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

Dear all, I am getting a new error regarding the PRINT function. I have never had this error and have gotten no clue from a bit of googling. Any help is appreciated.

Can't locate object method "PRINT" via package "IO::File" at addFeatInfo2clusterinfo.pl line 63. 

use strict;
use warnings;
use Data::Dumper;

my $in_clustInfo=$ARGV[0] || "output.clusterinfo";
open (IN,"<" ,$in_clustInfo);
my %HoMS2lines;
while (my $line=<IN>){
        chomp $line;
        my @cols=split(/\t/,$line);
        my $clust_indx=$cols[0];
        my $mz=$cols[2];
        my $rt=$cols[15];
        $HoMS2lines{$clust_indx}{mz}=$mz;
        $HoMS2lines{$clust_indx}{rt}=$rt;
        $HoMS2lines{$clust_indx}{line}=$line;
}
#print Dumper(%HoMS2lines);
close(IN);
##

my $in_featsInfo=$ARGV[1];
open (IN,"<" ,$in_featsInfo);
my %HoMS1feats;
while (my $line=<IN>){
        chomp $line;
        my @cols=split(/\t/,$line);
        my $mz=$cols[5];
        my $rt=$cols[6];
        my $feat=$cols[4];
        my $metab=$cols[10];
        $HoMS1feats{$feat}{mz}=$mz;
        $HoMS1feats{$feat}{rt}=$rt;
        $HoMS1feats{$feat}{metab}=$metab;
        $HoMS1feats{$feat}{line}=$line;
}
close(IN);
#print Dumper(%HoMS1feats);
##
my $out="$in_clustInfo.featsadded.txt";
open (OUT,">",$out);
##
my $mz_ppmWin=10;
my $rt_win=10;

foreach my $clust (keys %HoMS2lines){
        my $mz=$HoMS2lines{$clust}{'mz'}; 
        my $mz_win=($mz*$mz_ppmWin)/1000000;
        my $rt=$HoMS2lines{$clust}{'rt'};
        foreach my $feat (keys %HoMS1feats){
                my $ftmz=$HoMS1feats{$feat}{'mz'};
                my $ftrt=$HoMS1feats{$feat}{'rt'};
                my $ftmetab=$HoMS1feats{$feat}{'metab'};
                if (($ftmz < $mz+$mz_win && $ftmz > $mz-$mz_win) && ($
+ftrt < $rt+$rt_win && $ftrt > $mz-$rt_win)){
                        PRINT OUT join("\t",$HoMS2lines{$clust}{'line'
+},$feat,$ftmz,$ftrt,$ftmetab)."\n";
                }
                else{
                        PRINT OUT join("\t",$HoMS2lines{$clust}{'line'
+},"no matchin feat","NA","NA","NA")."\n";
                }
        }
}

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Replies are listed 'Best First'.
Re: Can't locate print error
by choroba (Cardinal) on Dec 03, 2015 at 10:18 UTC
    Perl is case sensitive. PRINT and print are two different strings. You wanted to use print. 
    ($q=q:Sq=~/;[c](.)(.)/;chr(-||-|5+lengthSq)`"S|oS2"`map{chr |+ord
}map{substrSq`S_+|`|}3E|-|`7**2-3:)=~y+S|`+$1,++print+eval$q,q,a,

    [download]
[reply]
[d/l]
[select]
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[d/l]
[select]
        Indirect object notation. Method names aren't checked for existence before runtime. 
        ($q=q:Sq=~/;[c](.)(.)/;chr(-||-|5+lengthSq)`"S|oS2"`map{chr |+ord
}map{substrSq`S_+|`|}3E|-|`7**2-3:)=~y+S|`+$1,++print+eval$q,q,a,

        [download]
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[d/l]
Re: Can't locate print error
by marto (Cardinal) on Dec 03, 2015 at 10:19 UTC

    The PRINT OUT... lines should be print OUT..., print in lower case, like your commented out examples of using print.

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[d/l]
[select]
      oops sorry. I was progrming in another language for a few months, and I guess forgot a few things. thanks
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