Re^2: Opening multiple files in directory

Just wanted to say thanks this helped me a lot making this:

grepcertainfilesgrepcertainlinesandputresultsinfiles.pl

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

# FIND THE PATH TO THE Directory:
 my $dir = $ARGV[0];
 opendir(DIR, $dir) or die $!;
# select for files with names containing txt.fit 
my @files= grep { /txt.fit/ } readdir DIR;
 closedir DIR;

# Read files line by line
foreach my $file(@files) {
 open IN, "<$file" or die $!;
 my $tree = ();
 while(<IN>) {
# skip everything in file not conatining Tree mixture
   next unless ($_ =~ m/Tree mixture/);
# remove content from line thats unwanted in output
   $tree = $_;
   $tree =~s/Tree mixtureTree=//;
}
#name output file after input file but add .tre
my $outfile = "$file.tre";
# here i 'open' the file, saying i want to write to it with the '>>' s
+ymbol
open (FILE, ">> $outfile") || die "problem opening $outfile\n";
print FILE $tree;

}
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Comment on Re^2: Opening multiple files in directory Download Code

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Re^3: Opening multiple files in directory
by Athanasius (Archbishop) on Aug 31, 2014 at 16:50 UTC

I haven’t tried to run this code, but just looking through it there are two obvious problems:

Within a regex, a dot matches any character other than a newline (unless the regex has an /s modifier). So /txt.fit/ matches “mytxt.fit”, but it also matches “yourtxtafit”, “histxt0fitandmore”, etc. You need to backslash the . to make it match a literal dot only: /txt\.fit/; and unless “fit” may be followed by other characters, you want: /txt\.fit$/.

$tree is a scalar variable. Within the inner while loop, each time the line $tree = $_; is executed, it overwrites whatever was in the variable. So when this inner loop finishes, only the last line containing “Tree mixture” is written to the output file. Here is one way to correct this (untested):

foreach my $file (@files)
{
    my $outfile = "$file.tre";

    open(IN,   '<',  $file)    or die $!;
    open(FILE, '>>', $outfile) or die $!;

    while (my $tree = <IN>)
    {
        next unless /Tree mixture/;
        $tree =~ s/Tree mixtureTree=//;
        print FILE $tree;
    }

    close FILE or die $!;
    close IN   or die $!;
}
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Hope that helps,

Athanasius <°(((>< contra mundum Iustus alius egestas vitae, eros Piratica,

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