Push, big file. Correct and improvement - perl

Question

dummy.pepmasses
YCL049C 1 511.2465 0 0 MFSK
YCL049C 2 4422.3098 0 0 YLVTASSLFVA
YCL049C 3 1131.5600 0 0 DFYQVSFVK
YCL049C 4 1911.0213 0 0 SIAPAIVNSSVIFHDVSR
YCL049C 5 774.4059 0 0 GVAMGNVK
YCL049C 6 261.1437 0 0 SR
my $dummyfile = "dummy.pepmasses"; #filename defined here
my #mzco = ();
open (IFILE, $dummyfile) or die "unable to open file $dummyfile\n ";
while (my $line = $dummyfile){
#read each line in file
chomp $line;
my $mz_value = (split/\s+/,$line)[3]; #pick column 3rd at every line
$mz_value = join "\n"; # add "\n" for data
push (#mzco,$mz_value); #add them all in one array #mzco
}
print "#mzco";
close IFILE;
There should be better way to express this one. How can it be ?
I want to pick up the third column and push it into an array. Are there better methods?

Answer 1

I'll just go through your code and comment
open (IFILE, $dummyfile) or die "unable to open file $dummyfile\n ";
You should use 3-argument open with explicit mode, and a lexical file handle. Also, you should not include newline in the die message unless you want to suppress line number. You should also include the error, $!.
open my $fh, "<", $dummyfile or die "Unable to open $dummyfile: $!";
while (my $line = $dummyfile){
#read each line in file
No, this just copies the file name. To read from the file handle, do this:
while (my $line = <IFILE>) {
Or <$fh> if you use a lexical file handle.
chomp $line;
my $mz_value = (split/\s+/,$line)[3]; #pick column 3rd at every line
This is actually the 4th column, since indexes start at zero 0.
$mz_value = join "\n"; # add "\n" for data
join does not work that way. It is join EXPR, LIST to join a list of values into a string. You want the concatenation operator .:
$mz_value = $mz_value . "\n";
Or more appropriately:
$mz_value .= "\n";
But why do it that way? It is simpler to just add the newline when you print.
print "#mzco";
You can do this:
print "$_\n" for #mzco;
Or if you are feeling daring:
use feature 'say';
say for #mzco;
And just to show you the power of Perl, this program can be reduced to a one-liner, using a lot of built-in features:
perl -lane ' print $F[3] ' dummy.pepmasses
-l chomp lines, add newline (by default) to print
-n put while (<>) loop around code: read input file or stdin
-a autosplit each line into #F.
The program as a file would look like this:
$\ = $/; # set output record separator to input record separator
while (<>) {
chomp;
my #F = split;
print $F[3];
}