In unix system
I have a directory called program_sets , and in the program_sets , there exists 8 directory and in each directory they have a program called A.pl
I want to launch and run 8 A.pl programs in the same time , but when I launch the first program , the procedure will be block until the first program call is finish . How can I solve this problems?
here is my code
#!/usr/bin/perl
opendir(Programs,"./program_sets");
#Each_names = readdir(Programs);
shift(#Each_names);
shift(#Each_names);
for($i=0;$i<=$#Each_names;$i++)
{
`perl ./program_sets/$Each_names[$i]/A.pl`;
}
thanks
Run them in the background with &, just like you would from the shell.
for($i=0;$i<=$#Each_names;$i++)
{
system("perl ./program_sets/$Each_names[$i]/A.pl >/dev/null 2>&1 &");
}
Also, backticks should be used when you're assigning the output to a variable. Use system() to run a command without saving the output.
In *NIX, you can add "&" to the command-line to launch the programs in the background.
Another option is to use fork() http://perldoc.perl.org/functions/fork.html
There looks to be some other issues here as well.
#!/usr/bin/perl
# warnings, strict
use warnings;
use strict;
# lexically scoped $dh
#opendir(Programs,"./program_sets");
my $cur_dir = "./program_sets";
opendir(my $dh, $cur_dir);
# what exactly is being shifted off here? "." and ".."??
##Each_names = readdir(Programs);
#shift(#Each_names);
#shift(#Each_names);
# I would replace these three lines with a grep and a meaningful name.
# -d: only directories. /^\./: Anything that begins with a "."
# eg. hidden files, "." and ".."
my #dirs = grep{ -d && $_ !~ /^\./ } readdir $dh;
close $dh;
for my $dir ( #dirs ) {
my $path = "$cur_dir/$dir";
system("perl $path/A.pl >/dev/null 2>&1 &");
}
Related
I have a master Perl script that needs to call another Perl script with options. I read many threads regarding arguments but I need both, arguments and options. Below is my sample code:
sub run_script_a{
my $script_path = "/home/sample/script.pl"
my #ARGS = "input.txt";
##I need to capture the result of the script run and fail if something went wrong
system($^X, $tool_path, #ARGS);
}
I tried the following:
my #ARGS = "input.txt -o output.txt";
It didn't work, gave me this error:
Cannot open input.txt -o output.txt for read: No such file or directory
How do I make it work? The second script runs as:
sample.pl input.txt -o output.txt
I am not good at coding bash scripts so I am using Perl.
my $tool_path = "/home/sample/script.pl"
my #args = "input.txt -o output.txt";
system($tool_path, #args);
is equivalent to the shell command
/home/sample/script.pl "input.txt -o output.txt"
You want
my $tool_path = "/home/sample/script.pl"
my #args = ( "input.txt", "-o", "output.txt" );
system($tool_path, #args);
Actually, if you want to capture the output, there's no need to involve a file. You want
use IPC::System::Simple qw( capturex );
my $tool_path = "/home/sample/script.pl"
my #args = "input.txt";
my $output = capturex($tool_path, #args);
Use backticks to run script with arguments and capture output (perldoc -f qx).
perl -E'say `echo 4 | $^X -p ./script.pl`'
Content of script.pl:
$_**=3
I'm able to do this on the command line and it works :
~/Tools/perl/edif_extr_cell.pl design.edif nmos1p8v | perl -p -e 's/^/\n/ if /portImplementation|figure\s+device/;' | perl -n -000 -e 'print if /portImplementation/;'
(basically, extracting a section of the EDIF file).
Now, I want to make a utility of this. And my script is below. Question : can this code be more efficient? If feel like it's very inelegant. I could pipe streams easily on the command line but, in a script, I feel lost.
#!/usr/bin/perl -w -p
BEGIN{ $file = '';}
s/^/\n/ if /portImplementation|figure\s+device/;
$file .= $_;
END{
$cmd = q{\rm -f /tmp/dump}.$$.'.txt';
system( $cmd );
open( OUT, ">/tmp/dump$$.txt");
print OUT $file;
close OUT;
$out = `perl -n -000 -e 'print if /portImplementation/;' /tmp/dump$$.txt`;
system( $cmd );
print $out;
}
If I understand correct, you want to be able to do
~/Tools/perl/edif_extr_cell.pl design.edif nmos1p8v | myfilter
Ideally, you'd merge the two Perl scripts into one rather than having one script launch two instances of Perl, but this turns out to be rather hard because of the change to $/ (via -00) and because you insert newlines in the first filter.
The simplest answer:
#!/bin/sh
perl -pe's/^/\n/ if /portImplementation|figure\s+device/' |
perl -00ne'print if /portImplementation/'
It appears that you were trying to write the equivalent of that sh script in Perl. It would look like the following:
#!/usr/bin/perl
use strict;
use warnings;
use IPC::Open qw( open3 );
# open3 has issues with lexical file handles.
pipe(local *PIPE_READER, local *PIPE_WRITER)
or die($!);
my $pid1 = open3('<&STDIN', '>&PIPE_WRITER', '>&STDERR',
'perl', '-pes/^/\n/ if /portImplementation|figure\s+device/');
my $pid2 = open3('<&PIPE_READER', '>&STDOUT', '>&STDERR',
'perl', '-00neprint if /portImplementation/');
waitpid($pid1);
waitpid($pid2);
I'd normally recommend IPC::Run3 or IPC::Run for launching and interfacing with child processes, but low-level open3 does the trick nicely in this particular situation.
I downloaded a random EDIF file from GitHub, running the following script on it gives the same output as your code:
#! /usr/bin/perl
use warnings;
use strict;
my #buffer;
my $found;
my $prepend = q();
while (<>) {
if (/portImplementation|figure\s+device/) {
if ($found && #buffer) {
print $prepend, #buffer;
$prepend = "\n";
}
undef $found;
#buffer = ();
}
$found ||= /portImplementation/;
push #buffer, $_;
}
# Don't forget to output the last paragraph!
print $prepend, #buffer if $found && #buffer;
I am writing a script for replacing 2 words from a text file. The script is
count=1
for f in *.pdf
do
filename="$(basename $f)"
filename="${filename%.*}"
filename="${filename//_/ }"
echo $filename
echo $f
perl -pe 's/intime_mean_pu.pdf/'$f'/' fig.tex > fig_$count.tex
perl -pi 's/TitleFrame/'$filename'/' fig_$count.tex
sed -i '/Pointer-rk/r fig_'$count'.tex' $1.tex
count=$((count+1))
done
But the replacing of words using the second perl command is giving error:
Can't open perl script "s/TitleFrame/Masses1/": No such file or directory
Please suggest what I am doing wrong.
You could change your script to something like this:
#!/bin/bash
for f in *.pdf; do
filename=$(basename "$f" .pdf)
filename=${filename//_/}
perl -spe 's/intime_mean_pu.pdf/$a/;
s/TitleFrame/$b/' < fig.tex -- -a="$f" -b="$filename" > "fig_$count.tex"
sed -i "/Pointer-rk/r fig_$count.tex" "$1.tex"
((++count))
done
As well as some other minor changes to your script, I have made use of the -s switch to Perl, which means that you can pass arguments to the one-liner. The bash variables have been double quoted to avoid problems with spaces in filenames, etc.
Alternatively, you could do the whole thing in Perl:
#!/usr/bin/env perl
use strict;
use warnings;
use autodie;
use File::Basename;
my $file_arg = shift;
my $count = 1;
for my $f (glob "*.pdf") {
my $name = fileparse($f, qq(.pdf));
open my $in, "<", $file_arg;
open my $out, ">", 'tmp';
open my $fig, "<", 'fig.tex';
# copy up to match
while (<$in>) {
print $out $_;
last if /Pointer-rk/;
}
# insert contents of figure (with substitutions)
while (<$fig>) {
s/intime_mean_pu.pdf/$f/;
s/TitleFrame/$name/;
print $out $_;
}
# copy rest of file
print $out $_ while <$in>;
rename 'tmp', $file_arg;
++$count;
}
Use the script like perl script.pl "$1.tex".
You're missing the -e in the second perl call
I tried to use some unix tools inside a perl driver script because I knew little about writing shell script. My purpose is to just combine a few simple unix commands together so I can run the script on 100 directories in one perl command.
The task is I have more than 100 folders, in each folder, there are n number of files. I want to do the same thing on each folder, which is to combine the files in them and sort the combined file and use bedtools to merge overlapping regions (quite common practice in bioinformatics)
Here is what I have:
#!/usr/bin/perl -w
use strict;
my $usage ="
This is a driver script to merge files in each folder into one combined file
";
die $usage unless #ARGV;
my ($in)=#ARGV;
open (IN,$in)|| die "cannot open $in";
my %hash;
my $final;
while(<IN>){
chomp;
my $tf = $_;
my #array =`ls $tf'/.'`;
my $tmp;
my $tmp2;
foreach my $i (#array){
$tmp = `cut -f 1-3 $tf'/'$i`;
$tmp2 = `cat $tmp`;
}
my $tmp3;
$tmp3=`sort -k1,1 -k2,2n $tmp2`;
$final = `bedtools merge -i $tmp3`;
}
print $final,"\n";
I know that this line isn't working at all..
$tmp2 = `cat $tmp`;
The issue is how to direct the output into another variable in perl and use that variable later on in another unix command...
Please let me know if you can point out where I can change to make it work. Greatly appreciated.
The output from backticks usually includes newlines, which usually have to be removed before using the output downstream. Add some chomp's to your code:
chomp( my #array =`ls $tf'/.'` );
my $tmp;
my $tmp2;
foreach my $i (#array){
chomp( $tmp = `cut -f 1-3 $tf'/'$i` );
chomp( $tmp2 = `cat $tmp` );
}
my $tmp3;
chomp( $tmp3=`sort -k1,1 -k2,2n $tmp2` );
$final = `bedtools merge -i $tmp3`;
To use a perl variable in the shell, this is an example :
#!/usr/bin/env perl
my $var = "/etc/passwd";
my $out = qx(file $var);
print "$out\n";
For the rest, it's very messy. You should take the time learning perl and not mixing coreutils commands and Perl, where perl itself is a better tool to do the whole joke.
OK. I gave it up on perl and decided to give it a try using shell script. It worked!!
Thanks for the above answers though!
for dir in `ls -d */`
do
name=$(basename $dir /)
cd $dir
for file in `ls`
do
cut -f 1-3 $file > $file.tmp
done
for x in `ls *tmp`
do
cat $x >> $name.tmp1
done
sort -k1,1 -k2,2n $name.tmp1 > $name.tmp2
bedtools merge -i $name.tmp2 > $name.combined
done
I'm writing a code to find the file which not contain a string pattern. Provided I have a list of files, I have to look into the content of each file, I would like to get the file name if the string pattern "clean" not appear inside the file. Pls help.
Here is the scenario:
I have a list of files, inside each file is having numerous of lines. If the file is clean, it will have the "clean" wording. But if the file is dirty, the "clean" wording not exist and there will be no clear indication to tell the file is dirty. So as long as inside each file, if the "clean" wording is not detect, I'll category it as dirty file and I would like to trace the file name
You can use a simple one-liner:
perl -0777 -nlwE 'say $ARGV if !/clean/i' *.txt
Slurping the file with -0777, making the regex check against the entire file. If the match is not found, we print the file name.
For perl versions lower than 5.10 that do not support -E you can substitute -E with -e and say $ARGV with print "$ARGV".
perl -0777 -nlwe 'print "$ARGV\n" if !/clean/i' *.txt
If you need to generate the list within Perl, the File::Finder module will make life easy.
Untested, but should work:
use File::Finder;
my #wanted = File::Finder # finds all ..
->type( 'f' ) # .. files ..
->name( '*.txt' ) # .. ending in .txt ..
->in( '.' ) # .. in current dir ..
->not # .. that do not ..
->contains( qr/clean/ ); # .. contain "clean"
print $_, "\n" for #wanted;
Neat stuff!
EDIT:
Now that I have a clearer picture of the problem, I don't think any module is necessary here:
use strict;
use warnings;
my #files = glob '*.txt'; # Dirty & clean laundry
my #dirty;
foreach my $file ( #files ) { # For each file ...
local $/ = undef; # Slurps the file in
open my $fh, $file or die $!;
unless ( <$fh> =~ /clean/ ) { # if the file isn't clean ..
push #dirty, $file; # .. it's dirty
}
close $fh;
}
print $_, "\n" for #dirty; # Dirty laundry list
Once you get the mechanics, this can be simplified a la grep, etc.
One way like this:
ls *.txt | grep -v "$(grep -l clean *.txt)"
#!/usr/bin/perl
use strict;
use warnings;
open(FILE,"<file_list_file>");
while(<FILE>)
{
my $flag=0;
my $filename=$_;
open(TMPFILE,"$_");
while(<TMPFILE>)
{
$flag=1 if(/<your_string>/);
}
close(TMPFILE);
if(!$flag)
{
print $filename;
}
}
close(FILE);