Is it possible to put elements of array to hash in perl? - arrays

Question

example of file content:
>random sequence 1 consisting of 500 residues.
VILVWRISEMNPTHEIYPEVSYEDRQPFRCFDEGINMQMGQKSCRNCLIFTRNAFAYGIV
HFLEWGILLTHIIHCCHQIQGGCDCTRHPVRFYPQHRNDDVDKPCQTKSPMQVRYGDDSD;
>random sequence 2 consisting of 500 residues.
KAAATKKPWADTIPYLLCTFMQTSGLEWLHTDYNNFSSVVCVRYFEQFWVQCQDHVFVKN
KNWHQVLWEEYAVIDSMNFAWPPLYQSVSSNLDSTERMMWWWVYYQFEDNIQIRMEWCNI
YSGFLSREKLELTHNKCEVCVDKFVRLVFKQTKWVRTMNNRRRVRFRGIYQQTAIQEYHV
HQKIIRYPCHVMQFHDPSAPCDMTRQGKRMNFCFIIFLYTLYEVKYWMHFLTYLNCLEHR;
>random sequence 3 consisting of 500 residues.
AYCSCWRIHNVVFQKDVVLGYWGHCWMSWGSMNQPFHRQPYNKYFCMAPDWCNIGTYAWK
I need an algorithm to build a hash $hash{$key} = $value; where lines starting with > are the values and following lines are the keys.
What I have tried:
open (DATA, "seq-at.txt") or die "blabla";
#data = <DATA>;
%result = ();
$k = 0;
$i = 0;
while($k != #data) {
$info = #data[$k]; #istrina pirma elementa
if(#data[$i] !=~ ">") {
$key .= #data[$i]; $i++;
} else {
$k = $i;
}
$result{$key} = $value;
}
but it doesn't work.

Answer 1

You don't have to previously use an array, you can directly build your hash:
use strict;
use warnings;
# ^- start always your code like this to see errors and what is ambiguous
# declare your variables using "my" to specify the scope
my $filename = 'seq-at.txt';
# use the 3 parameters open syntax to avoid to overwrite the file:
open my $fh, '<', $filename or die "unable to open '$filename' $!";
my %hash;
my $hkey = '';
my $hval = '';
while (<$fh>) {
chomp; # remove the newline \n (or \r\n)
if (/^>/) { # when the line start with ">"
# store the key/value in the hash if the key isn't empty
# (the key is empty when the first ">" is encountered)
$hash{$hkey} = $hval if ($hkey);
# store the line in $hval and clear $hkey
($hval, $hkey) = $_;
} elsif (/\S/) { # when the line isn't empty (or blank)
# append the line to the key
$hkey .= $_;
}
}
# store the last key/val in the hash if any
$hash{$hkey} = $hval if ($hkey);
# display the hash
foreach (keys %hash) {
print "key: $_\nvalue: $hash{$_}\n\n";
}

Answer 2

It is unclear what you want, the array seems to be the lines subsequent to the random sequence number... If the contenst of a file test.txt are:
Line 1:">"random sequence 1 consisting of 500 residues.
Line 2:VILVWRISEMNPTHEIYPEVSYEDRQPFRCFDEGINMQMGQKSCRNCLIFTRNAFAYGIV
Line 3:HFLEWGILLTHIIHCCHQIQGGCDCTRHPVRFYPQHRNDDVDKPCQTKSPMQVRYGDDSD;
You could try something like:
#!/usr/bin/perl
use strict;
use warnings;
use Data::Dumper;
my $contentFile = $ARGV[0];
my %testHash = ();
my $currentKey = "";
open(my $contentFH,"<",$contentFile);
while(my $contentLine = <$contentFH>){
chomp($contentLine);
next if($contentLine eq ''); # Empty lines.
if($contentLine =~ /^"\>"(.*)/){
$currentKey= $1;
}else{
push(#{$testHash{$currentKey}},$contentLine);
}
}
print Dumper(\%testHash);
Which results in a structure like this:
seb#amon:[~]$ perl test.pl test.txt
$VAR1 = {
'random sequence 3 consisting of 500 residues.' => [
'AYCSCWRIHNVVFQKDVVLGYWGHCWMSWGSMNQPFHRQPYNKYFCMAPDWCNIGTYAWK'
],
'random sequence 1 consisting of 500 residues.' => [
'VILVWRISEMNPTHEIYPEVSYEDRQPFRCFDEGINMQMGQKSCRNCLIFTRNAFAYGIV',
'HFLEWGILLTHIIHCCHQIQGGCDCTRHPVRFYPQHRNDDVDKPCQTKSPMQVRYGDDSD;'
],
'random sequence 2 consisting of 500 residues.' => [
'KAAATKKPWADTIPYLLCTFMQTSGLEWLHTDYNNFSSVVCVRYFEQFWVQCQDHVFVKN',
'KNWHQVLWEEYAVIDSMNFAWPPLYQSVSSNLDSTERMMWWWVYYQFEDNIQIRMEWCNI',
'YSGFLSREKLELTHNKCEVCVDKFVRLVFKQTKWVRTMNNRRRVRFRGIYQQTAIQEYHV',
'HQKIIRYPCHVMQFHDPSAPCDMTRQGKRMNFCFIIFLYTLYEVKYWMHFLTYLNCLEHR;'
]
};
You would be basically using each hash "value" as an array structure, the #{$variable} does the magic.