##########################字符串引用##########################
$value="ATGCN";
print $value,"\n";
$valueRef=\$value; #引用
print "$value and $valueRef\n";
$derefRalueRef=${$valueRef};
print "$value and $valueRef and $derefRalueRef\n";
##########################匿名字符串引用#######################
$value1=\ "ATGCNGG";
print ${$value1},"\n";
##########################数组引用#############################
@sequences=("ATTTAC","AACCGCTT","AACCTT");
print @sequences,"\n";
print "@sequences","\n";
$arrayRef=\@sequences;
print $arrayRef,"\n";
@deRefarray=@{$arrayRef};
print "@deRefarray","\n";
print "*******************","\n";
print @{$arrayRef}[0],"\n";
print "*******************","\n";
print ref($arrayRef),"\n";
print $arrayRef -> [0],"\n";
print $arrayRef -> [1],"\n";
print $arrayRef -> [2],"\n";
print $arrayRef -> [0]," ",$arrayRef -> [1]," ",$arrayRef -> [2],"\n";
###############################匿名数组引用############################
$sequences = ["ATACGCA","GGCCATA","CAGATATCAAA"];
print $sequences,"\n";
print ref($sequences),"\n";
print $sequences -> [0]," ",$sequences -> [1]," ",$sequences -> [2],"\n";
###############################多维数组的引用############################
$sequences=[["ATCGCGA","GCCAATG","GGAACCTT"],["AAATTTGGCCAGG","AGAGTACAGCAT","AGGC"],["ATTCA","GGCCAA","GGGAAAGGTTAAGGTT"]];
print "@{$sequences}","\n";
print $sequences,"\n";
print ref($sequences),"\n";
print $sequences -> [0],"\n";
print $sequences -> [1],"\n";
print $sequences -> [2],"\n";
print $sequences -> [0][0],"\n";
for $i (0..2){
for $j (0..2){
print $sequences -> [$i][$j],"\n";
}
}
print "########################","\n";
for $i (0..2){
for $j (0..2){
print $sequences -> [$i] -> [$j],"\n";
}
}
print "#########################","\n";
for $i (0..2){
print $sequences -> [$i],"\n";
}
##########################hash引用###########################
use Data::Dumper;
my %dzHash=(
"ID123" => "gff",
"ID124" => "gff1",
"ID125" => "gff3"
);
print %dzHash."\n";
print scalar(%dzHash),"\n";
print %dzHash,"\n";
my $refdzHash=\ %dzHash;
print Dumper($refdzHash);
print ref($refdzHash),"\n";
print %{$refdzHash},"\n";
print $refdzHash,"\n";
print $refdzHash -> {ID123},"\n";
print $refdzHash -> {ID125},"\n";
print %{$refdzHash},"\n";
print %{$refdzHash}{ID124},"\n";
for my $K (keys %{$refdzHash}){
print "keys:",$K,"\t","value:",$refdzHash -> {$K},"\n";
}
####################匿名hash##########################
$myniHash={
"ID123" => "gff",
"ID124" => "gff1",
"ID125" => "gff3"
};
print $myniHash,"\n";
print %{$myniHash},"\n";
print $myniHash -> {ID124},"\n";
for $d (keys %{$myniHash}){
print "keys:",$d,"\t","value:",$myniHash -> {$d},"\n";
}
$filename="test.gff3";
open(R,"$filename") || die "Can not open $filename\n";
open(W,">$filename.mRNA");
my %geneInfo=();
my $refgeneInfo=\ %geneInfo;
while (my $file=<R>){
chomp $file;
if ($file=~/^#/){
next;
}
my @temp=split("\t",$file);
if ($temp[2] eq "gene"){
$temp[-1]=~/ID=([^;]+)?/;
my $geneID=$1;
$refgeneInfo -> {$geneID} -> {'location'} = [$temp[0],$temp[3],$temp[4]];
}
if ($temp[2] eq "mRNA"){
$temp[-1]=~/ID=([^;]+).Parent=([^;]+)/;
push(@{$refgeneInfo->{$2}->{transcripts}},{"start" => $temp[3],"end" => $temp[4],"chr" =>$temp[0],"mRNA" =>$1});
}
}
for my $id (keys %{$refgeneInfo}){
print $refgeneInfo -> {$id} ->{location},"\n";
print $refgeneInfo -> {$id} -> {transcripts},"\n";
if ( ($refgeneInfo -> {$id} -> {transcripts}) ne ""){
print $refgeneInfo -> {$id} -> {transcripts} -> [0] ->{mRNA},"\n";
}
print "\n";
}
close R;
close W;
