error of "Use of uninitialized value" - perl

Question

previously I asked about a problem regarding my homework to calculate the alignment score of two protein sequences:
how to pass a variable to different if statement
However, I missed a significant amount of information in the question so I have to rewrite the code.
Now my code is done, but I have a warning as Use of uninitialized value $sequence2_new in split at alignment_sequence.pl line 52. Following this warning, there are numerous warning as Use of uninitialized value in string eq at alignment_sequence.pl line 56.I understand it because I have an uninitialized value, but I can't understand how it is uninitialized. My code is following:
#!/usr/in/perl
use warnings;
use strict;
use feature qw(say);
my $infile1 = "cystic_fibrosis.fasta";
my $inFH1;
unless (open($inFH1, "<", $infile1)){
die join (' ', "Can't open", $infile1, $!)
}
my #seq = <$inFH1>;
close $inFH1;
shift #seq;
my $sequence1 = join("", #seq);
$sequence1 =~ s/\n//g;
#parse the query sequence
my $infile2 = "sequence_collection.fasta";
my $inFH2;
unless (open($inFH2, "<", $infile2)){
die join (' ', "Can't open", $infile2, $!)
}
my $beginning = 1;
my #sequence2;
my $sequence2 = "";
while (my $line = <$inFH2>){
chomp $line;
my $chr = substr($line, 0, 1);
if ($chr ne ">"){
$sequence2 = $sequence2.$line;
}else {
if (! $beginning){
push #sequence2, $sequence2;
$sequence2 = "";
}elsif ($beginning){
$beginning = 0;
}
}
}
close $inFH2;
#parse multiple sequence
my $element = scalar(#sequence2);
for ($a = 0; $a < $element; $a++ ){
my $sequence2_new;
if (length $sequence1 < length $sequence2[$a]){
$sequence2_new = substr ($sequence2[$a], 0, length $sequence1);
}
my #sequence1_new = split('', $sequence1);
my #sequence2_new = split('', $sequence2_new);
my $element_new = scalar(#sequence1_new);
my $num = 0;
for ($b = 0; $b < $element_new; $b++){
if ($sequence1_new[$b] eq $sequence2_new[$b]){
$num++;
}
}
my $score = $num / length $sequence1;
say $sequence1;
say $sequence2[$a];
say "\n";
print "The alignment score is: ";
printf("%.2f", $score);
say "\n\n";
}
The file cystic_fibrosis.fasta contains:
>gi|90421313|ref|NP_000483.3| cystic fibrosis transmembrane conductance regulator [Homo sapiens]
MQRSPLEKASVVSKLFFSWTRPILRKGYRQRLELSDIYQIPSVDSADNLSEKLEREWDRELASKKNPKLI
NALRRCFFWRFMFYGIFLYLGEVTKAVQPLLLGRIIASYDPDNKEERSIAIYLGIGLCLLFIVRTLLLHP
AIFGLHHIGMQMRIAMFSLIYKKTLKLSSRVLDKISIGQLVSLLSNNLNKFDEGLALAHFVWIAPLQVAL
LMGLIWELLQASAFCGLGFLIVLALFQAGLGRMMMKYRDQRAGKISERLVITSEMIENIQSVKAYCWEEA
MEKMIENLRQTELKLTRKAAYVRYFNSSAFFFSGFFVVFLSVLPYALIKGIILRKIFTTISFCIVLRMAV
TRQFPWAVQTWYDSLGAINKIQDFLQKQEYKTLEYNLTTTEVVMENVTAFWEEGFGELFEKAKQNNNNRK
TSNGDDSLFFSNFSLLGTPVLKDINFKIERGQLLAVAGSTGAGKTSLLMVIMGELEPSEGKIKHSGRISF
CSQFSWIMPGTIKENIIFGVSYDEYRYRSVIKACQLEEDISKFAEKDNIVLGEGGITLSGGQRARISLAR
AVYKDADLYLLDSPFGYLDVLTEKEIFESCVCKLMANKTRILVTSKMEHLKKADKILILHEGSSYFYGTF
SELQNLQPDFSSKLMGCDSFDQFSAERRNSILTETLHRFSLEGDAPVSWTETKKQSFKQTGEFGEKRKNS
ILNPINSIRKFSIVQKTPLQMNGIEEDSDEPLERRLSLVPDSEQGEAILPRISVISTGPTLQARRRQSVL
NLMTHSVNQGQNIHRKTTASTRKVSLAPQANLTELDIYSRRLSQETGLEISEEINEEDLKECFFDDMESI
PAVTTWNTYLRYITVHKSLIFVLIWCLVIFLAEVAASLVVLWLLGNTPLQDKGNSTHSRNNSYAVIITST
SSYYVFYIYVGVADTLLAMGFFRGLPLVHTLITVSKILHHKMLHSVLQAPMSTLNTLKAGGILNRFSKDI
AILDDLLPLTIFDFIQLLLIVIGAIAVVAVLQPYIFVATVPVIVAFIMLRAYFLQTSQQLKQLESEGRSP
IFTHLVTSLKGLWTLRAFGRQPYFETLFHKALNLHTANWFLYLSTLRWFQMRIEMIFVIFFIAVTFISIL
TTGEGEGRVGIILTLAMNIMSTLQWAVNSSIDVDSLMRSVSRVFKFIDMPTEGKPTKSTKPYKNGQLSKV
MIIENSHVKKDDIWPSGGQMTVKDLTAKYTEGGNAILENISFSISPGQRVGLLGRTGSGKSTLLSAFLRL
LNTEGEIQIDGVSWDSITLQQWRKAFGVIPQKVFIFSGTFRKNLDPYEQWSDQEIWKVADEVGLRSVIEQ
FPGKLDFVLVDGGCVLSHGHKQLMCLARSVLSKAKILLLDEPSAHLDPVTYQIIRRTLKQAFADCTVILC
EHRIEAMLECQQFLVIEENKVRQYDSIQKLLNERSLFRQAISPSDRVKLFPHRNSSKCKSKPQIAALKEE
TEEEVQDTRL
The file sequence_collection.fasta contains 100 similar blocks:
>gi|1100985|gb|AAC48608.1| CFTR chloride channel [Oryctolagus cuniculus]
MQRSPLEKAGVLSKLFFSWTRPILRKGYRQRLELSDIYQIPSADSADNLSEKLEREWDRELASKKNPKLI
NALRRCFFWRFMFYGIFLYLGEVTKAVQPLLLGRIIASYDPDNKEERSIAIYLGIGLCLLFVVRTLLLHP
AIFGLHHIGMQMRIAMFSLIYKKGLALAHFVWISPLQVTLLMGLLWELLQASAFCGLAFLIVLALVQAGL
GRMMMKYRDQRAGKINERLVITSEMIENIQSVKAYCWEEAMEKMIENLRQTELKLTRKAAYVRYFNSSAF
FFSGFFVVFLSVLPYALTKGIILRKIFTTISFCIVLRMAVTRQFPWAVQTWYDSLGAINKIQDFLQKQEY
KTLEYNLTTTEVVMDNVTAFWEEGFGELFEKAKQNNSDRKISNGDNNLFFSNFSLLGAPVLEDISFKIER
GQLLAVAGSTGAGKTSLLMMITGELEPSEGKIKHSGRISFCSQFSWIMPGTIKENIIFGVSYDEYRYRSV
IKACQLEEDISKFTEKDNTVLGEGGITLSGGQRARISLARAVYKDADLYLLDSPFGYLDVLTEKEIFESC
VCKLMANKTRIMVTSKMEHLKKADKILILHEGSSYFYGTFSELQSLRPDFSSKLMGYDSFDQFSAERRNS
ILTETLRRFSLEGDASVSWNDTRKQSFKQNGELGEKRKNSILNPVNSMRKFSIVLKTPLQMNGIEEDSDA
TIERRLSLVPDSEQGEAILPRSNMINTGPMLQGCRRQSVLNLMTHSVSQGPSIYRRTTTSTRKMSLAPQT
NLTEMDIYSRRLSQESGLEISEEINEEDLKECFIDDVDSIPTVTTWNTYLRYITVHRSLIFVLIWCIVIF
LAEVAASLVVLWLFGNTAPQDKENSTKSGNSSYAVIITNTSSYYFFYIYVGVADTLLALGLFRGLPLVHT
LITVSKILHHKMLHSVLQAPMSTLNTLKAGGILNRFSKDIAILDDLLPLTIFDFIQLLLIVVGAIAVVSV
LQPYIFLATVPVIAAFILLRAYFLHTSQQLKQLESEGRSPIFTHLVTSLKGLWTLRAFGRQPYFETLFHK
ALNLHTANWFLYLSTLRWFQMRIEMIFVLFFIAVAFISILTTGEGEGRVGIILTLAMNIMSTLQWAVNSS
IDVDSLMQSVSRVFMFIDMPTEAKSTKSIKPSSNCQLSKVMIIENQHVKKDDVWPSGGQMTVKGLTAKYI
DSGNAILENISFSISPGQRVGLLGRTGSGKSTLLSAFLRLLSTEGEIQIDGVSWDSITLQQWRKAFGVIP
QKVFIFSGTFRKNLDPYEQWSDQEIWKVADEVGLRSVIEQFPGKLDFVLVDGGYVLSHGHKQLMCLARSV
LSKAKILLLDEPSAHLDPITYQIIRRTLKQAFADCTVILCEHRIEAMLECQRFLVIEENTVRQYESIQKL
LSEKSLFRQAISSSDRAKLFPHRNSSKHKSRPQITALKEEAEEEVQGTRL
Sorry I know it's very redundant. I will greatly appreciate any suggestions.

Answer 1

In this code, you do not assign a value to $sequence2_new when the if condition is false. That means it remains undef.
my $sequence2_new;
if (length $sequence1 < length $sequence2[$a]){
$sequence2_new = substr ($sequence2[$a], 0, length $sequence1);
}
Try assigning a value to it:
my $sequence2_new = '';
if (length $sequence1 < length $sequence2[$a]){
$sequence2_new = substr ($sequence2[$a], 0, length $sequence1);
}