Hi PerlMonks!

I'm not sure if this is a valid question to ask, but I can't debug a program and thus I require your help!

#!/usr/bin/perl
use Modern::Perl;
use File::Slurp qw/read_file write_file/;

my $uniprot = 'D:\\ARP\\Downloads\\uniprot-sfinal.txt';
my $activin = 'D:\\ARP\\Downloads\\Activator-Pfam.txt';
my $antioxin = 'D:\\ARP\Downloads\\AntiOxidant-Pfam.txt';
my $toxinin= 'D:\\ARP\\Downloads\\Toxin-Pfam.txt';


my $activout = 'D:\\ARP\\Downloads\\ActivACNPF.txt';
my $antioxout= 'D:\\ARP\\Downloads\\AntioxACNPF.txt';
my $toxinout= 'D:\\ARP\\Downloads\\ToxinACNPF.txt';
my @activline;
my @antioxline;
my @toxinline;

my %activ = map { /(.+)\s+\|\s+(PF.{5})/; $1 => $2 } read_file $activi
+n;
my %antiox = map{ /(.+)\s+\|\s+(PF.{5})/; $1 => $2 } read_file $antiox
+in;
my %toxin = map { /(.+)\s+\|\s+(PF.{5})/;$1=> $2} read_file $toxinin;
for ( read_file $uniprot ) {
/(.{6})\s+.+=([^\s]+)/;
push @activline, "$1 $2 $activ{$1}\n" if $activ{$1};
push @antioxline, "$1 $2 $antiox{$1}\n" if $antiox{$1};
push @toxinline, "$1 $2 $antiox{$1}\n" if $antiox{$1};
}

write_file $activout, @activline;
write_file $antioxout, @antioxline;
write_file $toxinout, @toxinline;

print STDOUT "DONE\n";

[download]

This is a program I'm writing for my research project. Here's a few lines from each input file:

D:\\ARP\\Downloads\\uniprot-sfinal.txt

Q6GZX4 ORFNames=FV3-001R ;PF04947
Q6GZX3 ORFNames=FV3-002L ;PF03003
Q197F8 ORFNames=IIV3-002R 
Q197F7 ORFNames=IIV3-003L 
Q6GZX2 ORFNames=FV3-003R 
Q6GZX1 ORFNames=FV3-004R 
Q197F5 ORFNames=IIV3-005L

[download]

D:\\ARP\\Downloads\\Activator-Pfam.txt

Q6GZX4 | PF04947.9
Q96355 | PF01486.12 PF00319.13
Q96356 | PF01486.12 PF00319.13
Q39371 | PF01486.12 PF00319.13

[download]

D:\\ARP\Downloads\\AntiOxidant-Pfam.txt

D0EYG3 | PF10262.4
E7QVU5 | PF10417.4 PF00578.16
D1JAS4 | PF10417.4 PF00578.16

[download]

D:\\ARP\\Downloads\\Toxin-Pfam.txt

C7T183 | PF02950.12
C7T1P5 | PF02950.12
E2E4E4 | PF00918.12
A2PU44 | PF01375.12

[download]

The error codes I got were as shown

Use of uninitialized value in list assignment at ARP//positivedatasetextractor.pl line 18

Line 18: my %activ = map { /(.+)\s+\|\s+(PF.{5})/; $1 => $2 } read_file $activin;

Use of uninitialized value in list assignment at ARP//positivedatasetextractor.pl line 20

Line 20: my %toxin = map { /(.+)\s+\|\s+(PF.{5})/;$1=> $2} read_file $toxinin;

Use of uninitialized value $1 in hash element at ARP//positivedatasetextractor.pl Line 23

Line 23: push @activline, "$1 $2 $activ{$1}\n" if $activ{$1};

Use of uninitialized value $1 in hash element at ARP//positivedatasetextractor.pl Line 24

Line 24: push @antioxline, "$1 $2 $antiox{$1}\n" if $antiox{$1};

Use of uninitialized value $1 in hash element at ARP//positivedatasetextractor.pl Line 25

Line 25: push @toxinline, "$1 $2 $antiox{$1}\n" if $antiox{$1};

I know this is pretty long, but I have no idea how to debug this, so I'm posting this here for help. Thanks in advance!

Update: Thanks for your help, everyone! Well, I have further problems which use the same datasets, but is quite unrelated to this matter, so I'll be posting it on another new thread. Thanks again!

In reply to Debugging help! by invaderzard

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