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abacas.pl
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abacas.pl
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#!/home/eklavya/miniconda3/bin/perl
# Copyright (C) 2008-10 Genome Research Limited. All Rights Reserved.
#
# This program is free software; you can redistribute it and/or
# modify it under the terms of the GNU General Public License
# as published by the Free Software Foundation; either version 2
# of the License, or (at your option) any later version.
#This program is distributed in the hope that it will be useful,
# but WITHOUT ANY WARRANTY; without even the implied warranty of
# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
# GNU General Public License for more details.
#
# You should have received a copy of the GNU General Public License
# along with this program; if not, write to the Free Software
# Foundation, Inc., 59 Temple Place - Suite 330, Boston, MA 02111-1307, USA.
#ABACAS.1.3.1
#--------------------------------
#Please report bugs to:
#sa4@sanger.ac.uk & tdo@sanger.ac.uk
use strict;
use warnings;
use POSIX qw(ceil floor);
use Getopt::Std;
our $version="1.3.1";
#-------------------------------------------------------------------------------
if (@ARGV < 1) { usage();}
my ($help, $reference, $query_file, $choice, $sen, $seed, $mlfas, $fasta_bin, $avoid_Ns,
$tbx, $min_id, $min_cov, $diff_cov, $min_len,$add_bin_2ps, $pick_primer,
$flank, $chk_uniq,$redoMummer, $is_circular,$escapeToPrimers, $debug, $gaps_2file, $prefix,$optionsLog)
=checkUserInput( @ARGV );
my $ref_inline;
if ($escapeToPrimers ==1)
{
pickPrimers ($reference, $query_file, $flank, $chk_uniq);
exit;
}
#BEGIN
#-------------------------------------------------------------------------------
print_header();
print $optionsLog;
$ref_inline = Ref_Inline($reference);
#Get length of the reference sequence
my $ref_len = length($ref_inline);
###################
# Running MUMmer #
###################
my ($path_dir, $run_mum, $path_toPass);
if ($debug)
{
print "the seed is $seed \n";
print "RedoMummer= ",$redoMummer."\n";
}
my @do_mum_return;
my $mummer_tiling;
if ($redoMummer==0)
{
print "PREPARING DATA FOR $choice \n";
@do_mum_return = doMummer($reference, $query_file, $choice,$sen,$seed,$min_id, $min_cov, $diff_cov,$min_len, $debug, $is_circular) or die "Couldn't run MUMmer\n";
$mummer_tiling = $do_mum_return[0];
$path_dir = $do_mum_return[2];
$path_toPass = $do_mum_return[1];
}
elsif ($redoMummer ==1)
{ print "not doing mummer\n";
my @check = checkProg ($choice);
$mummer_tiling = '$choice.tiling';
$path_dir = $check[2];
$path_toPass = $check[1];
}
else
{
print "Unknown option for -R\n";
exit;
}
####################################
# Processing tiling output #
####################################
if ($debug) {
print "Do tiling...\n";
}
#--------------------------------
##################
#Do Tiling
#-------------------------------------------
doTiling ($mummer_tiling, $path_toPass, $path_dir,$reference, $query_file, $choice, $prefix,$mlfas, $fasta_bin, $avoid_Ns, $ref_len, $gaps_2file, $ref_inline, $add_bin_2ps, $pick_primer, $flank, $chk_uniq, $tbx);
############################################## SUB ROUTINES for CONTIG ORDERING and PRIMER DESIGN ##########################################################
# Put in one file for ease of downloading. They could be placed in separate packages.
#----------------------------------------------------------------------------------------------------------
#################################Contig ordering ##########################################################
########
sub help
{
die <<EOF
***********************************************************************************
* ABACAS: Algorithm Based Automatic Contiguation of Assembled Sequences *
* *
* *
* Copyright (C) 2008-10 The Wellcome Trust Sanger Institute, Cambridge, UK. *
* All Rights Reserved. *
* *
***********************************************************************************
USAGE
abacas.pl -r <reference file: single fasta> -q <query sequence file: fasta> -p <nucmer/promer> [OPTIONS]
-r reference sequence in a single fasta file
-q contigs in multi-fasta format
-p MUMmer program to use: 'nucmer' or 'promer'
OR
abacas.pl -r <reference file: single fasta> -q <pseudomolecule/ordered sequence file: fasta> -e
OPTIONS
-h print usage
-d use default nucmer/promer parameters
-s int minimum length of exact matching word (nucmer default = 12, promer default = 4)
-m print ordered contigs to file in multifasta format
-b print contigs in bin to file
-N print a pseudomolecule without "N"s
-i int mimimum percent identity [default 40]
-v int mimimum contig coverage [default 40]
-V int minimum contig coverage difference [default 1]
-l int minimum contig length [default 1]
-t run tblastx on contigs that are not mapped
-g string (file name) print uncovered regions (gaps) on reference to file name
-a append contigs in bin to the pseudomolecule
-o prefix output files will have this prefix
-P pick primer sets to close gaps
-f int number of flanking bases on either side of a gap for primer design (default 350)
-R int Run mummer [default 1, use -R 0 to avoid running mummer]
-e Escape contig ordering i.e. go to primer design
-c Reference sequence is circular
EOF
}
########
sub usage
{
die <<EOF
---------------------------------------------------------------------------------------------------
ABACAS.$version
visit www.abacas.sourceforge.net for more information.
--------------------------------
Please report bugs to:sa4 (at)sanger.ac.uk and tdo (at) sanger.ac.uk
----------------------------------------------------------------------------------------------------
USAGE
abacas.pl -r <reference file: single fasta> -q <query sequence file: fasta> -p <nucmer/promer> [OPTIONS]
-r reference sequence in a single fasta file
-q contigs in multi-fasta format
-p MUMmer program to use: 'nucmer' or 'promer'
for contig ordering and primer design
OR
abacas.pl -r <reference file: single fasta> -q <pseudomolecule/ordered sequence file: fasta> -e
to escape contig ordering and go directly to primer design
OR
abacas.pl -h for help
EOF
}
########
##################
sub print_header
{
print "
***********************************************************************************
* ABACAS: Algorithm Based Automatic Contiguation of Assembled Sequences *
* *
* *
* Copyright (C) 2008-10 The Wellcome Trust Sanger Institute, Cambridge, UK. *
* All Rights Reserved. *
* *
***********************************************************************************
\n";
}
#########################################
sub checkUserInput{
my %options;
getopts('hr:q:p:ds:mbNi:v:V:l:tg:ao:Pf:Ru:ecD', \%options);
my $optionsLog="# Checking user options:";
my ($help, $reference, $query_file, $choice, $sen, $seed, $mlfas, $fasta_bin, $avoid_Ns,
$tbx, $min_id, $min_cov, $diff_cov, $min_len,$add_bin_2ps, $pick_primer,
$flank, $chk_uniq,$redoMummer, $is_circular,$escapeToPrimers, $debug, $gaps_2file, $prefix);
if($options{h}) {
$help = $options{h};
help();
}
if ($options{r} && $options{q} ){
($reference, $query_file) = ($options{r},$options{q});
$optionsLog.="\n#\t-r Reference=$reference\n#\t-q Query=$query_file\n";
}else{
usage() unless $options{e};
}
if ($options{p}){
$choice = $options{p};
$optionsLog.="#\t-p $choice\n";
unless ($choice eq "nucmer" || $choice eq "promer"){
print "Unknown MuMmer function\n Please use nucmer or promer\n";
exit;
}
}else{
usage() unless $options{e};
}
if ($options{e}){ #$escapeToPrimers)
print_header();
print "Primer design selected,... escaping contig ordering\n";
$escapeToPrimers = 1;
$chk_uniq = "nucmer";
$choice = "";
$optionsLog.="#\t-e Primer design selected,... escaping contig ordering\n";
}else{
$escapeToPrimers = 0;
}
if ($options{d}) {
$sen =1;
$optionsLog.="#\t-d use default setting i.e. --mumreference in $choice\n";
} else {
$sen =0;
$optionsLog.="#\t-d 0 use sensitive mapping in $choice i.e. --maxmatch\n";
} #print $sen , " ---sen\n";
#print $options{t}, "\n"; exit;
if($options{t}) {$tbx = 1;} else {$tbx = 0;} #print $tbx, " ---tbx\n"; #
if ($options{s}){
$seed = $options{s};
$optionsLog.="#\t-s seed=$seed\n";
}
else{
if ($choice eq "nucmer"){
$seed = 12;
}
else{
$seed =4;
}
}
if ($options{m}){
$mlfas =1;
$optionsLog.="#\t-m print multifasta file of ordered contigs\n"
} else { $mlfas =0; } #print $mlfas , " ---mlfasta\n";
if ($options{b}) {
$fasta_bin =1;
$optionsLog.="#\t-b print multifasta file of contigs in bin to file\n"
} else {$fasta_bin =0;}
if ($options {N}){
$avoid_Ns =1;
$optionsLog.="#\t-N don't print Ns in pseudo-molecule\n"
} else {$avoid_Ns=0;}
if($options{i}){
$min_id=$options{i};
$optionsLog.="#\t-i $min_id is the minimum identity cutoff\n";
}
else{$min_id =40;
# $optionsLog.="#\t-i not defined: $min_id is the default minimum identity cutoff\n";
}
if ($options{v}){
$min_cov = $options{v};
$optionsLog.="#\t-v $min_cov is the minimum contig-coverage cutoff\n";
}
else{
$min_cov =40;
#$optionsLog.="#\t-v not defined $min_id is the default contig-coverage cutoff\n";
}
if($options{V}){
$diff_cov = $options{V};
$optionsLog.="#\t-V $diff_cov\n";
}
else {$diff_cov =1;
# $optionsLog.="#\t-V $diff_cov using the default value\n";
}
if ($options {l}){
$min_len = $options {l};
$optionsLog.="#\t-l $min_len is the minimum length of contigs to be ordered\n";
}
else{$min_len = 1;
# $optionsLog.="#\t-l not defined: using 1 as the default minimum length of contigs to be ordered\n";
}
if ($options{a}) {$add_bin_2ps = 1; }else {$add_bin_2ps =0;}
if ($options{P}) {$pick_primer=1;} else {$pick_primer =0;}
if ($options{f}) {$flank = $options{f};} else {$flank = 1000;}
if ($options{u}) {$chk_uniq = $options{u}; } else {$chk_uniq = "nucmer";}
#unless ($options{R}) {$re}
if($options{R}) {$redoMummer = 1; } else {$redoMummer = 0;}
if($options{c}) {$is_circular = 1;}else {$is_circular =0;}
if ($options{g}) {$gaps_2file = $options{g};} else {$gaps_2file ="";}
if($options{o}) {$prefix = $options{o};} else {$prefix = "";}
if($options{D}){
$debug=1;
$optionsLog.="#\t-D debug\n";
}
else {$debug =0};
if ($tbx ==1 && $fasta_bin !=1)
{
print "ERROR: Please use -t -b if you want to run tblastx on contigs in bin\n";
exit;
}
# print $redoMummer , "\n"; exit;
$optionsLog.="#\tInput checking done!!\n";
#print $optionsLog;
return ($help, $reference, $query_file, $choice, $sen, $seed, $mlfas, $fasta_bin, $avoid_Ns,
$tbx, $min_id, $min_cov, $diff_cov, $min_len,$add_bin_2ps, $pick_primer,
$flank, $chk_uniq,$redoMummer, $is_circular,$escapeToPrimers, $debug, $gaps_2file, $prefix,$optionsLog);
} ## end of checkUserInput
#############
## get the reference sequence in one line
#--------------------------------------------------
sub Ref_Inline
{
my $ref = shift;
open (refFH, $ref) or die "Could not open file $ref\n";
my $seq ="";
my @r = <refFH>;
my $num_chr =0;
foreach(@r){
if ($_ =~ /\>/){
$num_chr +=1;
}
}
if ($num_chr > 1){
print "\nERROR: Please use a single fasta reference file. You can simply merge chromosomes in to a union fasta file.\n\n";
exit;
}
shift @r;
foreach(@r){
chomp;
$seq = $seq.$_;
}
return $seq;
}
################
# Run mummer
#--------------------------------------------
sub doMummer
{
my ($reference, $query_file, $choice, $sen,$seed,$min_id, $min_cov, $diff_cov,$min_len, $debug, $is_circular ) = @_;
my $df = 'delta-filter';
my $st = 'show-tiling';
my $ask = 'which';
my ($path_toPass, $run_mum); # params to return...
my ($command, $Path, $dir) = checkProg($choice);
my ($run_df, $df_path, $df_dir) = checkProg($df);
my ($run_st, $st_path, $st_dir) = checkProg($st);
my (@running, @deltaRes, @coordsRes);
if ($choice eq "nucmer")
{
if ($sen ==0)
{
@running = `$command --maxmatch -l $seed -p $choice $reference $query_file &> /dev/null`;
@deltaRes = `$run_df -q $choice.delta >$choice.filtered.delta`;
if ($is_circular == 1)
{
@coordsRes = `$run_st -c -i $min_id -v $min_cov -V $diff_cov -l $min_len -R -u unused_contigs.out $choice.filtered.delta > $choice.tiling`;
}
else
{
@coordsRes = `$run_st -i $min_id -v $min_cov -V $diff_cov -l $min_len -R -u unused_contigs.out $choice.filtered.delta > $choice.tiling`;
}
}
else
{
@running = `$command -p $choice $reference $query_file &> /dev/null`;
@deltaRes = `$run_df -q $choice.delta >$choice.filtered.delta`;
if ($is_circular ==1) {@coordsRes = `$run_st -c -i $min_id -v $min_cov -V $diff_cov -l $min_len -R -u unused_contigs.out $choice.filtered.delta > $choice.tiling`;}
else { @coordsRes = `$run_st -i $min_id -v $min_cov -V $diff_cov -l $min_len -R -u unused_contigs.out $choice.filtered.delta > $choice.tiling`;}
}
}
else
{
if ($sen ==0)
{
@running = `$command --maxmatch -l $seed -x 1 -p $choice $reference $query_file &> /dev/null`;
@deltaRes = `$run_df -q $choice.delta >$choice.filtered.delta`;
if ($is_circular == 1)
{
@coordsRes= `$run_st -c -i $min_id -v $min_cov -V $diff_cov -l $min_len -R -u unused_contigs.out $choice.filtered.delta > $choice.tiling`;
}
else
{
@coordsRes= `$run_st -i $min_id -v $min_cov -V $diff_cov -l $min_len -R -u unused_contigs.out $choice.filtered.delta > $choice.tiling`;
}
}
else
{
@running = `$command -l $seed -p $choice $reference $query_file &> /dev/null`;
@deltaRes = `$run_df -q $choice.delta >$choice.filtered.delta`;
if ($is_circular == 1) {
@coordsRes= `$run_st -c -i $min_id -v $min_cov -V $diff_cov -l $min_len -R -u unused_contigs.out $choice.filtered.delta > $choice.tiling`;
}
else
{
@coordsRes= `$run_st -i $min_id -v $min_cov -V $diff_cov -l $min_len -R -u unused_contigs.out $choice.filtered.delta > $choice.tiling`;
}
}
}
my $Coordsfull= "$choice.tiling";
return ($Coordsfull,$Path, $dir);
}
## #############################################################################
sub checkProg{ #checks if a given excutable is in the path...
my $prog = shift;
my $ask = 'which';
my @check_prog = `$ask $prog`;
my $path_toPass;
my $path_dir;
my $command;
if (defined $check_prog[0] && $check_prog[0] =~ /$prog$/)
{
$path_toPass = $prog;
$command = $prog;
}
else
{
print "\nENTER the directory for your ", $prog, " executables [default ./]: ";
my $path=<STDIN>;
chomp $path;
$path_dir = $path;
if ($path_dir =~/\/$/)
{
$path_dir = $path_dir;
}
else
{
$path_dir = $path_dir."/";
}
my @final_check = `$ask $command`;
if (exists $final_check[0] && $final_check[0] =~ /$prog$/)
{
$command = $path_dir.$prog;
$path_toPass = $command;
}
else
{
print "ERROR: Could not run ", $prog, ", please check if it is installed in your path\n or provide the directory \n";
exit;
}
}
return ($command, $path_toPass, $path_dir);
}
##############################
# converts a fasta file to an ordered single line
#--------------------------------------------------
sub Fasta2ordered
{
if( @_ != 1 )
{
print "Usage: Fasta2ordered <fasta_file>\n";
exit;
}
my $fast = shift; #print $fast; exit;
my @fasta = split (/\n/, $fast);
if ($fasta[0] =~ /\>/ ) #remove chromosome name if exists in the onput sequence.
{
my $ch_name = $fasta[0];
shift @fasta;
}
#print $fasta[0]; exit;
foreach(@fasta){chomp;}
my $num_lines = scalar(@fasta);
my $dna = '';
for(my $i=0; $i< $num_lines; $i+=1)
{
$dna = $dna.$fasta[$i];
}
my $ordered_dna = $dna;
return $ordered_dna;
}
##############################################################
# Hash input contigs
#------------------------------------------------
sub hash_contigs {
if( @_ != 1 )
{
print "Usage: hash_contigs contigs_file";
exit;
}
my $contigs_file = shift;
if( $contigs_file =~ /\.gz$/ )
{
open(CONTIGS, $contigs_file, "gunzip -c $contigs_file |" ) or die "Cant open contigs file: $!\n";
}
else
{
open( CONTIGS, $contigs_file) or die "Cant open contigs file: $!\n";
}
my %contigs_hash; # hash to store contig names and sequences
my $contigName;
while (<CONTIGS>) ##add error checking...
{
if (/^>(\S+)/) {
$contigName=$1;
}
else {
chomp;
$contigs_hash{$contigName} .= $_;
}
}
close(CONTIGS);
#tdo
## check if qual exists
my %contigs_qual_hash;
if (-r "$contigs_file.qual" or -r "$contigs_file.qual.gz") {
if( -r "$contigs_file.qual.gz" )
{
open(CONTIGS, "$contigs_file.qual.gz", "gunzip -c $contigs_file.qual.gz |" ) or die "Cant open contigs file: $!\n";
}
else
{
open( CONTIGS, "$contigs_file.qual" ) or die "Cant open contigs file: $!\n";
}
while (<CONTIGS>) {
if (/^>(\S+)/) {
$contigName=$1;
}
else {
chomp;
$contigs_qual_hash{$contigName} .= $_;
}
}
} # end tdo # end if exist
return (\%contigs_hash,\%contigs_qual_hash);
}
#######################
##############################
### it gets a delta name
sub getMummerComparison{
my $deltaName = shift;
### transform the delta file to coords
my $call ="show-coords -H -T -q $deltaName > $deltaName.coords ";
!system(" $call") or die "Problems doing the show-coords comparison: $call $!\n";
### willh old results
my %h;
### has as index the postion with the max hits
my %h_max;
my $tmp=0;
my $tmp_index;
my $key='';
my $is_promer =0;
if ($deltaName =~/^promer/)
{
$is_promer =1;
}
open (F,"$deltaName.coords") or die "Problem in getComparisonFile to open file $deltaName.coords\n";
my @File=<F>;
my @a;
@a=split(/\s+/,$File[0]);
$tmp=$a[5];
$tmp_index=$a[0];
if ($is_promer ==1)
{
$key=$a[12]; ## nucmer: $key = $a[8]
}
else
{
$key = $a[8];
}
foreach (@File) {
@a=split(/\s+/);
if ($is_promer ==1)
{
push @{ $h{$a[12]}}, "$a[12]\t$a[11]\t$a[7]\t$a[5]\t0\t0\t$a[2]\t$a[3]\t$a[0]\t$a[1]\t1\t$a[5]\n";
if ($key eq $a[12] and $a[5]>$tmp)
{
$tmp=$a[5]; # length
$tmp_index=$a[0]; # position reference
}
elsif ($key ne $a[12]) {
### here possible bugg...
$h_max{$tmp_index}=$key;
$key=$a[12];
$tmp=$a[5]; # length
$tmp_index=$a[0]; # position reference
}
} #end if
#else i.e. if nucmer
else
{
push @{ $h{$a[8]}}, "$a[8]\t$a[6]\t$a[6]\t$a[5]\t0\t0\t$a[2]\t$a[3]\t$a[0]\t$a[1]\t1\t$a[5]\n";
if ($key eq $a[8] and $a[5]>$tmp)
{
$tmp=$a[5]; # length
$tmp_index=$a[0]; # position reference
}
elsif ($key ne $a[8]) {
### here possible bugg...
$h_max{$tmp_index}=$key;
$key=$a[8];
$tmp=$a[5]; # length
$tmp_index=$a[0]; # position reference
}
}
}
$h_max{$tmp_index}=$key;
# print Dumper %h_max;
return (\%h,\%h_max);
}
##################################
###########################
sub writeBinContigs2Ref{
my $nameBin = shift;
my $name = shift;
open (F, "$nameBin") or die "Couldn't find file $nameBin: $!\n";
my @ar;
my $count=0;
while (<F>) {
push @ar, $_;
$count++;
}
#### sa4: added error checking:- if file is empty
if (scalar(@ar) < 1)
{
print "No contigs in unusedcontigs file\n";
$count = 0;
}
else
{
open (F, "> $name.notMapped.contigs.tab") or die "Couldn't write file $name.tab: $!\n";
print F doArt(\@ar);
close(F);
}
return $count;
}
##############################
sub doArt{
my ($ref) = @_;
## hash of array with all positions of the contig
my %Pos;
## Hash with note of result line of nucmer
my %lines;
foreach (@$ref) {
chomp;
my @ar=split(/\t/);
push @{ $Pos{$ar[12]}}, "$ar[0]..$ar[1]";
$lines{$ar[12]} .= "FT $_\n";
}
my $res;
foreach my $contig (keys %lines) {
if (scalar(@{ $Pos{$contig} } >1)) {
my $tmp;
foreach (@{ $Pos{$contig} }) {
$tmp.="$_,";
}
$tmp =~ s/,$//g; # get away last comma
$res .= "FT contig join($tmp)\n";
}
else {
$res .= "FT contig $Pos{$contig}[0]\n";
}
$res .= "FT /systematic_id=\"$contig\"\n";
$res .= "FT /note=\"Contig $contig couldn't map perfectly.\n";
$res .= $lines{$contig};
$res .= "FT \"\n";
}
return $res;
}
##########################################################################
#---------------------------
sub makeN #creates a string of Ns
{
my $n = shift;
my $Ns= "N";
for (my $i =1; $i < $n; $i+=1)
{
$Ns = $Ns."N";
}
return $Ns;
}
###########################################################################
## reverse complement a sequence
#---------------------------------------------
sub revComp {
my $dna = shift;
my $revcomp = reverse($dna);
$revcomp =~ tr/ACGTacgt/TGCAtgca/;
return $revcomp;
}
################################################################################
### function to visualize rep. regions in Reference genome.
sub findRepeats
{
my $reference = shift;
my $name = shift;
my $path_prog = shift;
# get path
my ($path_coords) = $path_prog;
$path_coords =~ s/nucmer/show-coords/;
my $call = "$path_prog --maxmatch -c 100 -b 40 -p $name.repeats -l 25 $reference $reference &> /dev/null ";
!system("$call") or die "Problems doing the nucmer comparison: $call $!\n";
$call ="$path_coords -r -c -l $name.repeats.delta > $name.repeats.coords ";
!system(" $call") or die "Problems doing the show-coords comparison: $call $!\n";
my @Res;
open (F, "$name.repeats.coords" ) or die "Problems to open file $reference.repeats.coords: Is MUMmer installed correctly and inserted in the PATH environment variable? ($!)\n";
$_=<F>; $_=<F>; $_=<F>; $_=<F>;$_=<F>;
while (<F>) {
my @ar = split(/\s+/);
if (!($ar[1] == $ar[4] or $ar[2] == $ar[5] or $ar[7] > 100000)) { # to exclude self alignment
foreach ($ar[1]..$ar[2]) {
$Res[($_-1)]++;
}
}
}
### write the result to the plot file
my $res;
foreach (@Res){
if (defined($_)) {
$res .= "$_\n";
}
else {
$res .= "0\n";
}
}
open (F, "> $name.Repeats.plot") or die "Couldn't open file $name.plot to write: $! \n";
print F $res;
close(F);
### delete files
unlink("$name.repeats.delta");
unlink("$name.repeats.coords");
unlink("$name.repeats.cluster");
}
################################################################################
# reverse a list of qualities
#------------------------------
sub reverseQual{
my $str = shift;
$str =~ s/\s+$//g;
my @ar = split(/\s/,$str);
my $res;
for (my $i=(scalar(@ar)-1);$i>=0;$i--) {
$res.="$ar[$i] ";
}
return $res;
}
##############################################################################
# ----------------
sub getPosCoords{
my $ref_ar = shift;
my $contig = shift;
my $offset = shift;
my $res;
# print Dumper $$ref_ar{$contig};
foreach (@{$$ref_ar{$contig}}) {
print "in getPos Coords: $_\n";;
my @ar=split(/\t/);
$ar[6]+=$offset;
$ar[7]+=$offset;
$res .= join("\t",@ar);;
}
return $res;
}
#############################################################################
# -----------------------------
sub getPosCoordsTurn{
my $ref_ar = shift;
my $contig = shift;
my $offset = shift;
my $res;
# print Dumper $$ref_ar{$contig};
foreach (@{$$ref_ar{$contig}}) {
my @ar=split(/\t/);
my $tmp_8=$ar[8];
my $tmp_9=$ar[9];
$ar[8]=$ar[6]+$offset;
$ar[9]=$ar[7]+$offset;
$ar[6]=$tmp_8;
$ar[7]=$tmp_9;
## change query subject
$res .= join("\t",@ar);;
}
return $res;
}
############################################################################
#------------------------
sub printStats{
my ($num_fortillingcontigs,$num_notsetTilling,$num_mapped, $num_contigs, $num_inComparisoncontigs, $ref_len, $total_bases_mpd) = @_;
$num_fortillingcontigs=$num_notsetTilling+$num_mapped;
my $res;
$res.= "Short statistics of run.\n";
$res.= "$num_contigs\t\tcontigs entered to be mapped against the reference.\n";
$res.= sprintf("$num_inComparisoncontigs\t%0.2f \%\tmade a hit against the reference to the given parameter (-s -d etc)\n",($num_inComparisoncontigs*100/$num_contigs));
$res.= sprintf("$num_fortillingcontigs\t%0.2f \%\twere considered for the tilling graph (-s -d etc)\n",($num_fortillingcontigs*100/$num_contigs));
$res.= sprintf("$num_mapped\t%0.2f \%\tare mapped in the tilling graph (-s -d etc)\n",($num_mapped*100/$num_contigs));
$res.= sprintf("\nCoverage: The reference is $ref_len long. Up to $total_bases_mpd bp (%0.2f \%) are covered by the contigs (This doesn't mean that these regions are really similar...)\n",($total_bases_mpd*100/$ref_len));
print $res;
}
##################################################
#### Do Tiling
#----------------------------------------------------
sub doTiling {
my ($mummer_tiling, $path_toPass, $path_dir,$reference, $query_file, $choice, $prefix,$mlfas, $fasta_bin, $avoid_Ns, $ref_len, $gaps_2file, $ref_inline, $add_bin_2ps, $pick_primer, $flank, $chk_uniq, $run_blast) = @_;
### these are also defined in the main script.... to be changed!!
my ($num_contigs , $num_inbincontigs, $avg_cont_size,$num_overlaps , $num_gaps,
$num_mapped,$total_bases_mpd,$p_ref_covered,$num_ambigus,$num_inComparisoncontigs,
$num_fortillingcontigs,$num_notsetTilling)= (0,0,0,0,0,0,0,0,0,0,0,0);
my ($href, $ref_contigs_qual) = hash_contigs($query_file);
my $qualAvailable=0;
my %contigs_hash = %{$href};
my @c_keys = keys %contigs_hash;
$num_contigs = scalar(@c_keys);
my @cont_lens;
my (@ids ,$id, $id_len);
my (@Rs, @Re, @G, @Len, @cov, @pid, @orient, @Cid);
my (@Ps, @Pe);
my ($total);
my $g; #define gap size between contigs
my $tiling_gap; #gap size from tiling graph
open (TIL, $mummer_tiling) or die "Could not open $mummer_tiling: $!";
while (<TIL>)
{
chomp;
if ($_ =~/^>/)
{
my $line = substr $_, 1;
my @splits = split /\s+/, $line;
$id = $splits[0];
push @ids, $id;
$id_len= $splits[1];
}
else
{
my @splits = split /\s+/, $_;
push @Rs, $splits[0];
push @Re, $splits[1];
push @G, $splits[2];
push @Len, $splits[3];
push @cov, $splits[4];
push @pid, $splits[5];
push @orient, $splits[6];
push @Cid, $splits[7];
}
}
close (TIL);
if (scalar(@Rs) != scalar(@Re))
{
print "ERROR: unequal array size\n";
exit;
}
else
{
$total = scalar(@Rs);
$num_mapped = scalar(@Rs);
}
my $ref_loc = $reference; # get locations of reference and query files
my $qry_loc = $query_file;
my $dif_dir =0; #assume query and reference are in the working directory
my @splits_reference = split (/\//, $reference);
my $new_reference_file = $splits_reference[(scalar(@splits_reference)-1)];
my @splits_query = split (/\//, $query_file);
my $new_query_file = $splits_query[(scalar(@splits_query)-1)];
if ($prefix eq "")
{
$prefix = $new_query_file."_".$new_reference_file;
}
#-------------------------------------------------------------------
#define file handles for output files and open files to write output
#-------------------------------------------------------------------
my ($seqFH,$tabFH,$binFH,$crunchFH, $gapFH, $gapFHT, $mlFH, $dbinFH, $avoidNFH,$ref_gapsFH);
open ($seqFH, '>', $prefix . '.fasta') or die "Could not open file $prefix.fasta for write: $!\n";
open ($tabFH, '>', $prefix . '.tab') or die "Could not open file $prefix.tab for write: $!\n";
open ($binFH, '>', $prefix . '.bin') or die "Could not open file $prefix.bin for write: $!\n";
open ($crunchFH, '>', $prefix . '.crunch') or die "Could not open file $prefix.crunch for write: $!\n";
open ($gapFH, '>', $prefix . '.gaps') or die "Could not open file $prefix.gaps for write: $!\n";
open ($gapFHT, '>', $prefix . '.gaps.tab') or die "Could not open file $prefix.gaps.tab for write: $!\n";
if ($mlfas ==1)
{
open ($mlFH, '>', $prefix . '.MULTIFASTA.fa') or die "Could not open file $prefix.contigs.fas for write: $!\n";
}
if ($fasta_bin ==1)
{
open ($dbinFH, '>', $prefix . '.contigsInbin.fas') or die "Could not open file $prefix.contigsInbin.fas for write: $!\n";
}
if ($avoid_Ns ==1)
{
open ($avoidNFH, '>', $prefix .'.NoNs.fasta') or die "Could not open file $prefix.NoNs.fasta for write: $!\n";
}
if ($gaps_2file ne "")
{
open ($ref_gapsFH, '>', $gaps_2file.'.Gaps_onRef') or die "Could not open file $gaps_2file.Gaps_onRef for write: $!\n";
}
#-------------------------------------------------------------------------
# Writing tiling graph and generating a pseudomolecule
# Note use use ps for pseudomolecule
#@Ps = start of ps, and @Pe = end of ps
my $ps_start =1;