Re^5: Key value pair in hash inside while loop

If that's all you want for output, the following would do that.

#!/usr/bin/perl
use strict;
use warnings;
use Inline::Files;

my %data;
while (<A>) {
    chomp;
    my (undef, $fragment, undef, $pos) = split /\t/;
    $data{$pos} = $fragment;
}

<B>; # throw away header '300     dG = -62.54 ...'
while (<B>) {
    my $pos = (split /\t/)[0];
    print "$data{$pos} $pos\n" if $data{$pos};
}

__A__
1-Match:    GGTGTTGTATGCCTTTAAA    5    3545
2-Match:    GGAAAGTCAAGCCCATCTA    9    3254
3-Match:    GTTCTTATTTGCACCTACT    6    180
4-Match:    GATGAGGAACAGCAACCTT    5    844
__B__
300     dG = -62.54   [initially -70.70] gi178893_M23263_rna_300-1 
1    G    0    2    0    1
2    A    1    3    0    2
3    A    2    4    0    3
4    U    3    5    0    4
5    U    4    6    0    5
6    C    5    7    0    6
7    C    6    8    0    7
8    G    7    9    34    8
9    G    8    10    33    9
........
........
179    A    178    180    231    179
180    G    179    181    230    180
181    U    180    182    229    181
........
........
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Comment on Re^5: Key value pair in hash inside while loop Download Code

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Re^6: Key value pair in hash inside while loop by newtoperlprog (Sexton) on Aug 28, 2014 at 20:01 UTC
Thanks Cristoforo, I modified the code as suggested by you but I thing the program is giving me error of uninitialized values. #!/usr/bin/perl -w + use strict; use warnings; my $matchfile = "match_super.dat"; my $ctfile = "M23263_rna_300-1.dat_1.ct"; my @match;my %data;my $fragment; my $pos; open (A, "<", $matchfile) or die "Check the file $!\n"; while (my $line = <A>) { chomp $line; (undef, $fragment, undef, $pos) = split(/\t/, $line); $data{$pos} = $fragment; } close (A); my ($num1, $base, $num2, $num3, $connect, $num4); open (B, "<", $ctfile) or die "Check the file $!\n"; while (my $ctline = <B>) { chomp $ctline; if ($ctline =~ /^(\d+\s+dG.*)/) { # print "$1\n"; next; + next; } $pos = (split /\s+/)[0]; print "$data{$pos} $pos\n" if $data{$pos}; } close (B); [download] Error: Use of uninitialized value $pos in hash element at ./second_str_map.pl + line 29, <B> line 298. Use of uninitialized value $_ in split at ./second_str_map.pl line 28, + <B> line 299. Use of uninitialized value $pos in hash element at ./second_str_map.pl + line 29, <B> line 299. Use of uninitialized value $_ in split at ./second_str_map.pl line 28, + <B> line 300. Use of uninitialized value $pos in hash element at ./second_str_map.pl + line 29, <B> line 300. Use of uninitialized value $_ in split at ./second_str_map.pl line 28, + <B> line 301. Use of uninitialized value $pos in hash element at ./second_str_map.pl + line 29, <B> line 301. [download]	[reply] [d/l] [select]
Re^7: Key value pair in hash inside while loop by Cristoforo (Curate) on Aug 28, 2014 at 20:55 UTC
Change `$pos = (split /\s+/)[0];` to `$pos = (split /\s+/, $ctline)[0];`	[reply] [d/l] [select]