Sorry about the lack of information. The data file itself is ~1000 lines of DNA sequence (e.g. NNNNNNAAACCTAGGAATACGCGT) separated by linebreaks. Again, it's very simple code, which is what makes this so frustrating:
#!/usr/bin/perl
use warnings;
use strict;
my $filename = 'T7.fa';
open(DNA, $filename);
my @lines = <DNA>;
close DNA;
chomp(@lines);
my $genome = join('',@lines);
print "$genome\n";
When I run this, I get no error messages, but $genome only prints out what appears to be a concatenation of the last two lines: roughly NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN.
In lieu of join, I tried the dot operator like this:
... # <DNA> opened
my $genome = '';
while (<DNA>) {
chomp($_);
$genome.=$_;
}
close(<DNA>);
print "$genome\n";
This too gives no errors and returns a short string of Ns. When I print $genome after each iteration of the while loop it doesn't seem to be adding to the string, but rather erasing the old string and inserting JUST the current line. As I mentioned before, in Windows, both versions return what I expect...a "paragraph" of ~20000 bases. I DO have the same problem on a SuSE 9.0 installation, which I believe includes 5.8.0, but haven't tried anything earlier. Packages that are obviously Perl-driven all seem to work fine on my machine. Thanks so much! | [reply]
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I think you have a line seperator problem. DOS lines end with CR LF. Unix lines end with LF. If you're reading a DOS text file in unix, the chomp will remove the LF but leave the CR in, causing every line being printed to apear on top of each other. Try $/ = "\x0D\x0A"; before the read, or try adding $genome =~ s/\x0D//g; or try using the following:
#!/usr/bin/perl
use warnings;
use strict;
my $filename = 'T7.fa';
open(DNA, $filename);
my $genome;
{ local $/; $genome = <DNA>; }
close DNA;
$genome =~ s/\x0D\x0A//g;
print "$genome\n";
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Thanks ikegami. Your suggestion did the trick! I would have never figured that out on my own.
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