#!/usr/bin/env perl
use warnings;
use strict;

local $SIG{__WARN__} = sub {
    my $message = shift;
    logger('warning', $message);
};
sub logger {
    my ($level, $msg) = @_;
    if (open my $out, '>>', 'convert2gn.log') {
        chomp $msg;
        print $out "$level - $msg\n"; #add newline after $msg
    }
}


my @files = glob( "\.\/IN" . '/*' );
print "select file for converting to gene names\n";
my $i = 0;
for (@files) {print "$i\t$_\n"; $i++};
chomp (my $will = <STDIN>);
my $fl = $files[$will];
print "$fl\n";

my (@out, $header) = ();
my $fasta = get_fasta();
my %fas = %{$fasta};
my (%t, @h, $idx);
open my $fh, "<", $fl or die "ERROR. Can not open $fl $!";
while (<$fh>) {
    chomp;
    if (m/.*ID\t.+/) {
        $header = $_;
        @h = split /\t/, $_;
    }
    else {
        my @aa = split /\t/, $_;
        @t{@h} = @aa;
        my $bb = rm_sht($t{ID});
        my @idx2 = grep {$h[$_] eq 'ID' } 0..$#h;
        $idx = $idx2[0];
        for (@{$bb}) {
            if ($fas{$_}){
                $aa[$idx] = "$fas{$_}\t$_";
                my $bb = join "\t", @aa;
                push @out, $bb
            }
        }
    }
}
close $fh or die "ERROR. can not close fh\n$!\n";
$h[$idx] = "GN\tID";
@out = uniq(@out);
writeO(\@out, "\.\/IN\/conv2gn_out.txt", join("\t", @h));


sub rm_sht {
    #receive a mq formatted string (multiple accession tremble and shit) and convert it to SINGLE accession
    my ($string) = @_;
    if ($string =~ m/(.+);(.+)/g){ #if multiple accession
        my %out;
        my @arr = split /;/, $string;
        #remove swissprot or tremble id
        for my $single (@arr) {

            #$single =~ s/sp\|.+\||tr\|.+\|//g;
            $single =~ s/sp\|(.+)\|[\w]+/$1/g;
            $out{$single} = 1; #so removing the duplicates by default
        }
        my @lol = keys %out;
        return (\@lol);
    }
    else {
        $string =~ s/sp\|(.+)\|[\w]+/$1/g;
        my @arr;
        push @arr, $string;
        return (\@arr);
    }
}

sub read_table {
    #read a table and return a hash of an array with everything in that
    my ($path, $firstcolumname, $sep) = @_;
    open my $fh, "<", $path or die "ERROR. can not open fh$:";
    my (@h, %t, %out);
    while (<$fh>) {
        chomp;
        if (/^$firstcolumname/) {
            @h = split /$sep/, $_;
            next;
        }
        else {
            my $string = $_;
            my @d;
            if ($sep eq "\t") {
                @d = split /\t/, $string;
            }
            elsif ($sep  eq ",") {
                @d = $string =~  m/("[^"]+"|[^,]*)(?:,s*)?/g;
            }
            @t{@h} = @d;
        }
        if (@h) {
            for my $headers (@h) {
                push @{$out{$headers}}, $t{$headers};
            }
        }
    }
    eval {
        close $fh or die "ERROR. can not close fh$!";
    };
    if ($@) {
        return ('error with close fh')
    }
    my $out_ref = \%out;
    return ($out_ref);
}

sub writeO {
    #print out to file giving an array ref, path to file and the headers
    #use writeO($uni_sec, "./$lst{second_flnm},uni.txt", "unique");
    my ($ref, $outfile, $headers) = @_;
    my @out = @{$ref};
    unshift @out, $headers; #headers
    @out =  map {$_ . "\n"}@out; #map newline
    open my $out_fh, ">", $outfile or die "$! can not open $outfile";
    print $out_fh @out;
    close $out_fh or die "can not close $outfile $!";
}

sub get_fasta {
    my ($wanted) = @_;
    my @res = glob( "\.\/FASTA" . '/*' );
    print "fasta files available are:\n";
    my $i = 0;
    for (@res) {print "$i\t$_\n"; $i++};
    print "select fasta file to use for the conversion\t";
    chomp (my $will = <STDIN>);
    my $fasta = $res[$will];
    print "$fasta\n";
    open my $fh, "<", $fasta or die "ERROR. Can not open FASTA file $!";
    my (@h, %t);
    my $dupl = 1;
    while (<$fh>) {
        chomp;
        #used before ^<sp|.*\|([\w]+) .*GN=([\w]+) then added the part for matching the hyphen and if anything after the hyphen
        if (/sp\|(.+)\|[\w]+ .*GN=([\w]+[\-]?[\w]+).*/) {
            my $gene = $2;
            my $prot = $1;
            if (grep {$_ eq $gene} values %t){
                $dupl++;
                $gene = "$gene\_$dupl";
                $t{$prot} = uc($gene);
            }
            else {
                $t{$prot} = uc($gene);
            }
        }
    }
    close $fh or die "ERROR. can not close fh$!";
    return \%t;
}

sub uniq {
    my %seen;
    grep !$seen{$_}++, @_;
}