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

Hello! I got a weird print output for the line of code: print "******processing <<<<${file}>>>\n\n"; One output is ******processing <<<</home/user/projects/database/bwa/index_bwa_human_b36_both.fasta.tar.gz>>> Another output is actually the following which is weird >>>***processing <<<</home/user/projects/database/bwa/index_bwa_human_b36_both.fasta.index.tar.gz.md5 The input file where I got the file name has the following line: 
[13:06 yunfei@bcl code]$ cat -T -E ../src/db_names | grep "hg18ibwa"
$g18ibwa^Iindex_bwa_human_b36_both.fasta.tar.gz^Iindex_bwa_human_b36_b
+oth.fasta.index.tar.gz.md5

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The code for reading file names is (file path is added thereafter by $file="$dir/$file";) 
102         while(<DBNAME>) {
103                 next if /^#/;
104                 1 while (chomp);
105                 s/ +/\t/g;
106                 s/\t+/\t/g;
107                 my @tmp=split('\t',$_);
108                 my $item=shift @tmp;
109                 $down_name{$item}=\@tmp;
110         }

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Also when I try 
130                         if ($file =~/(zip$)|(gz$)|(tar$)|(bz$)|(bz
+2$)/i) {
131                                 $untar{$file}=$untar_dir;
132                                 print STDERR "Got $file another ta
+r file\n";
133                         } elsif ($file =~/md5$/i) {
134                                 my ($source_file)= $file=~/(.*)\.m
+d5$/i;
135                                 print STDERR "Source file $source_
+file\n";
136                         }

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I only got output from line 132 but never from line 135. Any idea what's wrong here? Thank you very much! I'm new to this place, hope I'm asking the question at the right place.

Replies are listed 'Best First'.
Re: weird print output
by kcott (Archbishop) on Sep 30, 2012 at 21:07 UTC

    G'day yunfei,

    Welcome to the monastery.

    Please provide a self-contained piece of code which reproduces your problem. (Guidelines for doing this can be found in: How do I post a question effectively?)

    The following code simulates what you're describing but does not reproduce the problem. 

    #!/usr/bin/env perl

use strict;
use warnings;

while (my $file = <DATA>) {
    print '-' x 60, "\n";
    chomp $file;
    print "******processing <<<<${file}>>>\n\n";

    if ($file =~/(zip$)|(gz$)|(tar$)|(bz$)|(bz2$)/i) {
        print "IF: $file\n";
    }
    elsif ($file =~/md5$/i) {
        print "ELSIF: $file\n";
    }

    print '-' x 60, "\n";
}

__DATA__
/home/user/projects/database/bwa/index_bwa_human_b36_both.fasta.tar.gz
/home/user/projects/database/bwa/index_bwa_human_b36_both.fasta.index.
+tar.gz.md5

    [download]

    Output:

    $ pm_weird_print.pl
------------------------------------------------------------
******processing <<<</home/user/projects/database/bwa/index_bwa_human_
+b36_both.fasta.tar.gz>>>

IF: /home/user/projects/database/bwa/index_bwa_human_b36_both.fasta.ta
+r.gz
------------------------------------------------------------
------------------------------------------------------------
******processing <<<</home/user/projects/database/bwa/index_bwa_human_
+b36_both.fasta.index.tar.gz.md5>>>

ELSIF: /home/user/projects/database/bwa/index_bwa_human_b36_both.fasta
+.index.tar.gz.md5
------------------------------------------------------------

    [download]

    In your while(<DBNAME>) {...} loop, it would be useful to show the raw data before and after modification as well as how that ties in with $file="$dir/$file";.

    Also, please correct the typo in the title: s/wired/weird/

    -- Ken

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[d/l]
[select]
Re: weird print output
by jwkrahn (Abbot) on Oct 01, 2012 at 00:32 UTC

    In your second example you have a "\r" (carriage return) at the end of the file name.

[reply]

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