lomSpace has asked for the wisdom of the Perl Monks concerning the following question:

Hello, How do you print the return value from a subroutine to a file?
Particularly, when you are using pass by value. 
#!/usr/bin/perl -w
use strict;
use FileHandle;
use Data::Dumper;

open(my $in1, "/Users/mydir/Desktop/hw3_infile1.txt");
open(my $report, ">/Users/mydir/Desktop/hw3_report.txt");
my @aa_seqs = ("MPIGSKERPTFFEIFKTRCNKADLGPIS", "MDLSALRVEEVQNVINAMQKIL
+ECPIC", "MDLSAVQIQEVQNVLHAMQKILECPICLE");
my @nt_seqs = ("atgccgctaccgt", "cgcctagcgccgcatta","ccgtaggcattc", "g
+acctaggtcag");

#call subroutines

#pass by value $report

print $report "Values returned via pass by value:\n";
my @oligo_array = get_oligo_seqs($in1); # pass by value
print  "@oligo_array\n";
close($in1);

#print results
print  $report "Before calling subroutine:\n";
for my $aa_seqs(@aa_seqs){
    print $report "$aa_seqs\n";
}

print  $report "\n";
for my $nt_seqs(@nt_seqs){
    print $report "$nt_seqs\n";
}
print $report "\n";

#pass by reference
change_array(\@aa_seqs, \@nt_seqs);
#print results
print  $report "After calling subroutine:\n";
for my $aa_seqs(@aa_seqs){
    print $report "$aa_seqs\n";
}
print $report "\n";
for my $nt_seqs(@nt_seqs){
    print $report "$nt_seqs\n";
}
close($report);

######## Subroutines #########

sub get_oligo_seqs{
    my ($fh) = shift;
    
    while(<$fh>){
        my @fields = split /\t/;
        my $oligos = $fields[1];
        print "$oligos\n";
    }
}
    
sub change_array{
    my ($aa, $nt) = @_;
    push(@$nt, 'ggacttacgggccatataa');
    shift(@$aa);
}

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Replies are listed 'Best First'.
Re: printing sub return values to a file
by ikegami (Patriarch) on Nov 19, 2009 at 07:03 UTC
    You write to a file using 
    print $fh EXPR;

    [download]

    EXPR can be any expression, including a subroutine call.

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Re: printing sub return values to a file
by cdarke (Prior) on Nov 19, 2009 at 08:41 UTC
    So far as I can see your subroutines do not explicitly return anything. With no return statement they will return the value of the last statement within them. That's fine for change_array, but the line my @oligo_array = get_oligo_seqs($in1); looks suspicious to me, since get_oligo_seqs does not return an array (I think it will give a single element containing an empty string).

    I wonder if you are confusing the print statement with a return?
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      I think it will give a single element containing an empty string
      Not that it much matters, but it probably returns 1 (the return value of a successful print). The exceptions are if print fails for some reason, or if the file handled by $fh is empty—in which latter case I would have guessed that the return value would be $fh, but Data::Dumper suggests that it's ''—or, I suppose, if $fh isn't a readable filehandle, in which case something else happens.
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      Hi cdarke!
      I made a change to the subroutine, but it only returns the first element.
      Any ideas on how I can get around that to return the all of the elements?
      Read more... (420 Bytes)

      LomSpace
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        The following will loop through all lines of the input file (assuming you opened the file prior to calling the sub), populate the array, then return the array. I think your code was exiting the sub after reading only one line. 
        sub get_oligo_seqs{
    my ($fh) = shift;
    my @seqs;
    while(<$fh>){
        my @fields = split /\t/;
        my $oligos = $fields[1];
        push(@seqs,($oligos));
    }
    return @seqs;
}

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