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make_panacea_flatfile.pl
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make_panacea_flatfile.pl
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#!/usr/bin/env perl
#Copyright (C) 2016-2021 The J. Craig Venter Institute (JCVI). 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 3 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, see <http://www.gnu.org/licenses/>
=pod
=head1 NAME
make_panacea_flatfile.pl
=head1 SYNOPSIS
make_panacea_flatfile.pl [options] -d directory -t type -o outputFlatFile
Options:
-i --input Input directory of the Pangenome information. Required.
-o --output Output file. Default is PanACEA.[date].txt
-t --type Input type of the Pangenome. Currently supports "Pangenome" <default>, Pangenome "Iterative", "Panoct", and "Roary".
-v --verbose Turns on verbose output for debugging
=head1 DESCRIPTION
make_panacea_flatfile.pl generates the panchromosome PanACEA flat file from pangenome output
from various programs, including PanOCT and Roary. This file is required to run the PanACAExT
visualizer.
=head1 AUTHOR
Thomas Clarke ([email protected])
2017 J. Craig Venter Institute
=cut
use strict;
use warnings;
use Getopt::Long;
use Pod::Usage;
#load information from the files
my %types = ( "pangenome" => 1, "iterative" => 1, "panoct" => 1, "roary" => 1 );
my $core_cnt = 0;
my $CORE_PERCT = 0.75;
my %gene_num; #Matches the gene cluster name with the corresponding array number in the JSON matrix
my %clusters; #stores names and number of genomes in cluster
my %fgi_grps; #type = circular/linear; bound = the start and stop core genes; parent; sz = size; hit
my %fgi_member; #the fGI that a cluster belongs to
my %cores; #cores and their type
my %list; #used to make fGI gene array: contains bounding genes, and the different fGRs
my %core_list; #list of core genes
my %fgi_list; #c_start, c_end
my %core_size; #gets the core size for the number
my %fgi_gene_list; #hash of arrays
my %geneLenInfo; # hash containing the gene length mean, min, max and standard deviation for each cluster;
my %seqs;
#Directory to write the output
my $in_dir; #Default value for the output head directory
my $date = time();
my $output_id = "PanACEA.txt"; #Default value for the output file
my $type = "pangenome";
my $verb = 0;
#Doing the options here: need in_dir, out_dir, dir, func_file, output_id
my $help;
GetOptions(
"input|i:s" => \$in_dir,
"type|t:s" => \$type,
"output|o:s" => \$output_id,
"verbose|v" => \$verb,
"help|h|?" => \$help,
) or die "Can't get options!\n";
#Probably should set up a verbose tag to level the printing
if ( !$in_dir ) {
warn "Please enter in a directory from which to create the Flat File\n";
pod2usage( { -verbose => 2, -exitval => 0 } );
}
if ( !-e $in_dir ) {
warn "$in_dir does not exist. Please check...\n";
pod2usage( { -verbose => 2, -exitval => 0 } );
}
if ( !-d $in_dir ) {
warn "$in_dir is not a directory. Please check...\n";
pod2usage( { -verbose => 2, -exitval => 0 } );
}
if ( !$types{ lc($type) } ) {
my $tmp = "$type is not a recognized pangenome type. Please check the below and select the correct one.\n";
$tmp .= "Pangenome outputs able to be used: ";
$tmp .= join( ", ", keys %types );
die "$tmp\n";
}
if ( $verb == 1 ) {
warn "Welcome to PanACEA Creation Software\n\n";
warn "Using pangenome information located in $in_dir...\n\n\n";
}
if ( $output_id eq "PanACEA.txt" ) {
if ( -e $output_id ) {
$output_id = "PanACEA.$date.txt";
warn "PanACEA.txt already exists. Using $output_id instead...\n\n";
}
} else {
if ( -e $output_id ) {
warn "Warning: $output_id already exists, so it will be re-written...";
}
}
if ( lc($type) eq "pangenome" ) { read_in_pangenome(); }
if ( lc($type) eq "iterative" ) { read_in_pangenome(); }
if ( lc($type) eq "panoct" ) { read_in_panoct(); }
if ( lc($type) eq "roary" ) { read_in_roary(); }
write_files();
if ( $verb == 1 ) {
warn "Finished...\n\n";
}
exit(0);
sub read_in_panoct {
warn "PanOCT function is not currently working. Please check again later..\n";
#Pass data to gene_order
exit(1);
}
#Reading in Roary output
sub read_in_roary {
warn "Roary function is not currently working. Please check again later..\n";
#load in x,y,z
#make: cluster_wieghts
# num_core_adjacency_vector.txt consensus
# num_core_adjacency_
exit(1);
}
#Reading in the Pangenome pipeline
sub read_in_pangenome {
my ( $file_in1, $file_in2, $conses_in, $fgi_in, $fgi_arr, $comb_file, $frame_shift_file, $fasta_file, $sing_file );
if ( -e $in_dir ) {
if ( -d $in_dir ) {
my $res_dir = "results_all";
if ( !-e "$in_dir/$res_dir/" ) { $res_dir = "results"; }
my $fgi_dir = "fGI";
if ( !-e "$in_dir/$res_dir/$fgi_dir" ) { $fgi_dir = "fGIs"; }
$file_in1 = "$in_dir/$res_dir/$fgi_dir/Core.attfGI"; #
$file_in2 = "$in_dir/$res_dir/shared_clusters.txt"; #
$conses_in = "$in_dir/$res_dir/$fgi_dir/consensus.txt"; #
$fgi_in = "$in_dir/$res_dir/$fgi_dir/FGI_inserts.details"; #
if ( !-e $fgi_in ) { $fgi_in = "$in_dir/$res_dir/$fgi_dir/fGI_report.txt.details"; } # ./results/fGI/
$fgi_arr = "$in_dir/$res_dir/$fgi_dir/fGI.att"; # ./results/fGI/ #
$comb_file = "$in_dir/combined.att"; #./ Connects genes to different assemblies
$frame_shift_file = "$in_dir/$res_dir/frameshifts.txt"; #./results/ For when genes get rename
$sing_file = "$in_dir/$res_dir/singletons_clusters.txt";
} else {
die "$in_dir is not a directory. Please double check...\n\n";
}
} else {
die "Cannot find $in_dir for reading in pangenome files. Please double check...\n\n";
}
if ($verb) { warn "Reading in PanGenome information...\n"; }
$in_dir =~ s/([\/]+)\Z//g;
open( CORE1, "<", $file_in1 )
or die("Cannot read in the Core + fGI attributes file. Please check $file_in1.\n"); #Core+fGI attributes file
open( CLUSTER, "<", $file_in2 )
or die("Cannot read in the Cluster file. Please check $file_in2.\n"); #Shared Cluster information file
open( SINGLETON, "<", $sing_file ) or die("Cannot read in the Singleton Gene file. Please check $sing_file.\n");
open( CONSENS, "<", $conses_in ) or die("Cannot read in the Consensus file. Please check $conses_in.\n"); #
open( COMB, "<", $comb_file ) or die("Cannot read in the Combined File file. Please check $comb_file.\n");
open( FGI, "<", $fgi_in ) or die("Cannot read in the FGI details file. Please check $fgi_in.\n"); #Details file
open( CORE2, "<", $fgi_arr )
or die("Cannot read in the FGI Attributes file. Please check $fgi_arr.\n"); #fGI attributes file
my %oldGeneName;
if (-e $frame_shift_file) { open( FRAME_SHIFT, "<", $frame_shift_file )
or die("Cannot read in the Frameshift file. Please check $frame_shift_file.\n");
#get all the old sequence names in cases of frameshifts
#oldGeneName is the hash we used to store the old name -> new name
#my %oldGeneName;
while ( !eof(FRAME_SHIFT) ) {
my $in = <FRAME_SHIFT>;
chomp($in);
my @in = split "\t", $in;
for ( my $i = 1 ; $i < scalar(@in) ; $i++ ) {
$oldGeneName{ $in[0] } = $in[$i];
$oldGeneName{ $in[$i] } = $in[0];
}
}
}
my %gene2clust; #Hash with keys (1) gene name and (2) genomes, it gives value the cluster number
my %genomes;
warn "Reading in Clusters...\n";
#reads in the cluster id and the gene names associated with that cluster. From that gets the fasta sequenece associated with each cluster
#and with each cluster also the mean, sd, min and maxv length (it does take a while to run-> is that the calculation or in loading the multi-fasta?)
my $in = <CLUSTER>;
chomp($in);
my @head = split "\t", $in;
for ( my $i = 1 ; $i < scalar(@head) ; $i++ ) {
$head[$i] =~ s/\s/\_/g;
$genomes{ $head[$i] } = $i;
}
my $c = 0;
while ( !eof(CLUSTER) ) {
my $in = <CLUSTER>;
chomp($in);
my @n = split "\t", $in;
for ( my $i = 1 ; $i < scalar(@head) ; $i++ ) {
if ( $n[$i] ) {
$n[$i] =~ s/'//g;
$n[$i] =~ s/`//g;
$n[$i] =~ s/\"//g;
$clusters{ $n[0] }->{ $head[$i] } =
$n[$i]; #for each cluster id and genome returns the gene name; also includes centroid and number_of_genes
}
}
$c++;
$n[2] =~ s/\;//g;
$n[2] =~ s/\'//g;
#Fills up the cluster ids per genome/gene name; also gets the
my $minLen = -1;
my $maxLen = -1;
my $sum_len;
my $sum_len2;
my $n;
for ( my $i = 7 ; $i < scalar(@head) ; $i++ ) {
if ( $n[$i] ) {
$gene2clust{ $head[$i] }->{ $n[$i] } = $n[0];
$seqs{byClust}->{ $n[0] }->{ $head[$i] } = 1;
$seqs{byClustId}->{ $n[0] }->{ $head[$i] } = $n[$i];
}
}
$gene_num{ $n[0] } = $c;
#adding
#fills out the gene jso array: for this one gene cluster equals one row
# columns are 1: ID; 2: number; 3: 4: 5: function
#Tries to get the number of genomes in the total. Probably should be the scalar(@head)-7;
}
warn "Finished Reading in Clusters...\n";
warn "$c genes clusters identified...\n";
#Also get the ID of the singletons to connect geneID to cluster ID;
$in = <SINGLETON>;
chomp($in);
my @head2 = split "\t", $in;
for ( my $i = 1 ; $i < scalar(@head2) ; $i++ ) {
$head2[$i] =~ s/\s/\_/g;
}
while ( !eof(SINGLETON) ) {
my $in = <SINGLETON>;
chomp($in);
my @in = split "\t", $in;
$gene2clust{ $in[6] }->{ $in[5] } = $in[0];
$clusters{ $in[0] }->{ $in[6] } = $in[5];
$seqs{byClust}->{ $in[0] }->{ $in[6] } = 1;
$seqs{byClustId}->{ $in[0] }->{ $in[6] } = $in[5];
$clusters{ $in[0] }->{"centroid_locus"} = $in[5];
for ( my $i = 1 ; $i < scalar(@head2) ; $i++ ) {
$in[$i] =~ s/'//g;
$in[$i] =~ s/`//g;
$in[$i] =~ s/\"//g;
$clusters{ $in[0] }->{ $head2[$i] } =
$in[$i]; #for each cluster id and genome returns the gene name; also includes centroid and number_of_genes
}
}
my %genomeAttSort; #hash with key as the contif
my %genomeCnt;
my %genedir;
warn "Reading and Sorting Genes...\n";
#reads throught the combined attributes files; doesn't have to be sorted as the script does that below
while ( !eof(COMB) ) {
my $v = <COMB>;
chomp($v);
my @n = split "\t", $v;
my $genome_id = $n[5];
my $st = $n[2];
my $end = $n[3];
my $gene_id = $n[1];
my $id = $n[0];
my $gene_dir = 1;
if ( $st > $end ) { $n[2] = $end; $n[3] = $st; $gene_dir = -1; }
$genomeCnt{$genome_id}++;
$genomeAttSort{ $n[0] }->{ min( $st, $end ) } = [ $n[0], $n[1], $n[2], $n[3], $n[4], $n[5], $gene_dir ];
}
my %clust2genome; #Hash
my %genome_order; #hash of array
my %fgi_2_genome;
foreach my $keys (%genomeAttSort) {
#Sorts the
my @keys = sort { $b <=> $a } keys( %{ $genomeAttSort{$keys} } );
for ( my $i = 0 ; $i < scalar(@keys) ; $i++ ) {
my @n = @{ $genomeAttSort{$keys}->{ $keys[$i] } };
my $genome_id = $n[5];
my $st = $n[2];
my $end = $n[3];
my $gene_id = $n[1];
my $id = $n[0];
my $gene_dir = $n[6];
if ( $genomes{ $n[5] } ) {
if ( $gene2clust{$genome_id}->{$gene_id} ) {
$clust2genome{ "CL_" . $gene2clust{ $n[5] }->{$gene_id} }->{$genome_id} = "$st-$end";
if ( $genome_order{$genome_id}->{arr} ) {
push @{ $genome_order{$genome_id}->{arr} }, "CL_" . $gene2clust{$genome_id}->{ $n[1] };
} else {
$genome_order{$genome_id}->{arr}->[0] = "CL_" . $gene2clust{$genome_id}->{$gene_id};
}
$genome_order{$genome_id}->{list}->{ "CL_" . $gene2clust{$genome_id}->{$gene_id} } =
scalar( @{ $genome_order{$genome_id}->{arr} } );
$genome_order{$genome_id}->{id}->{ "CL_" . $gene2clust{$genome_id}->{$gene_id} } = $id;
$genedir{$genome_id}->{ $gene2clust{ $n[5] }->{$gene_id} } = $gene_dir;
} else {
if ( $oldGeneName{$gene_id} ) {
$gene_id = $oldGeneName{$gene_id};
}
if ( $gene2clust{$genome_id}->{$gene_id} ) {
$clust2genome{ "CL_" . $gene2clust{ $n[5] }->{$gene_id} }->{$genome_id} = "$st-$end";
if ( $genome_order{$genome_id}->{arr} ) {
push @{ $genome_order{$genome_id}->{arr} }, "CL_" . $gene2clust{$genome_id}->{$gene_id};
} else {
$genome_order{$genome_id}->{arr}->[0] = "CL_" . $gene2clust{$genome_id}->{$gene_id};
}
$genome_order{$genome_id}->{list}->{ "CL_" . $gene2clust{$genome_id}->{$gene_id} } =
scalar( @{ $genome_order{$genome_id}->{arr} } );
$genome_order{$genome_id}->{id}->{ "CL_" . $gene2clust{$genome_id}->{$gene_id} } = $id;
$genedir{$genome_id}->{ $gene2clust{$genome_id}->{$gene_id} } = $gene_dir;
} else {
print( STDERR "No hits..." . $n[5] . " " . $gene_id . " $id $st $end\n" );
}
}
} else {
die("Cannot find genome... quitting\n\n");
}
}
}
warn "Reading in Core and FGI Cluster Assignments...\n";
while ( !eof(CONSENS) ) {
my $in = <CONSENS>;
if ( $in =~ /\#Assembly_Core(\s+)(\d+)(\s+)(\S+)/ ) {
$cores{$2}->{type} = $4;
$core_cnt++;
}
if ( $in =~ /\#Assembly_fGI/ ) {
chomp($in);
my ( $type, $id_num, $dist, $gene_num, $nt_len ) = split "\t", $in;
$fgi_grps{$id_num}->{type} = $dist;
$in = <CONSENS>;
my $st;
my $end;
my $hit;
while ( $in =~ /\A[^\s\#]/ && !eof(CONSENS) ) {
chomp($in);
my @tmp = split "\t", $in;
if ( $tmp[2] && $tmp[2] eq "P" ) {
$fgi_member{ $tmp[0] } = $id_num;
foreach my $genome ( keys( %{ $gene2clust{ $tmp[0] } } ) ) {
$fgi_2_genome{$id_num}->{$genome}++;
}
$hit = 1;
}
$in = <CONSENS>;
}
}
}
warn "Assigning genomes to FGR orders...\n";
my %genome_fgi_list;
my %genome_fgi_by_start
; #This list the FGI by starting Core Cluster. Contains keys: list (non-core genes in between); break (is there a break?)
#st: the starting core cluster; end: the ending core cluster;
foreach my $genome ( keys(%genome_order) ) {
my $curr;
my $tmp = "";
my $back = 0;
my $curr_id = "";
my $tmp2 = "";
my $back2 = 0;
my $st_gene;
my $st_gene_rev;
my $st_gene_id;
my $break;
my $in_cnt;
foreach my $gene_cl ( @{ $genome_order{$genome}->{arr} } ) {
if ( $gene_cl =~ /CL_(\d+)/ ) {
my $gene = $1;
my $geneDir = $genedir{$genome}->{$gene};
my $num = 3;
my $revNum = 5;
if ( $geneDir == 1 ) { $num = 5; $revNum = 3; }
#$revNum=$num;
if ( $curr_id eq "" ) {
$curr_id = $genome_order{$genome}->{id}->{$gene_cl};
$break = 1;
}
if ( $curr_id ne $genome_order{$genome}->{id}->{$gene_cl} && $st_gene ) {
if ($tmp) {
$genome_fgi_list{$tmp}->{$genome} = 1;
$genome_fgi_list{$back}->{$genome} = 1;
$genome_fgi_list{$tmp2}->{$genome} = 1;
$genome_fgi_list{$back2}->{$genome} = 1;
$genome_fgi_by_start{ $st_gene . "_NA" }->{$genome}->{list} = $tmp2;
$genome_fgi_by_start{ $st_gene . "_NA" }->{$genome}->{break} = 1;
$genome_fgi_by_start{ $st_gene . "_NA" }->{$genome}->{st} = $st_gene_id;
$genome_fgi_by_start{ "NA_" . $st_gene_rev }->{$genome}->{list} = $back;
$genome_fgi_by_start{ "NA_" . $st_gene_rev }->{$genome}->{end} = $st_gene_id;
$genome_fgi_by_start{ "NA_" . $st_gene_rev }->{$genome}->{break} = 1;
} else {
$genome_fgi_by_start{ $st_gene . "_NA" }->{$genome}->{list} = "";
$genome_fgi_by_start{ $st_gene . "_NA" }->{$genome}->{break} = 1;
$genome_fgi_by_start{ $st_gene . "_NA" }->{$genome}->{st} = $st_gene_id;
$genome_fgi_by_start{ "NA_" . $st_gene_rev }->{$genome}->{end} = $st_gene_id;
$genome_fgi_by_start{ "NA_" . $st_gene_rev }->{$genome}->{list} = "";
$genome_fgi_by_start{ "NA_" . $st_gene_rev }->{$genome}->{break} = 1;
}
$back = "";
$back2 = "";
$break = 1;
$tmp = "";
$tmp2 = "";
$st_gene = "";
$in_cnt = 0;
if ( !$fgi_member{$gene_cl} ) {
$st_gene_id = $gene;
$st_gene = "$gene-$num";
$st_gene_rev = "$gene-$revNum";
}
}
$curr_id = $genome_order{$genome}->{id}->{$gene_cl};
$curr = $gene;
if ( !$fgi_member{$gene_cl} ) {
if ($tmp) {
$genome_fgi_list{ $tmp . $gene . ":" }->{$genome} = 1;
$genome_fgi_list{ $tmp2 . $gene . ":" }->{$genome} = 1;
if ( $st_gene && ( $st_gene ne $gene . "-" . $revNum ) ) {
$genome_fgi_by_start{ $st_gene . "_" . $gene . "-" . $revNum }->{$genome}->{list} = $tmp2;
$genome_fgi_by_start{ $st_gene . "_" . $gene . "-" . $revNum }->{$genome}->{st} = $st_gene_id;
$genome_fgi_by_start{ $st_gene . "_" . $gene . "-" . $revNum }->{$genome}->{end} = $gene;
$genome_fgi_by_start{ $st_gene . "_" . $gene . "-" . $revNum }->{$genome}->{break} = $break;
$genome_fgi_by_start{ $st_gene . "_NA" }->{$genome}->{list} = $tmp2;
$genome_fgi_by_start{ $st_gene . "_NA" }->{$genome}->{st} = $st_gene_id;
$genome_fgi_by_start{ $st_gene . "_NA" }->{$genome}->{end} = $gene;
$genome_fgi_by_start{ $st_gene . "_NA" }->{$genome}->{break} = $break;
$genome_fgi_by_start{ "NA_" . $gene . "-" . $revNum }->{$genome}->{list} = $tmp2;
$genome_fgi_by_start{ "NA_" . $gene . "-" . $revNum }->{$genome}->{st} = $st_gene_id;
$genome_fgi_by_start{ "NA_" . $gene . "-" . $revNum }->{$genome}->{end} = $gene;
$genome_fgi_by_start{ "NA_" . $gene . "-" . $revNum }->{$genome}->{break} = $break;
$genome_fgi_by_start{ $gene . "-" . $revNum . "_" . $st_gene }->{$genome}->{list} = $back;
$genome_fgi_by_start{ $gene . "-" . $revNum . "_" . $st_gene }->{$genome}->{st} = $gene;
$genome_fgi_by_start{ $gene . "-" . $revNum . "_" . $st_gene }->{$genome}->{end} = $st_gene_id;
$genome_fgi_by_start{ $gene . "-" . $revNum . "_" . $st_gene }->{$genome}->{break} = $break;
$genome_fgi_by_start{ $gene . "-" . $revNum . "_NA" }->{$genome}->{list} = $back;
$genome_fgi_by_start{ $gene . "-" . $revNum . "_NA" }->{$genome}->{st} = $gene;
$genome_fgi_by_start{ $gene . "-" . $revNum . "_NA" }->{$genome}->{end} = $st_gene_id;
$genome_fgi_by_start{ $gene . "-" . $revNum . "_NA" }->{$genome}->{break} = $break;
$genome_fgi_by_start{ "NA_" . $st_gene }->{$genome}->{list} = $back;
$genome_fgi_by_start{ "NA_" . $st_gene }->{$genome}->{st} = $gene;
$genome_fgi_by_start{ "NA_" . $st_gene }->{$genome}->{end} = $st_gene_id;
$genome_fgi_by_start{ "NA_" . $st_gene }->{$genome}->{break} = $break;
} else {
$genome_fgi_by_start{ "NA_" . $gene . "-" . $revNum }->{$genome}->{list} = $tmp2;
$genome_fgi_by_start{ $gene . "-" . $revNum . "_NA" }->{$genome}->{list} = $back;
$genome_fgi_by_start{ $gene . "-" . $revNum . "_NA" }->{$genome}->{st} = $gene;
$genome_fgi_by_start{ "NA_" . $gene . "-" . $revNum }->{$genome}->{end} = $gene;
$genome_fgi_by_start{ "NA_" . $gene . "-" . $revNum }->{$genome}->{break} = $break;
$genome_fgi_by_start{ $gene . "-" . $revNum . "_NA" }->{$genome}->{break} = $break;
}
$genome_fgi_list{$back2}->{$genome} = 1;
$genome_fgi_list{$back}->{$genome} = 1;
$back = "";
$back2 = "";
$tmp2 = "";
$tmp = "";
$break = 0;
$in_cnt = 0;
$st_gene_id = $gene;
$st_gene_rev = $gene . "-" . $revNum;
$st_gene = $gene . "-" . $num;
} else {
if ( $st_gene && ( $st_gene ne $gene . "-" . $revNum ) ) {
$genome_fgi_list{ $gene . ":" }->{$genome} = 1;
$genome_fgi_by_start{ $st_gene . "_" . $gene . "-" . $revNum }->{$genome}->{list} = "";
$genome_fgi_by_start{ $st_gene . "_" . $gene . "-" . $revNum }->{$genome}->{end} = $gene;
$genome_fgi_by_start{ $st_gene . "_" . $gene . "-" . $revNum }->{$genome}->{st} = $st_gene_id;
$genome_fgi_by_start{ $st_gene . "_" . $gene . "-" . $revNum }->{$genome}->{break} = $break;
$genome_fgi_by_start{ $gene . "-" . $revNum . "_" . $st_gene }->{$genome}->{list} = "";
$genome_fgi_by_start{ $gene . "-" . $revNum . "_" . $st_gene }->{$genome}->{end} = $gene;
$genome_fgi_by_start{ $gene . "-" . $revNum . "_" . $st_gene }->{$genome}->{st} = $st_gene_id;
$genome_fgi_by_start{ $gene . "-" . $revNum . "_" . $st_gene }->{$genome}->{break} = $break;
$back = "";
$back2 = "";
$tmp2 = "";
$tmp = "";
$break = 0;
$in_cnt = 0;
$st_gene_id = $gene;
$st_gene_rev = $gene . "-" . $revNum;
$st_gene = $gene . "-" . $num;
}
}
} else {
my $fgi_tmp = $fgi_member{$gene_cl};
$in_cnt++;
if ( !$tmp2 || $tmp2 !~ /$gene:/ ) {
$tmp2 .= "$gene:";
$back = "$gene:$back";
}
if ( $tmp !~ /$fgi_tmp/ ) {
$tmp .= "$fgi_tmp:";
}
}
} else {
die("Cannot find any gene clusters under the ID $gene_cl... Quiting...\n");
}
}
}
warn "Reading in Core and FGI Cluster Assignments II...\n";
my ( $prev_n, $prev );
while ( !eof(CORE1) ) {
my $in = <CORE1>;
chomp($in);
my @n = split "\t", $in;
#$fgi_member{$n[1]} = $n[0];
push( @{ $core_list{ $n[0] } }, \@n );
$core_size{ $n[1] } = $n[3] - $n[2];
if ( !$cores{ $n[0] }->{sz} ) {
$cores{ $n[0] }->{sz} = $n[3];
}
if ( $n[3] > $cores{ $n[0] }->{sz} ) {
$cores{ $n[0] }->{sz} = $n[3];
}
if ( $n[2] > $cores{ $n[0] }->{sz} ) {
$cores{ $n[0] }->{sz} = $n[2];
}
if ( $prev && $prev =~ /INS/ ) {
$fgi_list{$prev}->{c_end} = $n[1];
}
if ( $n[4] && $n[4] =~ /fGI/ ) {
$fgi_list{ $n[1] }->{c_start} = $prev;
}
$prev = $n[1];
}
my ( $st, $prev2, $end, $hit );
while ( !eof(CORE2) ) {
my $in = <CORE2>;
chomp($in);
my @n = split "\t", $in;
$fgi_grps{ $n[0] }->{sz} = 0;
if ( $prev2 && $prev2 ne $n[0] ) {
$fgi_grps{$prev2}->{bound} = $st . "_" . $end;
my $st_1 = "";
if ( $fgi_member{ "CL_" . $st } ) { $st_1 = $fgi_member{ "CL_" . $st }; }
my $end_1 = "";
if ( $fgi_member{ "CL_" . $end } ) { $end_1 = $fgi_member{ "CL_" . $end }; }
$fgi_grps{$prev2}->{parent} = $st_1 . "_" . $end_1;
$st = "";
$end = "";
$hit = "";
}
$prev2 = $n[0];
if ( $n[1] !~ /CONTEXT/ ) {
push( @{ $core_list{ $n[0] } }, \@n );
$core_size{ $n[1] } = $n[3] - $n[2];
$fgi_gene_list{ $n[1] } = \@n;
if ( $n[3] > $fgi_grps{ $n[0] }->{sz} ) {
$fgi_grps{ $n[0] }->{sz} = $n[3];
}
if ( $n[2] > $fgi_grps{ $n[0] }->{sz} ) {
$fgi_grps{ $n[0] }->{sz} = $n[2];
}
$prev = $n[1];
$hit = 1;
} else {
if ( !$hit && $n[1] =~ /CL_(\d+)/ ) { $st = $1; }
if ( $hit && !$end && $n[1] =~ /CL_(\d+)/ ) { $end = $1; }
}
}
my $ins_id;
my $st_1 = "";
my $end_1 = "";
my $st_id = "";
my $end_id = "";
open( FGI, "<", $fgi_in ) or die();
while ( !eof(FGI) ) {
my $in = <FGI>;
chomp($in);
my @n = split "\t", $in;
my $line = $in;
if ( $n[0] =~ /INS/ ) {
my $cnt_i;
$ins_id = $n[0];
$st_id = "";
$end_id = "";
if ( scalar(@n) > 1 ) {
$n[1] =~ /(\d+)\_(\d+)/;
$st_1 = $1 . "-" . $2;
$st_id = $1;
}
if ( scalar(@n) > 2 ) {
$n[2] =~ /(\d+)\_(\d+)/;
$end_1 = $1 . "-" . $2;
$end_id = $1;
}
if ( $st_id eq $end_id ) { die( $in . " $st_id $end_id" ); }
my %out_list;
my %hits;
my $hit_type = 0;
foreach my $a ( keys( %{ $genome_fgi_by_start{ $st_1 . "_" . $end_1 } } ) ) {
my $in = $st_id . ":" . $genome_fgi_by_start{ $st_1 . "_" . $end_1 }->{$a}->{list} . $end_id . ":";
if (!$end_id) {
$end_1 =~ /(\d+)\-(\d+)/;
$end_id = $1;
}
if (!$st_id) {
$st_1 =~ /(\d+)\-(\d+)/;
$st_id = $1;
}
if ($st_id ne $end_id) {
if ($verb) { warn "$a\t$ins_id\t$in\t$st_id\t$st_1\t$end_1\t$in\n"; }
$out_list{$in}->{st} = "CL_" . $st_id;
$out_list{$in}->{list} = $genome_fgi_by_start{ $st_1 . "_" . $end_1 }->{$a}->{list};
$out_list{$in}->{en} = "CL_" . $end_id;
$out_list{$in}->{cnt}++;
$out_list{$in}->{gen_list} .= $a . ":";
$hits{$a} = 1;
$hit_type = 1;
}
}
foreach my $a ( keys( %{ $genome_fgi_by_start{ $st_1 . "_NA" } } ) ) {
if ( !$hits{$a} && $st_id ) {
my $in = $st_id . ":" . $genome_fgi_by_start{ $st_1 . "_NA" }->{$a}->{list};
my $oth = "";
my $oth_t = "";
if ( $genome_fgi_by_start{ $st_1 . "_NA" }->{$a}->{end}
&& !$fgi_member{ "CL_" . $genome_fgi_by_start{ $st_1 . "_NA" }->{$a}->{end} } ) {
#$in .= $genome_fgi_by_start{$st_1 . "_NA"}->{$a}->{end} .":";
$out_list{$in}->{en} = "CL_" . $genome_fgi_by_start{ $st_1 . "_NA" }->{$a}->{end};
} else {
if ( $genome_fgi_by_start{ "NA_" . $end_1 }->{$a}
&& $genome_fgi_by_start{ $st_1 . "_" }->{$a}->{break} ) {
$in .= $genome_fgi_by_start{ "NA_" . $end_1 }->{$a}->{list} . $end_id . ":";
$hits{$a} = 1;
$out_list{$in}->{en} = "CL_" . $end_id;
$oth .= $genome_fgi_by_start{ "NA_" . $end_1 }->{$a}->{list};
$oth_t .= $genome_fgi_by_start{ "NA_" . $end_1 }->{$a}->{type} . ":";
}
}
$out_list{$in}->{st} = "CL_" . $st_id;
if ($verb) { warn "$a\t$ins_id\t$st_id\t$st_1\t$end_1\t$in\n"; }
#$out_list{$in}->{en} = "";
$out_list{$in}->{cnt}++;
$out_list{$in}->{gen_list} .= $a . ":";
$out_list{$in}->{list} = $genome_fgi_by_start{ $st_1 . "_NA" }->{$a}->{list} . $oth;
$hit_type = 2;
}
}
foreach my $a ( keys( %{ $genome_fgi_by_start{ "NA_" . $end_1 } } ) ) {
if ( !$hits{$a} && $end_id ) {
if ($verb) { warn "$a\t$ins_id\t$in\t$st_id\t$st_1\t$end_1\n"; }
my $in = $genome_fgi_by_start{ "NA_" . $end_1 }->{$a}->{list} . "$end_id:";
if ( $genome_fgi_by_start{ "NA_" . $end_1 }->{$a}->{st}
&& !$fgi_member{ "CL_" . $genome_fgi_by_start{ "NA_" . $end_1 }->{$a}->{st} } ) {
#$in = $genome_fgi_by_start{ "NA_" . $end_1}->{$a}->{st} .":$in";
$out_list{$in}->{st} = "CL_" . $genome_fgi_by_start{ "NA_" . $end_1 }->{$a}->{st};
}
$out_list{$in}->{cnt}++;
$out_list{$in}->{gen_list} .= $a . ":";
$out_list{$in}->{en} = "CL_" . $end_id;
#$out_list{$in}->{st} = "";
$out_list{$in}->{list} = $genome_fgi_by_start{ "NA_" . $end_1 }->{$a}->{list};
$hit_type = 3;
}
}
foreach my $a ( keys(%out_list) ) {
if ($verb) { warn("$ins_id\t$a\t" . $out_list{$a}->{gen_list}. "\n"); }
if ( $a eq ":" ) {
die( $hit_type . " " . $ins_id . " S-" . $st_id . " E-" . $end_id . " " . $out_list{$a}->{gen_list} );
}
my @in = split ":", $out_list{$a}->{list};
$cnt_i->{$ins_id} += $out_list{$a}->{cnt};
$list{$ins_id}->{$a}->{arr} = \@in;
$list{$ins_id}->{$a}->{cnt} = $out_list{$a}->{cnt};
$list{$ins_id}->{$a}->{st} = $out_list{$a}->{st};
$list{$ins_id}->{$a}->{end} = $out_list{$a}->{en};
$list{$ins_id}->{$a}->{gen} .= $out_list{$a}->{gen_list};
}
} else {
my $start;
my $st_dir;
my $end;
my $end_dir;
my $fam = "";
my @in;
$n[0] .= ":";
my $chain = "";
my $chain2 = "";
#my $hits; my $curr;
while ( $n[0] =~ /(\D*)(\d+)([\-\+])(\:*)/g ) {
my $core_id = $1;
my $id = $2;
my $dir_pl = $3;
my $dir;
if ( $dir_pl eq "+" ) { $dir = 1; }
else { $dir = -1; }
if ($core_id) {
$chain .= "$id:";
$chain2 .= "$id:";
if ( $core_id =~ /START/ ) {
$start = "CL_$id";
$st_dir = $dir;
if ( $id eq $end_1 ) {
$end = "CL_$id";
$end_dir = 1;
if ( $dir_pl eq "+" ) { $end_dir = -1; $dir = 1; }
else { $dir = -1; }
$start = "";
$st_dir = 0;
}
}
if ( $core_id =~ /STOP/ ) {
$end = "CL_$id";
$end_dir = $dir;
}
if ( $core_id =~ /U/ ) {
$end = "CL_$id";
$end_dir = $dir;
}
} else {
if ( !$fgi_member{ "CL_" . $id } ) { die($id); }
my $tst = $fgi_member{ "CL_" . $id } . ":";
if ( $fam !~ /$tst/ ) { $fam .= $tst; $chain .= $tst; }
push @in, $id;
$chain2 .= "$id:";
}
}
}