Getting error while replacing word using perl - perl

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

Related

Perl wildcards in the file paths

I am working on my project where the GNU Makefile should automatically test my Perl program with different input files. I have this code which reads only one file from inputs directory, searches stop words and outputs out.txt file with frequency table of non-stop words.
#!/usr/bin/perl
use strict;
use warnings;
use Lingua::StopWords qw(getStopWords);
my %found;
my $src = '/programu-testavimas/1-dk/trunk/tests/inputs/test.txt';
my $des = '/programu-testavimas/1-dk/trunk/tests/outputs/out.txt';
open(SRC,'<',$src) or die $!;
open(DES,'>',$des) or die $!;
my $stopwords = getStopWords('en');
while( my $line = <SRC>){
++$found{$_} for grep { !$stopwords->{$_} }
split /\s+/, lc $line;
}
print DES $_, "\t\t", $found{$_}, $/ for sort keys %found;
close(SRC);
close(DES);
My goal is to test many files with separate case.sh scripts where the input files should be different in each case, this is one of the case:
#!/bin/sh
perl /programu-testavimas/1-dk/trunk/scripts/test.pl /programu-testavimas/1-dk/trunk/tests/inputs/test.txt > /home/aleksandra/programų-testavimas/1-dk/trunk/tests/outputs/out.txt
Then, my Makefile at once should test program with different inputs in each case. So, right now I'm struggling with my Perl code where my input file is only one individual and I need to make it read different files in inputs directory. How can I change path correctly that bash scripts could have each case with individual input file?
EDIT: I tried this with glob function but it outputs empty file
open(DES,'>',$des) or die $!;
my $stopwords = getStopWords('en');
for my $file ( glob $src ) {
open(SRC,'<',$file) or die "$! opening $file";
while( my $line = <SRC>){
++$found{$_} for grep { !$stopwords->{$_} }
split /\s+/, lc $line;
}
print DES $_, "\t\t", $found{$_}, $/ for sort keys %found;
close(SRC);
}
close(DES);
Correct me if I'm wrong, but to me it sounds like you have different shell scripts, each calling your perl script with a different input, and redirecting your perl's script output to a new file.
You don't need to glob anything in your perl script. It already has all the information it needs: which file to read. Your shell script/Makefile is handling the rest.
So given the shell script
#!/bin/sh
perl /path/to/test.pl /path/to/input.txt > /path/to/output.txt
Then in your perl script, simply read from the file provided via the first positional parameter:
#!/usr/bin/perl
use strict;
use warnings;
use Lingua::StopWords qw(getStopWords);
my %found;
my $stopwords = getStopWords('en');
while(my $line = <>) {
++$found{$_} for grep { !$stopwords->{$_} }
split /\s+/, lc $line;
}
print $_, "\t\t", $found{$_}, $/ for sort keys %found;
while(<>) will read from STDIN or from ARGV.
Your shell script could then call your perl script with different inputs and define outputs:
#!/bin/sh
for input in /path/to/*.txt; do
perl /path/to/test.pl "$input" > "$input.out"
done

How to extract a specific string using perl?

I have set of strings say "-f /path/filename1.f", "-f $path/filename2.f", etc in a single file file.f I want to read file.f and extract /path/filename1.f, $path/filename2.f, etc in another file.
I tried finding solution online but it looks like a mess.
Is there any clean and simple solution there for these kind of simple pattern searching?
below is the requirement
Example,
file.f (input file to perl script)
-f /path/filename1.f
-f $path1/filename2.f
-f /path/filename3.f
-f $path2/filename4.f
outputfile.f
/path/filename1.f
$path1/filename2.f
/path/filename3.f
$path2/filename4.f
Basically I just want path string from the file.f
Some perl code to solve your problem:
use strict;
use warnings;
open my $fhi, "<", "file.f" or die "Error: $!";
open my $fho, ">", "output.f" or die "Error: $!";
while( <$fhi> ) { # Read each line in $_ variable
s/^-f //; # Remove "-f " at the beginning of $_
print $fho $_; # print $_ to output.f file
}
close $fhi;
close $fho;
The simplest way is using cut:
cut -f2 -d’ ‘ input_file > output_file
Or you can use Perl:
perl -lane ‘print $F[1]’ input_file > output_file
These solutions extract the second field of the input and print it.
Look into the below solution -
Here everything after -f will be taken out.
#!/usr/bin/perl
use strict;
use warnings;
open(FILE,"<file.f");
while(<FILE>)
print "$1\n" if($_ =~ /^-f\s(.*)/);
}

perl : making a script as efficient as a perl one-liner

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;

unix functions inside perl

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

One-liner Perl command to rename files

So far this one-liner is stripping off one line and renaming the file, but I need help to alter it so that it strips that line I am looking for Data for and remove the old file extension .csv instead of adding to it. (.csv.out). I am not sure if this can be done with one-liner.
Instead it's adding on the the extension filename.csv.out
Example
test_20110824.csv.out
One-liner:
find -type f -name '*.csv' -exec perl -i.out -wlne '/^Data for/ or print' {} \;
I want to replace the extension:
test_20110824.out
perl -MFile::Copy -we 'for (glob "*.csv") { my ($name) = /^(.+).csv/i; move($_, $name . ".out"); }'
To remove the header matching Data for:
perl -MFile::Copy -MTie::File -wE 'for (glob '*x.csv') { tie my #file,
"Tie::File", $_ or die $!; shift #file if $file[0] =~ /^Data for/;
untie #file; my ($name) = /^(.*).csv/i; move($_, $name . ".out"); }'
But then it's really not a one-liner anymore...
use strict;
use warnings;
use Tie::File;
use File::Copy;
use autodie;
for (#ARGV) {
tie my #file, "Tie::File", $_;
shift #file if $file[0] =~ /^Data for/;
untie #file;
my ($name) = /^(.*).csv/i;
move($_, $name . ".out");
}
And use with:
$ script.pl *.csv
A simple Bash shell script will suffice
(shopt -s failglob; for i in *.csv.out; do echo mv $i ${i%csv.out}out; done)
The shopt -s failglob is needed to ensure that if there are no matches the command will fail instead of trying to rename *.csv.out to *.out. The construct ${i%csv.out}out removes a trailing csv.out and replaces it with just out.
As I have coded it here, this will just echo the commands it would execute. When you're satisfied it does what you want, remove the word echo.