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create_any_complete_site_with_flanking.pl
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create_any_complete_site_with_flanking.pl
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#!/usr/bin/perl -w
use strict;
use Bio::DB::Fasta;
use Bio::SeqIO;
## need refFasta, TEFasta, RelocaTEouput, padding
my $dbfile = shift;
my $TEfile = shift;
my $range_file = shift;
my $padding = shift;
my $usr_TE; #to be determined from range_file = 'mping';#shift; ## ping or mping
open GFF, ">$range_file.gff" or die "can't open $range_file.gff for writing\n";
if ( !defined $padding ) {
$padding = 0;
}
if ( !defined $dbfile or !defined $range_file ) {
die "Please provide fasta file and RelocaTE output\n
example:
./create_any_complete_site_with_flanking.pl RefFastaFile TEFastaFile location_File padding
"
}
my $db_obj = Bio::DB::Fasta->new($dbfile);
#my $db_TE_obj = Bio::DB::Fasta->new($TEfile);
my %TEs;
my $seqIO_obj = Bio::SeqIO->new( -format => 'fasta', -file => $TEfile );
while ( my $seq_obj = $seqIO_obj->next_seq ) {
my $TE = $seq_obj->id;
my $seq = $seq_obj->seq;
$TEs{$TE} = $seq;
}
my %inserts;
open IN, $range_file or die "Can't open range_file\n";
while ( my $range = <IN> ) {
chomp $range;
my @range = split /\t/, $range;
next if $range =~ /^TE.+insertion_site/;
#TE TSD Exper insertion_site strand left_flanking_read_count right_flanking_read_count left_flanking_seq right_flanking_seq
#Dasheng ATCCA A119_2 Chr1:861881..861885 - 32 28 CCACAGAAATTACAACAGCCAAACAACACATGTGGCCAATTTTCACACATAACGAGATAACATCCCAATCACAACTTTATGATAAACGAAAGCTTCCATC CAGTTCACGGCAAAGAGATTACTCATCATAAATAAATAGTGTACAATAAAATATATCACTGTTTACAAATATTATTTCTAGCTTCAGCATTTTACCACCT
my ( $ref, $start, $end ) = $range[3] =~ /^(\S+):(\d+)\.\.(\d+)/;
$inserts{$ref}{$start}{$end}{strains}{ $range[2] }++;
$inserts{$ref}{$start}{$end}{strand}{ $range[4] }++;
#$inserts{$ref}{$start}{$end}{TSD} = $range[1];
$inserts{$ref}{$start}{$end}{TE}{ $range[0] } = $range[1]; ##TSD info
}
foreach my $ref ( keys %inserts ) {
foreach my $start ( keys %{ $inserts{$ref} } ) {
foreach my $end ( keys %{ $inserts{$ref}{$start} } ) {
my @TEs;
foreach my $TE_name ( keys %{ $inserts{$ref}{$start}{$end}{TE} } ) {
my $TSD = $inserts{$ref}{$start}{$end}{TE}{$TE_name};
my @strains = sort keys %{ $inserts{$ref}{$start}{$end}{strains} };
push @TEs, $TE_name;
my $desc = join( "/", @strains );
my $plus =
defined $inserts{$ref}{$start}{$end}{strand}{'+'}
? $inserts{$ref}{$start}{$end}{strand}{'+'}
: 0;
my $minus =
defined $inserts{$ref}{$start}{$end}{strand}{'-'}
? $inserts{$ref}{$start}{$end}{strand}{'-'}
: 0;
my $strand_ref =
defined $inserts{$ref}{$start}{$end}{strand}{'.'}
? $inserts{$ref}{$start}{$end}{strand}{'.'}
: 0;
my $strand = 'fwd';
if ( $minus > $plus ) {
$strand = 'rc';
} elsif ( $strand_ref > $minus and $strand_ref > $plus ) {
$strand = 'ref';
}
my $name = $TE_name . "." . join( '_', $ref, $start, $end );
my $seq_obj = $db_obj->get_Seq_by_id($ref);
if ($seq_obj) {
my $seq = $seq_obj->seq;
my %coords;
my ( $padded_start, $padded_end, $pre_TE, $post_TE, $justTE );
my $rev_TE;
my $revcomp_TE;
my $revcomp_rev_TE;
if ( defined $seq ) {
#Chr1:2640500..2640502 Ping1 shared in H/E/19/23 and is in a stowawy
if ($TE_name eq 'ping' and $ref eq 'Chr1' and $start == 2640500 and $end == 2640502){
print_special_ping($start,$end,$seq,$name);
next;
}
my $TE = substr $seq, $start - 1, ( $end - $start ) + 1;
#if this is a reference mPing, add the TSD inaddition to flanking
if ( length $TE > length $TSD or $TSD eq 'TSD') {
$justTE= $TE;
$padded_start = $start - $padding;
$padded_end = $end + $padding;
$pre_TE = substr $seq, $padded_start - 1, $padding;
$post_TE = substr $seq, $end, ($padding);
}
## if TE length is 3, then we need to add the TE and dup the TSD
elsif ( length $TE == length $TSD ) {
$TSD = $TE; ## reset the $TSD to be exactly what is in the genomeSeq, just incase
$justTE = $TEs{$TE_name};
my $rev_justTE = reverse $justTE;
my $revcomp_justTE = $rev_justTE;
$revcomp_justTE =~ tr/ATGC/TACG/;
$TE = $justTE . $TSD;
$revcomp_TE = $revcomp_justTE . $TSD;
$padded_start = $end - $padding;
$padded_end = $end + $padding - ( length $TSD ) - 1;
$pre_TE = substr $seq, $end - $padding, $padding;
$post_TE = substr $seq, $end, $padding - ( length $TSD );
}
my $subseq = $pre_TE . $TE . $post_TE;
## coords are relative to subseq, always starts with 1 and ends at length of substr
$coords{flank_1_start} = 1;
$coords{flank_1_end} = $padding;
$coords{TE_start} = $padding + 1;
$coords{TE_end} = $padding + ( length $justTE );
$coords{TSD_2_start} = $TSD ne 'TSD' ? $coords{TE_end} + 1 : 'ref';
$coords{TSD_2_end} = $TSD ne 'TSD' ? $coords{TE_end} + ( length $TSD ) : 'ref';
$coords{TSD_1_start} = $TSD ne 'TSD' ? $coords{TE_start} - ( length $TSD ) : 'ref';
$coords{TSD_1_end} = $TSD ne 'TSD' ? $coords{TE_start} - 1 : 'ref' ;
$coords{flank_2_start} = $coords{TE_end} + 1;
$coords{flank_2_end} = $padding * 2 + ( length $justTE );
my $coords =
"FLANK1:$coords{flank_1_start}..$coords{flank_1_end} TSD1:$coords{TSD_1_start}..$coords{TSD_1_end} TE:$coords{TE_start}..$coords{TE_end} TSD2:$coords{TSD_2_start}..$coords{TSD_2_end} FLANK2:$coords{flank_2_start}..$coords{flank_2_end}";
my $revcomp_subseq;
if ( defined $revcomp_TE ) {
$revcomp_subseq = $pre_TE . $revcomp_TE . $post_TE;
}
my $TE_Orient = $strand;
$desc = defined $desc ? "$desc " : '';
my $TE_names = join( "/", @TEs );
my $GFF_strand = $TE_Orient eq 'fwd' ? '+' : '-';
if ($TE_Orient eq 'ref'){
$GFF_strand = '.';
}
if ( $padding == 0 ) {
my $header = "$TE_names $desc$ref:$start..$end $coords";
if ( !$TE_Orient or $TE_Orient eq 'fwd' or $TE_Orient eq 'unk' or $TE_Orient eq 'ref' ) {
print ">$name $TE_name.$TE_Orient $header\n$subseq\n";
print GFF
"$name\t.\tchromosome\t$coords{flank_1_start}\t$coords{flank_2_end}\t.\t.\t.\tID=$name;Name=$name;Note=$header\n";
print GFF
"$name\t.\ttransposable_element_insertion_site\t$coords{TE_start}\t$coords{TE_end}\t.\t$GFF_strand\t.\tID=$name.$start.$end;Name=$name;Note=$header\n";
}
if ( defined $revcomp_TE ) {
if ( !$TE_Orient or $TE_Orient eq 'rc' or $TE_Orient eq 'unk' )
{
print ">$name $TE_name.$TE_Orient $header\n$revcomp_subseq\n";
print GFF
"$name\t.\tchromosome\t$coords{flank_1_start}\t$coords{flank_2_end}\t.\t.\t.\tID=$name;Name=$name;Note=$header\n";
print GFF
"$name\t.\ttransposable_element_insertion_site\t$coords{TE_start}\t$coords{TE_end}\t.\t$GFF_strand\t.\tID=$name.$start.$end;Name=$name;Note=$header\n";
}
}
} else {
my $header = "$TE_names $desc$ref:$start..$end $coords";
if ( !defined $name ) {
$name = $header;
}
if ( !$TE_Orient or $TE_Orient eq 'fwd' or $TE_Orient eq 'unk' or $TE_Orient eq 'ref') {
print ">$name $TE_name.$TE_Orient $header\n$subseq\n";
print GFF
"$name\t.\tchromosome\t$coords{flank_1_start}\t$coords{flank_2_end}\t.\t.\t.\tID=$name;Name=$name;Note=$header\n";
print GFF
"$name\t.\ttransposable_element_insertion_site\t$coords{TE_start}\t$coords{TE_end}\t.\t$GFF_strand\t.\tID=$name.$start.$end;Name=$name;Note=$header\n";
}
if ( defined $revcomp_TE ) {
if ( !$TE_Orient or $TE_Orient eq 'rc' or $TE_Orient eq 'unk' )
{
print ">$name $TE_name.$TE_Orient $header\n$revcomp_subseq\n";
print GFF
"$name\t.\tchromosome\t$coords{flank_1_start}\t$coords{flank_2_end}\t.\t.\t.\tID=$name;Name=$name;Note=$header\n";
print GFF
"$name\t.\ttransposable_element_insertion_site\t$coords{TE_start}\t$coords{TE_end}\t.\t$GFF_strand\t.\tID=$name.$start.$end;Name=$name;Note=$header\n";
}
}
}
}
}
else {
warn "error retrieving $ref:$start..$end\n";
}
}
}
}
}
### SOUBROUTINE ####
sub print_special_ping {
my ($start,$end,$seq,$name) = @_;
my $ref = 'Chr1';
my $before_ping = 'TACTCCCTCCAGTTCCTAATTTATTGGCGTTTTAGACATGATTACACATACCAACGAGTGATTAATTAGTGTGCCTACTTCCTGTTTTACCCCTAATAAATACGGTTTTGAGGTATACCAAATCATAACCTGCTCTTGGTTTGAGTGGCCATCCCATGCAAAAGTGAAGCTACCAGTTCTGAGTTTGATTTTTGGTGGCCACATTTTTTTGCATGGCACTGTGGACGCGTGACTGTTGGCATGCATGCACTTTTTTCAGGCGTTCACGCGCGCAGTCACCGGGAAAGATTTTTCACTCGCGCGCTGCTAA';
my $len_beforePing = length $before_ping;
my $after_ping = 'TAACAAAAATTTTGCCAGGTGCGTTTGCCGCCAATAACTCAAATTTTGGCGCTGGTTTGCAGCAGAATCCCCTTTGCCATCTCCATCTATTTATGCTGTGCAATACTAGCTAGTTTGACGCTCCAACTCCCTACATACTCCATCTGTTTAACATGAACTTAAACATGGAGCCATTACCTGCTCCATGGCGAAAATGGCGAAAGTAGTACAAGGAGACGAGTAGAAGGCAAAGAGCCAACAAGCAGGCATAGAAGAAGAAAATTACTCAGCGCGTGGGAGAGCAATGGTTGAACAGGAAACGAGAAGGCAAAGCATGCATGACGTTGGAAATAATGGGAGTAGTAATGGCCGGCTGCATGCATGCAGGGGCAAGCAGGTCCAAGATGCACCAAAAAAGCTAAAACGTCAAAAAATATCACACAATGCTTCAAGAGCTAAAACGTCAACTAATTTCAAACTGGAGGGAGTA';
my $stowaway_with_ping = 'TACTCCCTCCAGTTCCTAATTTATTGGCGTTTTAGACATGATTACACATACCAACGAGTGATTAATTAGTGTGCCTACTTCCTGTTTTACCCCTAATAAATACGGTTTTGAGGTATACCAAATCATAACCTGCTCTTGGTTTGAGTGGCCATCCCATGCAAAAGTGAAGCTACCAGTTCTGAGTTTGATTTTTGGTGGCCACATTTTTTTGCATGGCACTGTGGACGCGTGACTGTTGGCATGCATGCACTTTTTTCAGGCGTTCACGCGCGCAGTCACCGGGAAAGATTTTTCACTCGCGCGCTGCTAAGGCCAGTCACAATGGAGGTTTCACTGGTGTGTCATGCACATTTAATAGGGGTAAGACTGAATAAAAAATGATTATTTGCATGAAATGGGGATGAGAGAGAAGGAAAGAGTTTCATCCTGGTGAAACTCGTCAGCGTCGTTTCCAAGTCCTCGGTAACAGAGTGAAACCCCCGTTGAGGCCGATTCGTTTCATTCACCGGATCTCTTGCGTCCGCCTCCGCCGTGCGACCTCCGCATTCTCCCGCGCCGCGCCGCGCCACGCCTCCTTCCCGCGTGAACATTCCTCCTTCCCGCGCGAGCGATTCCACCATCTCCCCCGTCCGGCGCCTACGGAGTACACCGCAACCGGTCGCCCCAATCCGGCGCCTAGACCGTGACCCACCCGCCATCTTCCGCAAGACCGAATCCCCAACCCACCCACCATCTTCCGCCGCCCCCGTCCCCGTCCCCGGCCATGGATCCGTCGCCGGCCGTGGATCCGTCGCCGGCCGTGGATCCGTCGCCGGCTGCTGAAACCCGGCGGCGTGCAACCGGGAAAGGAGGCAAACAGCGCGGGGGCAAGCAACTAGGATTGAAGAGGCCGCCGCCGATTTCTGTCCCGGCCACCCCGCCTCCTGCTGCGACGTCTTCATCCCCTGCTGCGCCGACGGCCATCCCACCACGACCACCGCAATCTTCGCCGATTTTCGTCCCCGATTCGCCGAATCCGTCACCGGCTGCGCCGACCTCCTCTCTTGCTTCGGGGACATCGACGGCAAGGCCACCGCAACCACAAGGAGGAGGATGGGGACCAACATCGACCATTTCCCCAAACTTTGCATCTTTCTTTGGAAACCAACAAGACCCAAATTCATGGTACATGTATTTTCTTCTTTTTCTGTTACTTTCAACCTACGGTAACTCTAATTCATGGATGAGACTACTGCCATTGTGCAGTTCAATGCTTTTTCTTCATGTTATATTTCGTCCAGCTGTGAGTTATGGTTTGAAGATTGCTGTGGTTGTTTCATTGCTGAGTATGTGAAAGATAGATGGATGAAAGAGAGAATTATATTTTAGTCTGTAATCTTGCTCATCCAGTTGCTCATGTATGACCTTGGTTCTAGAATGTTGCCCTGACTGTATGCTTAATGTTCAGAGAAGTGATGCCTAAAGCAGTGAGATCAGTGGGATCAGATTAGCTATCGACATATAATATTAGCTATCTCAGTTGTGAAAGAGAGATGGGTGAAAAGGCACCCCTTGGATTAATTCTGTAGTATCAAATTCTGCACCTTGTCTGTCCATATGTTCTGCTTGGTTGGTGGGTGCAGTGCATTTGTAAAAAATAGTTTGCTTCTGATCCTTAATATATGTAACAGGGAATGAATTTTCACCCATCTCAGTTGTAAAGGTACTGTCTTGCTATGCAATATGTGTAAATTGACAAACCTGAAAATAGTCTGTTTGGAATTTGCAAAAGCAATTCGATAGTTTGGAATTTCCAAACCTCAGTCAGCAGTAGGCAATCCATTTTAGTTCTTGCTATGCACAAAAACAGTACACCTGATATGCTCATTTTAATACAACTTTTTTGTCTCTGTTACAGTTTGGTCAGGGGTTATCCTCCAGGAGGGTTTGTCAATTTTATTCAACAAAATTGTCCGCCGCAGCCACAACAGCAAGGTGAAAATTTTCATTTCGTTGGTCACAATATGGGATTCAACCCAATATCTCCACAGCCACCAAGTGCCTACGGAACACCAACACCCCAAGCTACGAACCAAGGCACTTCAACAAACATTATGATTGATGAAGAGGACAACAATGATGACAGTAGGGCAGCAAAGAAAAGATGGACTCATGAAGAGGAAGAGAGACTGGTATTCATCGGATACTTTTACATTTCCATATGTCTTTGTTTTGACTAATACTTGACAGGTCATTAACTGATTCTTGTAGGCCAGTGCTTGGTTGAATGCTTCTAAAGACTCAATTCATGGGAATGATAAGAAAGGTGATACATTTTGGAAGGAAGTCACTGATGAATTTAACAAGAAAGGGAATGGAAAACGTAGGAGGGAAATTAACCAACTGAAGGTTCACTGGTCAAGGTTGAAGTCAGCGATCTCTGAGTTCAATGACTATTGGAGTACGGTTACTCAAATGCATACAAGCGGATACTCCGACGACATGCTTGAGAAAGAGGCACAGAGGCTGTATGCAAACAGGTTTGGAAAACCTTTTGCGTTGGTCCATTGGTGGAAGATACTCAAAGATGAGCCCAAATGGTGTGCTCAGTTTGAATCAGAGAAAGACAAGAGCGAAATGGATGCTGTTCCAGAACAGCAGTCACGTCCTATTGGTAGAGAAGCAGCAAAGTCTGAGCGCAATGGAAAGCGCAAGAAAGAAAATGTTATGGAAGGCATTGTCCTCCTAGGGGACAATGTCCAGAAAATTATAAAGGTCCACGAAGACCGGAGGGTGGATCGTGAAAAGGCCACCGAAGCACAGATTCAGATATCAAATGCAACATTGTTGGCCGCTAAGGAGCAGAAGGAAGCAAAGATGTTCGATGTGTACAATACTCTATTAAGTAAGGATACAAGCAACATGTCTGAAGATCAAATGGCTAGCCACCAGAGGGCAATACGGAAATTAGAGGAGAAGCTATTTGCGGATTAAGGTGAGTTTTATAAACTGACCACTATTTTCTGAAATGTATGAATTCTGAAATTTATATACAATTGTGTAAACATGGAAAATTAGATAATGTATGCATGATGCACAACATGTGCGTGCAGCACTATTTAATGGCAGTTTCACAAGTGTGAAAACTGACCACTATAGTACTATTGTGGTGTGAAAACTGACCACTACTATTGTGGTGTGAATGCTACTGTGGTGTGAAAACTGACCACTATAGTTTCACATTCCTGGATGCAGCCCTCCTCTATATATATAGATACAGTCCTCATCTCTTCCTGGCATACACACAGCCCTCTTCTCTAATTCCTGGACGCAGTCCTCATCTCTTCCTGGCATAGACGCAGCCCTTCTCTCTTCCTGTTTAGTTCAACAACATTGAGGTGATCTGCCTTTCTTTGAAGTTTCTATCTTTTTTCACTGCTGTGAATGATTATTTCTCTGCTGTGAATGATTATTTCTCCAATCTTCCTTTGTTCACCTTCTCTCTTTCTCTGCTGTGAAGATGTCTGGAAATGAAAATCAGATTCCTGTGTCCTTGTTGGACGAGTTTCTCGCTGAGGATGAGATCATGGATGAGATAATGGATGATGTTCTCCATGAAATGATGGTGTTATTGCAGTCCTCCATCGGAGATCTTGAAAGAGAGGCTGCTGACCATCGTTTGCATCCAAGGAAGCACATCAAGAGGCCACGAGAGGAAGCACATCAAAATTTGGTGAATGATTATTTCTCTGAAAATCCTCTATATCCTTCCAATATTTTTCGCCGAAGATTTCGTATGTACAGGCCGCTGTTTTTACGTATTGTGGACGCATTAGGCCAGTGGTCAGATTACTTTACTCAGAGGGTAGATGCCGCTGGTAGGCAAGGGCTTAGTCCATTACAAAAGTGTACTGCAGCAATTCGCCAATTGGCTACTGGTAGTGGTGCTGATGAACTAGATGAGTATTTGAAGATTGGAGAGACTACTGCTATGGATGCTATGAAAAATTTTGTGAAAGGAATTAGAGAAGTATTTGGTGAAAGATATCTCAGGCGTCCCACTGTAGAAGATACTGAACGACTACTCGAGCTTGGTGAGAGACGCGGTTTTCCTGGTATGTTCGGTAGCATTGACTGTATGCATTGGCAATGGGAAAGGTGCCCAACTGCGTGGAAGGGTCAGTTCACTCGTGGTGATCAAAAAGTGCCAACGCTGATTCTTGAGGCAGTGGCATCACATGATCTTTGGATTTGGCATGCGTTCTTTGGAGTAGCAGGTTCTAACAATGATATCAATGTTTTGAGCCGATCTACTGTGTTTATCAATGAGCTGAAAGGACAAGCTCCTAGAGTGCAGTACATGGTAAATGGGAATCAATACAACGAAGGTTATTTTCTTGCTGATGGAATTTACCCTGAATGGAAGGTATTTGCTAAGTCATATCGACTCCCTATCACTGAGAAGGAGAAGTTGTATGCACAACATCAAGAAGGGGCAAGAAAGGATATCGAGAGAGCATTTGGTGTTCTACAACGTCGATTCTGCATCTTAAAACGACCAGCCCGTCTATATGACCGAGGTGTACTCCGTGATGTTGTCCTAGGTTGCATCATACTTCACAATATGATAGTTGAAGATGAGAAGGAAGCGCGACTTATTGAAGAAAATCTAGATTTAAATGAGCCTGCTAGTTCATCAACGGTTCAGGCACCAGAATTCTCTCCTGACCAGCATGTTCCATTAGAAAGAATTTTAGAAAAGGATACTAGTATGAGAGATCGTTTGGCTCATCGCCGACTCAAGAATGATTTGGTGGAACATATATGGAATAAGTTTGGTGGTGGTGCACATTCATCTGGTAATTATGTTTTTATTTTGCATTATTAGTTATCTATGGTACTAAGATATGTACAAGTTTCTCTAAATTGCACTAAATCTGTGGTTCATATTGGATATGTGTAAACTATGAATGTAGCCTGACTAAAACCATCATTCATGCTGAACTGGTTTTTGTTTTGTATATGCAGGATGAAACAAGGAACTAGGTTTCTGAACGCATTACGGACTGAAGGTTGAGGGGCAGAATGATCCACCCAGTTGCTTCTATCAGATCACTAAAGTTTCATTTCACTGTTTTATTTTGGACACTTGATGCTTGTGTGCATCCGATGAATGTTTAATTTGGTCACCTGATGCTTGTGTGCATCCGATGAATGTTTAATTTGGTCACCTGATGCTTGTATGCAGTTATCTATCTTATTTGTTAATGTTGCTGGTACTGAGGATTTTTAGAAGTGAAATGCACAAGTTGCTGTGTTTTTTGACTGATCCTTGTGTGCACTTGACGTTGTATGTGACAAATGATGGTTCCCAGTTGTGCACCTGATTCATGATTCAGTTATTCAGTTTAAATTGACGTTGTTTGTGTGCACCTTTTGTCAGTTAGCCAGTTACGGCTGGAAGTTGTGTAAGTTTGTGTGACGCCTGGCTACAGGATTTTGGGTACAAATGATCCCAGCAACTTGTATCAATTAAATGCTTTGCTTAGTCTTGGAAACGTCAAAGTGAAACCCCTCCACTGTGGGGATTGTTTCATAAAAGATTTCATTTGAGAGAAGATGGTATAATATTTTGGGTAGCCGTGCAATGACACTAGCCATTGTGACTGGCCTAACAAAAATTTTGCCAGGTGCGTTTGCCGCCAATAACTCAAATTTTGGCGCTGGTTTGCAGCAGAATCCCCTTTGCCATCTCCATCTATTTATGCTGTGCAATACTAGCTAGTTTGACGCTCCAACTCCCTACATACTCCATCTGTTTAACATGAACTTAAACATGGAGCCATTACCTGCTCCATGGCGAAAATGGCGAAAGTAGTACAAGGAGACGAGTAGAAGGCAAAGAGCCAACAAGCAGGCATAGAAGAAGAAAATTACTCAGCGCGTGGGAGAGCAATGGTTGAACAGGAAACGAGAAGGCAAAGCATGCATGACGTTGGAAATAATGGGAGTAGTAATGGCCGGCTGCATGCATGCAGGGGCAAGCAGGTCCAAGATGCACCAAAAAAGCTAAAACGTCAAAAAATATCACACAATGCTTCAAGAGCTAAAACGTCAACTAATTTCAAACTGGAGGGAGTA';my $len_afterPing = length $after_ping;
#my $pre_TE_len = $padding - $len_beforePing + 3;
#my $post_TE_len = $padding - $len_afterPing + 3;
my $pre_TE_len = $padding - $len_beforePing ;
my $post_TE_len = $padding - $len_afterPing ;
my $pre_TE = substr $seq, ($start - ($pre_TE_len)-1) ,$pre_TE_len;
my $post_TE = substr $seq, $end ,$post_TE_len;
my $special_ping_plus_flank = $pre_TE . $stowaway_with_ping . $post_TE;
my $total_len = length $special_ping_plus_flank;
my $stowaway_start = $pre_TE_len + 1;
my $stowaway_break_end = $padding;
my $ping_start = $padding + 1;
my $ping_end = $total_len - $padding;#length $pre_TE . $stowaway_with_ping;
my $stowaway_break_start = $ping_end + 1;
my $stowaway_end = $ping_end + $len_afterPing;
my $flank2_start = $ping_end +1;
my $info = "$ref:$start..$end FLANK1:1..$padding STOWAWAY_prePing:$stowaway_start..$stowaway_break_end TE:$ping_start..$ping_end STOWAWAY_postPing:$stowaway_break_start..$stowaway_end FLANK2:$flank2_start..$total_len";
print ">$name HEG4/EG4/A119/A123 $info\n$special_ping_plus_flank\n";
print GFF "$name\t.\tchromosome\t1\t$total_len\t.\t.\t.\tID=$name;Name=$name;Note=shared:HEG4/EG4/A119/A123 $info\n";
print GFF "$name\t.\ttransposable_element_insertion_site\t$ping_start\t$ping_end\t.\t.\t.\tID=$name.$start.$end;Name=$name;Note=ping HEG4/EG4/A119/A123 $info\n";
}
# my $header = "$TE_names $desc$ref:$start..$end $coords";
#"$name\t.\ttransposable_element_insertion_site\t$coords{TE_start}\t$coords{TE_end}\t.\t$GFF_strand\t.\tID=$name.$start.$end;Name=$name;Note=$header\n";