Empty lines in a files using Perl

[lewindha]

Hello al

I am working on a BioInformatics assignment and I am using Perl to parse a few input files. I am new to Perl. Here is my question:

I am using this to parse the lines:

($ID, $Rest) = split ( " ", $_, 2);

The first variable is an ID and the rest of the line is a description.

My problem is when a line is blank or empty. My program terminates giving this error:

use of unitialized string in concatenation . or string a line 33.

I get one of these for every line that is blank. Can anyone tell me how to just ignore blank lines?

Thanks

[sykkn]

Try something like this:

$someVar .= $Rest if($Rest);


This is as much as I can tell you without a little more of the code you are using.

[lewindha]

I'm sorry. The input file is a little different than I described earlier.

The lines in the file look like this:

1.1.1.1 00010 00071 00120 00350 00561

I want to create an output file like so:

1.1.1.1 00010
1.1.1.1 00071
1.1.1.1 00120
1.1.1.1 00350
1.1.1.1 00561

Here is the code that I am using:

#!/usr/bin/perl -w
use FileHandle;

print "Type the name of the input file: ";
$in_file = <STDIN>;
chomp ($in_file);

$_ = $in_file;


$dot_index = rindex($in_file, ".");

$out_file = substr($in_file, 0, $dot_index) . ".dat";

open(INFILE, $in_file) || die "Can't open $in_file: $!";
open(OUT, ">$out_file") || die "Can't create $out_file: $!";

while(<INFILE>) {
chomp;

($ID, $Rest) = split ( ' ', $_, 2) if ($ID);

@maps = split ( ' ', $Rest) if ($ID);

$i = 0;

while ( @maps )
{
print $ID;
print OUT "$ID\t$maps[$i]\n";
$i++;
}

}

close(INFILE) || die "Can't close $in_file: $!";
close(OUT) || die "Can't close $out_file: $!";

I made the changes you suggested. I don't get errors any more, but it doesn't write to the output file. Thanks for the help.

[genlee]

I made a few changes to your while loop you might want to look at.

while&#40;<INFILE>&#41; &#123;
chomp;
                                                                                
&#40;@line&#41;= split&#40;' ', $_&#41;;
$len=@line;
$i=1;
while &#40;$i < $len&#41; &#123;
  print "$line&#91;0&#93;\n";
  print OUT "$line&#91;0&#93;\t$line&#91;$i&#93;\n";
  $i++;
&#125;

That works correctly on my box with the test line you gave me. If you want, I can probably shorten a few more lines.

[lewindha]

That worked. Thank you very much.

One more problem:

The input file has ID numbers that come in the form 'x.x.x.x'

Some of them are full like

1.1.1.1
1.1.1.21

but some come like this:

1.1.1.-
1.-.-.-

I need to disregard the IDs that are not full ( the ones with dashes instead of numbers ).

How do I check for this? I've read about the /d flag, but how do I use it correctly?

Thanks again

[genlee]

Revision #2

while&#40;<INFILE>&#41; &#123;
chomp;
if &#40;!/-/&#41; &#123;                                                                     
&#40;@line&#41;= split&#40;' ', $_&#41;;
$i=0;
while&#40;$i < @line&#41; &#123;
  print "$line&#91;0&#93;\n";
  print OUT "$line&#91;0&#93;\t$line&#91;$i&#93;\n";
  $i++;
&#125;
&#125;                                                                     
&#125;

[lewindha]

You are a life saver. Thank you.

One more question and I'll leave you alone

In the input file, some lines look like this:

1.1.1.10 00040

When I run the script, the second element in the array is ' 00040'. I need it to be '00040'.

How do I fix this?

Thanks again

[Dolda2000]

Try (@line) = split(' +', $_);

[genlee]

Revision #3. The foreach line should run through the @line array and remove any white space in an element. Though I am not sure how you were getting spaces since we were using ' ' to split up the line.

while&#40;<INFILE>&#41; &#123;
chomp;
if&#40;! /-/&#41; &#123;
&#40;@line&#41;= split&#40;' ', $_&#41;;
$i=1;
foreach &#40;@line&#41; &#123;s/ //;&#125;
while&#40;$i < @line&#41; &#123;
  print "$line&#91;0&#93;\n";
  print OUT "$line&#91;0&#93;\t$line&#91;$i&#93;\n";
  $i++;
&#125;
&#125;
&#125;

[lewindha]

Hey guys

Thanks a lot for all of your help. I've almost got it. The revision you sent ,genlee, that contained:

foreach (@line) {s/ //};

did not work so I still have that problem. I suppose that it means to replace all white space in a value with nothing. I don't know why it doesn't work, but I still get variables with white space like
' 00010'.

I'm still working on it. If you have any other suggestions, please let me know.

Thanks again