";
print STDERR "\t\t5LTR Len LST: $ls_5ltr_len\n";
print STDERR "\t\t5LTR Lem PAR: $par_5ltr_len\n";
print STDERR "\t\t3LTR Len LST: $ls_3ltr_len\n";
print STDERR "\t\t3LTR Len PAR: $par_3ltr_len\n";
print STDERR "\n\t\tEXTRACTED COORDINATES:\n";
print STDERR "\t\t5\'LTR Start: $ltr5_start\n";
print STDERR "\t\t5\'LTR End: $ltr5_end\n";
print STDERR "\t\t3\'LTR Start: $ltr3_start\n";
print STDERR "\t\t3\'LTR End: $ltr3_end\n";
print STDERR "\t\tPBS Start: $pbs_start\n";
print STDERR "\t\tPBS end : $pbs_end\n";
print STDERR "\t\tPPT Start: $ppt_start\n";
print STDERR "\t\tPPT End: $ppt_end\n";
print STDERR "\t\tRetro Start: $full_retro_start\n";
print STDERR "\t\tRetro End: $full_retro_end\n";
# SEQUENCE DATA
print STDERR "\n\t\tSEQUENCE DATA:\n";
print STDERR "\t\t5Dinuc: $ls_5dinuc\n";
print STDERR "\t\t3Dinuc: $ls_3dinuc\n";
print STDERR "\n\t\t=====================\n";
print STDERR "\t\t5\' TSD TEST:\n";
print STDERR "\t\tLTR_STRUC: $ls_5tsr_seq\n";
print STDERR "\t\t=====================\n";
print STDERR "\n\t\t=====================\n";
print STDERR "\t\t3\' TSD TEST:\n";
print STDERR "\t\tLTR_STRUC: $ls_3tsr_seq\n";
print STDERR "\t\t=====================\n";
print STDERR "\n\t\t=====================\n";
print STDERR "\t\tPBS STRING TEST:\n";
print STDERR "\t\tLTR_STRUC: $ls_pbs_seq\n";
print STDERR "\t\tFROM RETRO: $pbs_from_full_retro\n";
print STDERR "\t\t=====================\n";
print STDERR "\n\t\t=====================\n";
print STDERR "\t\tPPT STRING TEST:\n";
print STDERR "\t\tLTR_STRUC: $ls_ppt_seq\n";
print STDERR "\t\tFROM RETRO: $ppt_from_full_retro\n";
print STDERR "\t\t=====================\n";
print STDERR "\n";
print STDERR "\t\t5\'Flank: $ls_5flank_seq\n";
print STDERR "\t\t3\'Flank: $ls_3flank_seq\n";
#print "\t\t5\'LTR: $ls_5ltr_seq\n";
#print "\t\t3\'LTR: $ls_3ltr_seq\n";
#print "$ls_full_retro_seq\n";
}
# 05/16/2008 - Added the following back into the code
#-----------------------------+
# 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);
}
close (GFFOUT);
}
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;