I'm attempting to assign the Linux system command top -n1 to an array and then eliminate the first seven lines of the text that is written to a text file. When I go to print elements from my array, I get an error saying use of uninitialized value. Can someone show what I'm doing wrong when assigning my array to the system command? Thank you.
Edit: I might also add, I'm looking to delete the first seven lines by using array slicing.
sub processlist
{
my $num_of_lines = 0;
my #top_command = `top -bn1 >toptmp.txt`;
#opening temp file, and output file.
open(my $in, '<' , "toptmp.txt") or die "Can't read the file: $!"; #file used for initial reading
open(my $out, '>', "top.txt") or die "can't write to file: $!";
print $top_command[0], "\n";
#looping deleting first 7 lines
while(<$in>)
{
if($num_of_lines > 6) #starts writing to top.txt past line 7 (counting starts at 0)
{
print $out $_;
}
$num_of_lines++;
}
close $out;
close $in;
system("rm toptmp.txt"); #erasing tmp file.
}
Use instead
top -bn1 | tail -n +8
No need to reinvent the wheel when the tail command will already do what you want
You are writing the top results to a file, if you want to get them to the variable you should not do that.
Use top -bn1 instead of top -bn1 >toptmp.txt
Related
This question already has answers here:
How to get the current line number of a file opened using Perl
(3 answers)
Closed 3 years ago.
I've made a Perl script to list the contents of a specified file, but I also want to see the line number of the file content. What functions in Perl enable this?
This is my code:
#!/usr/local/bin/perl
use warnings;
use strict;
print "Specify the file you want to look at:\n";
my $file_name = <STDIN>;
chomp $file_name;
open(FH, '<', $file_name) or die "Cannot open $file_name: $!";
print "This is the listed content of: $file_name\n";
while(<FH>){
print $_;
}
close(FH);
This is what happens when I run the script, and this is what I would like it to do.
Actual result Wished result
Hello 1. Hello
my 2. my
name 3. name
is 4. is
Janne 5. Janne
You can do something like this:
my $line_n = 1;
while(<FH>){
print "$line_n. $_";
$line_n++;
}
I would like to add a unique one line header that pertains to each file FOCUS*.tsv file in a specified directory. After that, I would like to combine all of these files into one file.
First I’ve tried sed command.
`my $cmd9 = `sed -i '1i$SampleID[4]' $tsv_file`;` print $cmd9;
It looked like it worked but after I’ve combined all of these files into one file in the next section of the code, the inserted row was listed four times for each file.
I’ve tried the following Perl script to accomplish the same but it deleted the content of the file and only prints out the added header.
I’m looking for the simplest way to accomplish what I’m looking for.
Here is what I’ve tried.
#!perl
use strict;
use warnings;
use Tie::File;
my $home="/data/";
my $tsv_directory = $home."test_all_runs/".$ARGV[0];
my $tsvfiles = $home."test_all_runs/".$ARGV[0]."/tsv_files.txt";
my #run_directory = (); #run_directory = split /\//, $tsv_directory; print "The run directory is #############".$run_directory[3]."\n";
my $cmd = `ls $tsv_directory/FOCUS*\.tsv > $tsvfiles`; #print "$cmd";
my $cmda = "ls $tsv_directory/FOCUS*\.tsv > $tsvfiles"; #print "$cmda";
my #tsvfiles =();
#this code opens the vcf_files.txt file and passes each line into an array for indidivudal manipulation
open(TXT2, "$tsvfiles");
while (<TXT2>){
push (#tsvfiles, $_);
}
close(TXT2);
foreach (#tsvfiles){
chop($_);
}
#this loop works fine
for my $tsv_file (#tsvfiles){
open my $in, '>', $tsv_file or die "Can't write new file: $!";
open my $out, '>', "$tsv_file.new" or die "Can't write new file: $!";
$tsv_file =~ m|([^/]+)-oncomine.tsv$| or die "Can't extract Sample ID";
my $sample_id = $1;
#print "The sample ID is ############## $sample_id\n";
my $headerline = $run_directory[3]."/".$sample_id;
print $out $headerline;
while( <$in> ) {
print $out $_;
}
close $out;
close $in;
unlink($tsv_file);
rename("$tsv_file.new", $tsv_file);
}
Thank you
Apparently, the wrong '>' when opening the file for reading was the problem and it got solved.
However, I'd like to make a few comments on some of the rest of the code.
The list of files is built by running external ls redirected to a file, then reading this file into an array. However, that is exactly the job of glob and all of that is replaced by
my #tsvfiles = glob "$tsv_directory/FOCUS*.tsv";
Then you don't need the chomp either, and the chop that is used would actually hurt since it removes the last character, not only the newline (or really $/).
Use of chop is probably not what you want. If you are removing the linefeed ($/) use chomp
To extract a match and assign it, a common idiom is
my ($sample_id) = $tsv_file =~ m|([^/]+)-oncomine.tsv$|
or die "Can't extract Sample ID: $!";
Note that I also added $!, to actually print the error. Otherwise we just don't know what it was.
The unlink and rename appear to be overwriting one file with another. You can do that by using move from the core module File::Copy
use File::Copy qw(move);
move ($tsv_file_new, $tsv_file)
or die "Can't move $tsv_file to $tsv_file_new: $!";
which renames the _new into $tsv_file, so overwriting it.
As for how the files need to be combined, more precise explanation would be needed.
Closed. This question is not reproducible or was caused by typos. It is not currently accepting answers.
This question was caused by a typo or a problem that can no longer be reproduced. While similar questions may be on-topic here, this one was resolved in a way less likely to help future readers.
Closed 8 years ago.
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I'm writing a Perl script that searches a kml file and I need to print a very long line of latitude/longitude coordinates. The following script successfully finds the string I'm looking for, but just prints a blank line instead of the value of the string:
#!/usr/bin/perl
# Strips unsupported tags out of a QGIS-generated kml and writes a new one
$file = $ARGV[0];
# read existing kml file
open( INFO, $file ); # Open the file
#lines = <INFO>; # Read it into an array
close(INFO); # Close the file
#print #lines; # Print the array
$x = 0;
$coord_string = "<coordinates>";
# go through each line looking for above string
foreach $line (#lines) {
$x++;
if ( $x > 12 ) {
if ( $line =~ $coord_string ) {
$thisCooordString = $line;
$var_startX = $x;
print "Found coord string: $thisCoordString\n";
print " on line: $var_startX\n";
}
}
}
The file that it's reading is here
and this is the output I get:
-bash-4.3$ perl writekml.pl HUC8short.kml
Found coord string:
on line: 25
Found coord string:
on line: 38
Is there some cap on the maximum length that a string can be in Perl? The longest line in this file is ~151,000 characters long. I've verified that all the lines in the file are read successfully.
You've misspelled the variable name (two os vs three os):
$thisCooordString = $line;
...
print "Found coord string: $thisCoordString\n";
Add use strict and use warnings to your script to prevent these sorts of errors.
Always include use strict and use warnings in EVERY perl script.
If you had done this, you would've gotten the following error message to clue you into your bug:
Global symbol "$thisCoordString" requires explicit package name
Adding these pragmas and simplifying your code results in the following:
#!/usr/bin/env perl
# Strips unsupported tags out of a QGIS-generated kml and writes a new one
use strict;
use warnings;
local #ARGV = 'HUC8short.kml';
while (<>) {
if ( $. > 12 && /<coordinates>/ ) {
print "Found coord string: $_\n";
print " on line: $.\n";
}
}
You can even try with perl one liners as shown below:
Perl One liner on windows command prompt:
perl -lne "if($_ =~ /<coordinates>/is && $. > 12) { print \"Found coord string : $_ \n"; print \" on line : $. \n\";}" HUC8short.kml
Perl One liner on unix prompt:
perl -lne 'if($_ =~ /<coordinates>/is && $. > 12) { print "Found coord string : $_ \n"; print " on line : $. \n";}' HUC8short.kml
As others have pointed out, you need. No, you MUST always use use strict; and use warnings;.
If you used strict, you would have gotten an error message telling you that your variable $thisCoordString or $thisCooordString was not declared with my. Using warnings would have warned you that you're printing an undefined string.
Your whole program is written in a very old (and obsolete) Perl programming style. This is the type of program writing I would have done back in Perl 3.0 days about two decades ago. Perl has changed quite a bit since then, and using the newer syntax will allow you to write easier to read and maintain programs.
Here's your basic program written in a more modern syntax:
#! /usr/bin/env perl
#
use strict; # Lets you know when you misspell variable names
use warnings; # Warns of issues (using undefined variables
use feature qw(say); # Let's you use 'say' instead of 'print' (No \n needed)
use autodie; # Program automatically dies on bad file operations
use IO::File; # Lots of nice file activity.
# Make Constants constant
use constant {
COORD_STRING => qr/<coordinates>/, # qr is a regular expression quoted string
};
my $file = shift;
# read existing kml file
open my $fh, '<', $file; # Three part open with scalar filehandle
while ( my $line = <$fh> ) {
chomp $line; # Always "chomp" on read
next unless $line =~ COORD_STRING; #Skip non-coord lines
say "Found coord string: $line";
say " on line: " . $fh->input_line_number;
}
close $fh;
Many Perl developers are self taught. There is nothing wrong with that, but many people learn Perl from looking at other people's obsolete code, or from reading old Perl manuals, or from developers who learned Perl from someone else back in the 1990s.
So, get some books on Modern Perl and learn the new syntax. You might also want to learn about things like references which can lead you to learn Object Oriented Perl. References and OO Perl will allow you to write longer and more complex programs.
I want to write a perl program for opening a file and reading its content and the printing the number of lines, words and characters there are. I also want to print the number of times a specific word appeared in the file. Here is what I have done:
#! /usr/bin/perl
open( FILE, "test1.txt" ) or die "could not open file $1";
my ( $line, $word, $chars ) = ( 0, 0, 0 );
while (<FILE>) {
$line++;
$words += scalar( split( /\s+/, $_ ) );
$chars += length($_);
print $_;
}
$chars -= $words;
print(
"Total number of lines in the file:= $line \nTotal number of words in the file:= $words \nTotal number of chars in the file:= $chars\n"
);
As you can clearly see, I don't have any provision for taking user input of the words whose occurrence is to be counted. Because I don't know how to do it. Please help with counting of the number of occurrence part. Thank you
I guess you're doing this for learning purposes, so here is a good readable version of your problem (there might be a thousand others, because it's perl). If not, there's wc on the linxux command line.
Note that I'm using three argument open, it's generally better to do that.
For counting single words you'll most probably need a hash. And I used <<HERE docs, because they are nicer for formating. If you have any doubts, just look in the perldoc and ask your questions.
#!/usr/bin/env perl
use warnings; # Always use this
use strict; # ditto
my ($chars,$word_count ,%words);
{
open my $file, '<', 'test.txt'
or die "couldn't open `test.txt':\n$!";
while (<$file>){
foreach (split){
$word_count++;
$words{$_}++;
$chars += length;
}
}
} # $file is now closed
print <<THAT;
Total number of lines: $.
Total number of words: $word_count
Total number of chars: $chars
THAT
# Now to your questioning part:
my $prompt= <<PROMPT.'>>';
Please enter the words you want the occurrences for. (CTRL+D ends the program)
PROMPT
print $prompt;
while(<STDIN>){
chomp; # get rid of the newline
print "$_ ".(exists $words{$_}?"occurs $words{$_} times":"doesn't occur")
." in the file\n",$prompt;
}
This question already has an answer here:
Why does my file content/user input not match? (missing chomp canonical) [duplicate]
(1 answer)
Closed 8 years ago.
I'm pretty new in perl so please try to understand me.
I have in a .txt file defined some lines like this:
doc1.20131010.zip
doc2.20131010.zip
doc3.20131010.zip
doc4.20131010.zip
I made this code:
#! /usr/bin/env perl
use strict;
use warnings;
use feature qw(say);
use autodie;
use Net::SFTP::Attributes;
use Net::SFTP;
use constant {
HOST => "x.x.x.x",
USER_NAME => "sftptest",
PASSWORD => "**********",
DEBUG => "0",
};
my $REMOTE_DIR = "IN";
my $LOCAL_DIR = "/home/rec";
my $sftp = Net::SFTP->new (
HOST,
timeout => 240,
user => USER_NAME,
password => PASSWORD,
autodie => 1,
);
#
# Fetch Files
#
#my $res = $sftp->ls($REMOTE_DIR,sub { print $_[0]{longname}, "\n" });
#print "$res";
my $ls = $sftp->ls($REMOTE_DIR)
or die "ls failed: " . $sftp->error;
open my $fh, '>', '/home/rec/listing' or die "unable to create file: $!";
print $fh $_->{filename}, "\n" for #$ls;
close $fh;
open F, "</home/docs/listing";
for my $line (<F>)
{
#print "$line";
$sftp->get("$line","$line") ;
}
Now when I run the above code it should give me the above files listed, instead I get this:
Couldn't stat remote file: No such file or directory at ./r.pl line 40.
You probably need to remove newline after reading file names from filehandle:
for my $line (<F>) {
chomp($line);
$sftp->get($line, $line);
}
or more commonly,
while (my $line = <F>) {
chomp($line);
$sftp->get($line, $line);
}
You use use autodie;, yet you have:
open my $fh, '>', '/home/rec/listing' or die "unable to create file: $!";
No need for the or die... since the program will automatically die.
You also have use feature qw(say);, yet you use print instead of say. The whole purpose of say is to prevent issues that might be the cause of your error.
You also should check the return results of your $sftp->get($line, $line); line to see if it was successful or not.
If you did both of these, you would have seen that your $sftp->get($line, $line) was failing because you forgot to chomp that NL at the end of the file.
Instead, you used:
`print $line;`
which printed the file out, but since the file name had a NL, it looked fine. Otherwise, you would have see the extra space and immediately seen the problem.