Even though I answered this on StackOverflow, I'll paste my solution here for completeness purposes:
Here's one way using split() hackery:
#!/usr/bin/perl
use strict;
use warnings;
my $f1 = 'file1.txt';
my $f2 = 'file2.txt';
my @pdb;
open my $pdb_file, '<', $f2
or die "Can't open the PDB file $f2: $!";
while (my $line = <$pdb_file>){
chomp $line;
push @pdb, $line;
}
close $pdb_file;
open my $shifts_file, '<', $f1
or die "Can't open the SHIFTS file $f1: $!";
while (my $line = <$shifts_file>){
chomp $line;
my $pdb_line = shift @pdb;
# - inner split: get the third element from the $pdb_line
# - outer split: get the first element (character) from the
# result of the inner split
my $criteria = (split('', (split('\s+', $pdb_line))[2]))[0];
# - compare the 2nd element of the file1.txt line against
# the above split() operations
if ((split('\s+', $line))[1] eq $criteria){
print "$pdb_line\n";
}
else {
print "**** >$pdb_line< doesn't match >$line<\n";
}
}
Files:
file1.txt (note I changed line two to ensure a non-match worked):
1 H 35
1 A 22
1 H 20
file2.txt:
A 1 HB2 MET 1
A 2 CA MET 1
A 3 HA MET 1
Output:
./app.pl
A 1 HB2 MET 1
****>A 2 CA MET 1< doesn't match >1 A 22<
A 3 HA MET 1
-stevieb
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