separate data and print to two files

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

Hello, I need to parse a file and print to two files. The records go to different files
based on whether the values in field[0] has a dash and a number at the end of the string
or not. Example: 10002TU or 10002TU-2.

#!/usr/bin/perl -w
use strict;
use warnings;


open(my $reg_out, ">C:/Documents and Settings/mydir/Desktop/RegularOli
+gos.txt");
open(my $irreg_out, ">C:/Documents and Settings/mydir/Desktop/Irregula
+rOligos.txt");
open(my $out, ">C:/Documents and Settings/mydir/Desktop/mfrp.txt");
my $first_line = <$in>;
chomp $first_line;

while(<DATA>){
    chomp;
    my @fields = split /\t/;
    my $maid = $fields[0];
    my $forward = $fields[1];
    my $reverse = $fields[2];
    my $probe = $fields[3];
    if ($probe =~ /^\d{5}TU|TD$/){
        print $reg_out "$maid\t$forward\t$reverse\t$probe\n";
    }
    else{
        print $irreg_out "$maid\t$forward\t$reverse\t$probe\n";
    }
}
#close $in;
close $irreg_out;
close $reg_out;

__DATA__
10002TU    AGACATTACCTGTGAGACACCTTTC    GCCTCCACCTCAGAGTCAG    TCCATGG
+GAAGGATCTCCGTGAAATCA
10002TU-2    GCTCCAGCTAGAAGAGAATCC    CCCACCAGGGCTGTGTAAG    CCTGTGAGA
+TAGTACAGCTGAAGAGTTGGC
10002TD    TGTGTTGATTCTCAGCCTCTTG    GACGGAGCACATAGGCAAAG    TCTGTTCTT
+CTCAGCTGTCTTTGTTGCTGC
10003TU    CAGCAAGCCCTGAGGTGTG    CAGTGAACTGAGAAAGACGAGAGG TGCAAGTCCAG
+ATGGAGGCCACC
10174TU-2    ACCTGAACAGCCTGACATGAAC    TGGGATGGAGGGCAAAGTC    CCACCTAG
+TATGACCCAGCACACCTCC
[download]

Any direction will be appreciated.

Comment on separate data and print to two files Download Code

Replies are listed 'Best First'.
Re: separate data and print to two files by zwon (Abbot) on Jul 08, 2009 at 18:42 UTC
Isn't `$probe =~ /^\d{5}TU\|TD$/` [download] should be `$maid =~ /^\d{5}TU\|TD$/` [download]	[reply] [d/l] [select]
Re^2: separate data and print to two files by lomSpace (Scribe) on Jul 08, 2009 at 18:50 UTC
Yeah, I just figured out the SIMPLE mistake! Thanks anyway! Lom Space	[reply]
Re: separate data and print to two files by toolic (Bishop) on Jul 08, 2009 at 18:55 UTC
Since you did not specify, I will assume your Regular file will contain the dashes. If this does not do what you want, then you must show the desired output: use strict; use warnings; open my $reg_out , '>', 'RegularOligos.txt' or die "can not open fi +le RegularOligos.txt:$!"; open my $irreg_out, '>', 'IrregularOligos.txt' or die "can not open fi +le IrregularOligos.txt:$!"; while(<DATA>){ chomp; my @fields = split; my $line = join "\t", @fields; if ($fields[0] =~ /-/){ print $reg_out "$line\n"; } else{ print $irreg_out "$line\n"; } } close $irreg_out; close $reg_out; __DATA__ 10002TU AGACATTACCTGTGAGACACCTTTC GCCTCCACCTCAGAGTCAG TCCATGGG +AAGGATCTCCGTGAAATCA 10002TU-2 GCTCCAGCTAGAAGAGAATCC CCCACCAGGGCTGTGTAAG CCTGTGAGA +TAGTACAGCTGAAGAGTTGGC 10002TD TGTGTTGATTCTCAGCCTCTTG GACGGAGCACATAGGCAAAG TCTGTTCTT +CTCAGCTGTCTTTGTTGCTGC 10003TU CAGCAAGCCCTGAGGTGTG CAGTGAACTGAGAAAGACGAGAGG TGCAAGTCCAG +ATGGAGGCCACC 10174TU-2 ACCTGAACAGCCTGACATGAAC TGGGATGGAGGGCAAAGTC CCACCTAGT +ATGACCCAGCACACCTCC [download]	[reply] [d/l]
Re^2: separate data and print to two files by graff (Chancellor) on Jul 08, 2009 at 19:47 UTC
... I will assume your Regular file will contain the dashes. Actually, it appears to be the other way around. And here's an even simpler way (no need to split): #!/usr/bin/perl use strict; use warnings; my @filenames = qw/Reg Irreg/; my %ofh = map { open( my $fh, ">", $_.'ularOlios.txt' ) or die $!; $_ => $fh + } @filenames; while (<DATA>) { my $o = ( /^\w+-/ ) ? $ofh{Irreg} : $ofh{Reg}; print $o $_; } close $_ for ( values %ofh ); __DATA__ 10002TU AGACATTACCTGTGAGACACCTTTC GCCTCCACCTCAGAGTCAG TCCATGGG +AAGGATCTCCGTGAAATCA 10002TU-2 GCTCCAGCTAGAAGAGAATCC CCCACCAGGGCTGTGTAAG CCTGTGAG +ATAGTACAGCTGAAGAGTTGGC 10002TD TGTGTTGATTCTCAGCCTCTTG GACGGAGCACATAGGCAAAG TCTGTTCT +TCTCAGCTGTCTTTGTTGCTGC 10003TU CAGCAAGCCCTGAGGTGTG CAGTGAACTGAGAAAGACGAGAGG TGCAAGTC +CAGATGGAGGCCACC 10174TU-2 ACCTGAACAGCCTGACATGAAC TGGGATGGAGGGCAAAGTC CCACCTAG +TATGACCCAGCACACCTCC [download]	[reply] [d/l]