Searching for two matches in perl - perl

I'm looking for a way to match two terms in a single string. For instance if I need to match both "foo" and "bar" in order for the string to match and be printed, and the string is "foo 121242Z AUTO 123456KT 8SM M10/M09 SLP02369", it would not match. But if the string was "foo 121242Z AUTO 123456KT 8SM bar M10/M09 SLP02369", it would match and then go on to be printed. Here's the code that I have currently but I am a bit stuck. Thanks!
use strict;
use warnings;
use File::Find;
use Cwd;
my #folder = ("/d2/aschwa/archive_project/METAR_data/");
open(OUT , '>', 'TEKGEZ_METARS.txt') or die "Could not open $!";
print OUT "Date (YYYYMMDD), Station, Day/Time, Obs Type, Wind/Gust (Kt), Vis (SM),
Sky, T/Td (C), Alt, Rmk\n";
print STDOUT "Finding METAR files\n";
my $criteria = sub {if(-e && /^/) {
open(my $file,$_) or die "Could not open $_ $!\n";
my $dir = getcwd;
my #dirs = split ('/', $dir);
while(<$file>) {
$_ =~ tr/\015//d;
print OUT $dirs[-1], ' ', $_ if /foo?.*bar/;
}
}
};
find($criteria, #folder);
close OUT;
print STDOUT "Done Finding Station METARS\n";

Why not just simple:
perl -ne'print if /foo.*bar/'
If you want process more files from some directory use find
find /d2/aschwa/archive_project/METAR_data/ -type f -exec perl -MFile::Spec -ne'BEGIN{$dir = (File::Spec->splitdir($ARGV[0]))[-2]} print $dir, ' ', $_ if /foo.*bar/' {} \; > TEKGEZ_METARS.txt

You can achieve it with positive look-ahead for both strings:
print OUT $dirs[-1], ' ', $_ if m/(?=.*foo)(?=.*bar)/;

#!/usr/bin/perl
use warnings;
use strict;
my $string1 = "foo 121242Z AUTO 123456KT 8SM M10/M09 SLP02369";
my $string2 = "foo 121242Z AUTO 123456KT 8SM bar M10/M09 SLP02369";
my #array = split(/\s+/, $string2);
my $count = 0;
foreach (#array){
$count++ if /foo/;
$count++ if /bar/;
}
print join(" ", #array), "\n" if $count == 2;
This will print for $string2, but not for $string1

Related

perl- extract duplicate sequences from a multi-fasta file

I have a big fasta file input.fasta which consists many duplicate sequences. I want to enter a header name and extract out all the sequences with the matching header. I know this could be done easily done with awk/sed/grep but I need a Perl code.
input.fasta
>OGH38127_some_organism
PAAALGFSHLARQEDSALTPKHYTWTAPGEGDVRAPCPVLNTLANHEFLPHNGKNITVDK
AITALGDAMNISPALATTFFTGGLKTNPTPNATWFDLDMLHKHNVLEHDGSLSRRDMHFD
TSNKFDAATFANFLSYFDANATVLGVNETADARARHAYDMSKMNPEFTITSSMLPIMVGE
SVMMMLVWGSVEEPGAQRDYFEYFFRNERLPVELGWTPGETEIGVPVVTAMITAMVAASP
TDVP
>ABC14110_some_different_org_name
WWVAPGPGDSRGPCPGLNTLANHGYLPHDGKGITLSILADAMLDGFNIARSDALLLFTQ
AIRTSPQYPATNSFNLHDLGRDQLNRHNVLEHDASLSRADDFFGSNHIFNETVFDESRAY
AMLANSKIARQINSKAFNPQYKFTSKTEQFSLGEIAAPIIAFGNSTSGEVNRTLVEYFFM
NERLPIELGWKKSEDGIALDDILRVTQMISKAASLITPSALSWTAETLTP
>OGH38127_some_organism
LPWSRPGPGAVRAPCPMLNTLANHGFLPHDGKNISEARTVQALGRALNIEKELSQFLFEK
ALTTNPHTNATTFSLNDLSRHNLLEHDASLSRQDAYFGDNHDFNQTIFDETRSYWPHPVI
DIQAAALSRQARVNTSIAKNPTYNMSELGLDFSYGETAAYILILGDKDFGKVNRSWVEYL
FENERLPVELGWTRHNETITSDDLNTMLEKVVN
.
.
.
I have tried with the following script but it is not giving any output.
script.pl
#!/perl/bin/perl -w
use strict;
use warnings;
print "Enter a fasta header to search for:\n";
my $head = <>;
my $file = "input.fasta";
open (READ, "$file") || die "Cannot open $file: $!.\n";
my %seqs;
my $header;
while (my $line = <READ>){
chomp $line;
$line =~ s/^>(.*)\n//;
if ($line =~ m/$head/){
$header = $1;
}
}
close (READ);
open( my $out , ">", "out.fasta" ) or die $!;
my #count_seq = keys %seqs;
foreach (#count_seq){
print $out $header, "\n";
print $out $seqs{$header}, "\n";
}
exit;
Please help me correct this script.
Thanks!
If you use the Bioperl module Bio::SeqIO to handle the parsing of the fasta files, it becomes really simple:
#!/usr/bin/perl
use warnings;
use strict;
use Bio::SeqIO;
my ($file, $name) = #ARGV;
my $in = Bio::SeqIO->new(-file => $file, -format => "fasta");
my $out = Bio::SeqIO->new(-fh => \*STDOUT, -format => "fasta");
while (my $s = $in->next_seq) {
$out->write_seq($s) if $s->display_id eq $name;
}
run with perl grep_fasta.pl input.fasta OGH38127_some_organism
There's no need to store the sequences in memory, you can print them directly when reading the file. Use a flag variable ($inside in the example) that tells you whether you're reading the desired sequence or not.
#! /usr/bin/perl
use warnings;
use strict;
my ($file, $header) = #ARGV;
my $inside;
open my $in, '<', $file or die $!;
while (<$in>) {
$inside = $1 eq $header if /^>(.*)/;
print if $inside;
}
Run as
perl script.pl file.fasta OGH38127_some_organism > output.fasta

Make the same edit for edit for each column in a multi-column file

I have multiple CSV files with varying numbers of columns that I need to reformat into a fixed-format text file.
At this stage, I hash and unhash the columns that need to be edited, but its tedious and I can't add new columns without changing the program first.
Is there a simpler way of reading, splitting and editing all columns, regardless of the number of columns in the file?
Here is my code thus far:
use strict;
use warnings;
my $input = 'FILENAME.csv';
my $output = 'FILENAME.txt';
open (INPUT, "<", "$input_file") or die "\n !! Cannot open $input_file: $!";
open (OUTPUT, ">>", "$output_file") or die "\n !! Cannot create $output_file: $!";
while ( <INPUT> ) {
my $line = $_;
$line =~ s/\s*$//g;
my ( $a, $b, $c, $d, $e, $f, $g, $h, $i, $j ) = split('\,', $line);
$a = sprintf '%10s', $a;
$b = sprintf '%10s', $b;
$c = sprintf '%10s', $c;
$d = sprintf '%10s', $d;
$e = sprintf '%10s', $e;
$f = sprintf '%10s', $f;
$g = sprintf '%10s', $g;
$h = sprintf '%10s', $h;
$i = sprintf '%10s', $i;
$j = sprintf '%10s', $j;
print OUTPUT "$a$b$c$d$e$f$g$h$i$j\n";
}
close INPUT;
close OUTPUT;
exit;
Do you mean something like this?
perl -aF/,/ -lne 'print map sprintf("%10s", $_), #F' FILENAME.csv > FILENAME.txt
Any time you're using sequential variables, you should be using an array. And in this case, since you only use the array once, you don't even need to do more than hold it temporarily.
Also: Use lexical filehandles, it's better practice.
#!/usr/bin/env perl
use strict;
use warnings;
my $input_file = 'FILENAME.csv';
my $output_file = 'FILENAME.txt';
my $format = '%10s';
open( my $input_fh, "<", $input_file ) or die "\n !! Cannot open $input_file: $!";
open( my $output_fh, ">>", $output_file ) or die "\n !! Cannot create $output_file: $!";
while (<$input_fh>) {
print {$output_fh} join "", map { sprintf $format, $_ } split /,/;
}
close $input_fh;
close $output_fh;
exit;

How to replace string dynamically using perl script

I am trying to solve below issues.
I have 2 files. Address.txt and File.txt. I want to replace all A/B/C/D (File.txt) with corresponding string value (Read from Address.txt file) using perl script. It's not replacing in my output file. I am getting same content of File.txt.
I tried below codes.
Here is Address.txt file
A,APPLE
B,BAL
C,CAT
D,DOG
E,ELEPHANT
F,FROG
G,GOD
H,HORCE
Here is File.txt
A B C
X Y X
M N O
D E F
F G H
Here is my code :
use strict;
use warnings;
open (MYFILE, 'Address.txt');
foreach (<MYFILE>){
chomp;
my #data_new = split/,/sm;
open INPUTFILE, "<", $ARGV[0] or die $!;
open OUT, '>ariout.txt' or die $!;
my $src = $data_new[0];
my $des = $data_new[1];
while (<INPUTFILE>) {
# print "In while :$src \t$des\n";
$_ =~ s/$src/$des/g;
print OUT $_;
}
close INPUTFILE;
close OUT;
# /usr/bin/perl -p -i -e "s/A/APPLE/g" ARGV[0];
}
close (MYFILE);
If i Write $_ =~ s/A/Apple/g;
Then output file is fine and A is replacing with "Apple". But when dynamically coming it's not getting replaced.
Thanks in advance. I am new in perl scripting language . Correct me if I am wrong any where.
Update 1: I updated below code . It's working fine now. My questions Big O of this algo.
Code :
#!/usr/bin/perl
use warnings;
use strict;
open( my $out_fh, ">", "output.txt" ) || die "Can't open the output file for writing: $!";
open( my $address_fh, "<", "Address.txt" ) || die "Can't open the address file: $!";
my %lookup = map { chomp; split( /,/, $_, 2 ) } <$address_fh>;
open( my $file_fh, "<", "File1.txt" ) || die "Can't open the file.txt file: $!";
while (<$file_fh>) {
my #line = split;
for my $char ( #line ) {
( exists $lookup{$char} ) ? print $out_fh " $lookup{$char} " : print $out_fh " $char ";
}
print $out_fh "\n";
}
Not entirely sure how you want your output formatted. Do you want to keep the rows and columns as is?
I took a similar approach as above but kept the formatting the same as in your 'file.txt' file:
#!/usr/bin/perl
use warnings;
use strict;
open( my $out_fh, ">", "output.txt" ) || die "Can't open the output file for writing: $!";
open( my $address_fh, "<", "address.txt" ) || die "Can't open the address file: $!";
my %lookup = map { chomp; split( /,/, $_, 2 ) } <$address_fh>;
open( my $file_fh, "<", "file.txt" ) || die "Can't open the file.txt file: $!";
while (<$file_fh>) {
my #line = split;
for my $char ( #line ) {
( exists $lookup{$char} ) ? print $out_fh " $lookup{$char} " : print $out_fh " $char ";
}
print $out_fh "\n";
}
That will give you the output:
APPLE BAL CAT
X Y X
M N O
DOG ELEPHANT FROG
FROG GOD HORCE
Here's another option that lets Perl handle the opening and closing of files:
use strict;
use warnings;
my $addresses_txt = pop;
my %hash = map { $1 => $2 if /(.+?),(.+)/ } <>;
push #ARGV, $addresses_txt;
while (<>) {
my #array;
push #array, $hash{$_} // $_ for split;
print "#array\n";
}
Usage: perl File.txt Addresses.txt [>outFile.txt]
The last, optional parameter directs output to a file.
Output on your dataset:
APPLE BAL CAT
X Y X
M N O
DOG ELEPHANT FROG
FROG GOD HORCE
The name of the addresses' file is implicitly popped off of #ARGV for use later. Then, a hash is built, using the key/value pairs in File.txt.
The addresses' file is read, splitting each line into its single elements, and the defined-or (//) operator is used to returned the defined hash item or the single element, which is then pushed onto #array. Finally, the array is interpolated in a print statement.
Hope this helps!
First, here is your existing program, rewritten slightly
open the address file
convert the address file to a hash so that the letters are the keys and the strings the values
open the other file
read in the single line in it
split the line into single letters
use the letters to lookup in the hash
use strict;
use warnings;
open(my $a,"Address.txt")||die $!;
my %address=map {split(/,/) } map {split(' ')} <$a>;
open(my $f,"File.txt")||die $!;
my $list=<$f>;
for my $letter (split(' ',$list)) {
print $address{$letter}."\n" if (exists $address{$letter});
}
to make another file with the substitutions in place alter the loop that processes $list
for my $letter (split(' ',$list)) {
if (exists $address{$letter}) {
push #output, $address{$letter};
}
else {
push #output, $letter;
}
}
open(my $o,">newFile.txt")||die $!;
print $o "#output";
Your problem is that in every iteration of your foreach loop you overwrite any changes made earlier to output file.
My solution:
use strict;
use warnings;
open my $replacements, 'Address.txt' or die $!;
my %r;
foreach (<$replacements>) {
chomp;
my ($k, $v) = split/,/sm;
$r{$k} = $v;
}
my $re = '(' . join('|', keys %r) . ')';
open my $input, "<", $ARGV[0] or die $!;
while (<$input>) {
s/$re/$r{$1}/g;
print;
}
#!/usr/bin/perl -w
# to replace multiple text strings in a file with text from another file
#select text from 1st file, replace in 2nd file
$file1 = 'Address.txt'; $file2 = 'File.txt';
# save the strings by which to replace
%replacement = ();
open IN,"$file1" or die "cant open $file1\n";
while(<IN>)
{chomp $_;
#a = split ',',$_;
$replacement{$a[0]} = $a[1];}
close IN;
open OUT,">replaced_file";
open REPL,"$file2" or die "cant open $file2\n";
while(<REPL>)
{chomp $_;
#a = split ' ',$_; #replaced_data = ();
# replace strings wherever possible
foreach $i(#a)
{if(exists $replacement{$i}) {push #replaced_data,$replacement{$i};}
else {push #replaced_data,$i;}
}
print OUT trim(join " ",#replaced_data),"\n";
}
close REPL; close OUT;
########################################
sub trim
{
my $str = $_[0];
$str=~s/^\s*(.*)/$1/;
$str=~s/\s*$//;
return $str;
}

Use of uninitialized value within XXXX in concatenation (.) or string at image_magick.pl line XX

I wrote a program to compare the image files of two folders(having 1000 files each) with some logic (see this SO question).
While executing it is comparing successfully until 900 images but then it gives an error like Use of uninitialized value within #tfiles2 in concatenation (.) or string at C:\dropbox\Image_Compare\image_magick.pl line 55 (#3).
And then I get a popup error like Perl Command Line Interpreter has stopped working, so I close the program.
My code is as follows:
#!/usr/bin/perl
use Image::Magick;
no warnings 'uninitialized';
use warnings;
use diagnostics;
#use strict;
use List::Util qw(first);
my $directory1="C:/dropbox/Image_Compare/folder1";
opendir(DIR, $directory1) or die "couldn't open $directory1: $!\n";
my #files1 = grep { (!/^\./) && -f "$directory1/$_" } readdir(DIR);
closedir DIR;
print #files1;
print 'end of files1';
my $directory2="C:/dropbox/Image_Compare/folder2";
opendir(DIR, $directory2) or die "couldn't open $directory2: $!\n";
my #files2= grep { (!/^\./) && -f "$directory2/$_" } readdir(DIR);
closedir DIR;
print #files2;
print 'end of files2';
print $files1[0];
foreach my $fils2 (#files2)
{
$g1 = Image::Magick->new;
$g2 = Image::Magick->new;
$temp1 = $g1->Read( filename=>"C:/dropbox/Image_Compare/folder1/".$files1[0]."");
$temp1 = $g2->Read( filename=>"C:/dropbox/Image_Compare/folder2/".$fils2."");
$g3 = $g1->Compare( image=>$g2, metric=>'AE' ); # compare
$error1 = $g3->Get( 'error' );
#print $error1;
if ($error1 == '0')
{
print "Matching image is:";
print $fils2 . "\n";
my $tdirectory2="C:/dropbox/Image_Compare/folder2";
opendir(DIR, $tdirectory2) or die "couldn't open $directory2: $!\n";
my #tfiles2 = grep { (!/^\./) && -f "$tdirectory2/$_" } readdir(DIR);
closedir DIR;
#my $index = firstidx { $_ eq'"' .$fils2.'"' } #tfiles2;
my $index = first { $tfiles2[$_] eq $fils2} 0..$#tfiles2;
#print $fils2;
print $index;
my $i=0;
foreach my $fils1 (#files1)
{
print 'ganesh';
print $files1[$i];
print $tfiles2[$index];
print 'gowtham'; print "<br />";
#print #tfiles2;
$g4 = Image::Magick->new;
$g5 = Image::Magick->new;
$temp2 = $g4->Read( filename=>"C:/dropbox/Image_Compare/folder1/".$files1[$i]."");
$temp2 = $g5->Read( filename=>"C:/dropbox/Image_Compare/folder2/".$tfiles2[$index]."");
$g6 = $g4->Compare( image=>$g5, metric=>'AE' ); # compare
$error2 = $g6->Get( 'error' );
$i++;
$index++;
if ($error2 == '0') {}
else {print "Image not matching:"; print $tfiles2[$index]; last;}
#if ($i == '800') {last;}
}
last
}
}
Can anyone please help, where i am doing a mistake.
Folder 1 file names: 0025.bmp to 1051.bmp;
Folder 2 file names: 0000.bmp to 1008.bmp;
Thanks
Ganesh
I don't know which the offending line is, but one of these is likely to be the candidate:
$temp2 = $g5->Read( filename=>"C:/dropbox/Image_Compare/folder2/".$tfiles2[$index]."");
or
else {print "Image not matching:"; print $tfiles2[$index]; last;}
Do note that you increment $index whether or not it is inside the array bounds. You do not check for the condition $index > $#tfiles, which should break the loop.
You might want to assert that both input arrays contain >> 900 elements, by printing the length like print "length: ", scalar #array, "\n";.
You can test at which index the undefined error actually happens by testing for definedness of the elements in the arrays:
if (not defined $tfiles[$index] or not defined $files1[$i]) {
die "There was an undefined element at index=$index, i=$i";
}
But then again, the offset between $i, and $index is constant (as mentioned in my answer), so you don't have to actually carry two variables.
A simple comparator subroutine could make your code more readable, thus aiding debugging (see procedural programming).
# return true if matching, false otherwise.
sub compare_images {
my ($file1, $file2) = #_;
my $image1 = Image::Magick->new;
$image1->Read(filename => $file1);
my $image2 = Image::Magick->new;
$image2->Read(filename => $file2);
my $result = $image1->Compare(image => $image2, metric => 'AE')->Get('error');
# free memory
undef $image1;
undef $image2;
return 0 == $result;
}
called like
my $image_root = "C:/dropbox/Image_Compare";
my ($folder1, $folder2) = qw(folder1 folder2);
unless (compare_images("$image_root/$folder1/$files1[$i]",
"$image_root/$folder2/$tfiles[$index]")) {
print "Images not matching at index=$index, i=$i\n";
print "filename: $tfiles[$index]\n";
last;
}
You could read your directories like
sub get_images_from_dir {
my ($dirname) = #_;
-d $dirname or die qq(The path "$dirname" doesn't point to a directory!);
opendir my $dir => $dirname or die qq(Can't open "$dirname": $!);
my #files = grep {!/^\./ and -f "$dirname/$_"} readdir $dir;
closedir $dir;
unless (#files) { die qq(There were no interesting files in "$dirname".) }
return #files;
}
Steps like these make code more readable and make it easy to insert checks.

How many different ways are there to concatenate two files line by line using Perl?

Suppose file1 looks like this:
bye bye
hello
thank you
And file2 looks like this:
chao
hola
gracias
The desired output is this:
bye bye chao
hello hola
thank you gracias
I myself have already come up with five different approaches to solve this problem. But I think there must be more ways, probably more concise and more elegant ways, and I hope I can learn more cool stuff :)
The following is what I have tried so far, based on what I've learnt from the many solutions of my previous problems. Also, I'm trying to sort of digest or internalize the knowledge I've acquired from the Llama book.
Code 1:
#!perl
use autodie;
use warnings;
use strict;
open my $file1,'<','c:/file1.txt';
open my $file2,'<','c:/file2.txt';
while(defined(my $line1 = <$file1>)
and defined(my $line2 = <$file2>)){
die "Files are different sizes!\n" unless eof(file1) == eof(file2);
$line1 .= $line2;
$line1 =~ s/\n/ /;
print "$line1 \n";
}
Code 2:
#!perl
use autodie;
use warnings;
use strict;
open my $file1,'<','c:/file1.txt';
my #file1 = <$file1>;
open my $file2,'<','c:/file2.txt';
my #file2 =<$file2>;
for (my $n=0; $n<=$#file1; $n++) {
$file1[$n] .=$file2[$n];
$file1[$n]=~s/\n/ /;
print $file1[$n];
}
Code 3:
#!perl
use autodie;
use warnings;
use strict;
open my $file1,'<','c:/file1.txt';
open my $file2,'<','c:/file2.txt';
my %hash;
while(defined(my $line1 = <$file1>)
and defined(my $line2 = <$file2>)) {
chomp $line1;
chomp $line2;
my ($key, $val) = ($line1,$line2);
$hash{$key} = $val;
}
print map { "$_ $hash{$_}\n" } sort keys %hash;
Code 4:
#!perl
use autodie;
use warnings;
use strict;
open my $file1,'<','c:/file1.txt';
open my $file2,'<','c:/file2.txt';
while(defined(my $line1 = <$file1>)
and defined(my $line2 = <$file2>)) {
$line1 =~ s/(.+)/$1 $line2/;
print $line1;
}
Code 5:
#!perl
use autodie;
use warnings;
use strict;
open my $file1,'<','c:/file1.txt';
my #file1 =<$file1>;
open my $file2,'<','c:/file2.txt';
my #file2 =<$file2>;
while ((#file1) && (#file2)){
my $m = shift (#file1);
chomp($m);
my $n = shift (#file2);
chomp($n);
$m .=" ".$n;
print "$m \n";
}
I have tried something like this:
foreach $file1 (#file2) && foreach $file2 (#file2) {...}
But Perl gave me a syntactic error warning. I was frustrated. But can we run two foreach loops simultaneously?
Thanks, as always, for any comments, suggestions and of course the generous code sharing :)
This works for any number of files:
use strict;
use warnings;
use autodie;
my #handles = map { open my $h, '<', $_; $h } #ARGV;
while (#handles){
#handles = grep { ! eof $_ } #handles;
my #lines = map { my $v = <$_>; chomp $v; $v } #handles;
print join(' ', #lines), "\n";
}
close $_ for #handles;
The most elegant way doesn't involve perl at all:
paste -d' ' file1 file2
If I were a golfing man, I could rewrite #FM's answer as:
($,,$\)=(' ',"\n");#_=#ARGV;open $_,$_ for #_;print
map{chomp($a=<$_>);$a} #_=grep{!eof $_} #_ while #_
which you might be able to turn into a one-liner but that is just evil. ;-)
Well, here it is, under 100 characters:
C:\Temp> perl -le "$,=' ';#_=#ARGV;open $_,$_ for #_;print map{chomp($a =<$_>);$a} #_=grep{!eof $_ }#_ while #_" file1 file2
If it is OK to slurp (and why the heck not — we are looking for different ways), I think I have discovered the path the insanity:
#_=#ARGV;chomp($x[$.-1]{$ARGV}=$_) && eof
and $.=0 while<>;print "#$_{#_}\n" for #x
C:\Temp> perl -e "#_=#ARGV;chomp($x[$.-1]{$ARGV}=$_) && eof and $.=0 while<>;print qq{#$_{#_}\n} for #x" file1 file2
Output:
bye bye chao
hello hola
thank you gracias
An easier alternative to your Code 5 which allows for an arbitrary number of lines and does not care if files have different numbers of lines (hat tip #FM):
#!/usr/bin/perl
use strict; use warnings;
use File::Slurp;
use List::AllUtils qw( each_arrayref );
my #lines = map [ read_file $_ ], #ARGV;
my $it = each_arrayref #lines;
while ( my #lines = grep { defined and chomp and length } $it->() ) {
print join(' ', #lines), "\n";
}
And, without using any external modules:
#!perl
use autodie; use warnings; use strict;
my ($file1, $file2) = #ARGV;
open my $file1_h,'<', $file1;
my #file1 = grep { chomp; length } <$file1_h>;
open my $file2_h,'<', $file2;
my #file2 = grep { chomp; length } <$file2_h>;
my $n_lines = #file1 > #file2 ? #file1 : #file2;
for my $i (0 .. $n_lines - 1) {
my ($line1, $line2) = map {
defined $_ ? $_ : ''
} $file1[$i], $file2[$i];
print $line1, ' ', $line2, "\n";
}
If you want to concatenate only the lines that appear in both files:
#!perl
use autodie; use warnings; use strict;
my ($file1, $file2) = #ARGV;
open my $file1_h,'<', $file1;
my #file1 = grep { chomp; length } <$file1_h>;
open my $file2_h,'<', $file2;
my #file2 = grep { chomp; length } <$file2_h>;
my $n_lines = #file1 < #file2 ? #file1 : #file2;
for my $i (0 .. $n_lines - 1) {
print $file1[$i], ' ', $file2[$i], "\n";
}
An easy one with minimal error checking:
#!/usr/bin/perl -w
use strict;
open FILE1, '<file1.txt';
open FILE2, '<file2.txt';
while (defined(my $one = <FILE1>) or defined(my $twotemp = <FILE2>)){
my $two = $twotemp ? $twotemp : <FILE2>;
chomp $one if ($one);
chomp $two if ($two);
print ''.($one ? "$one " : '').($two ? $two : '')."\n";
}
And no, you can't run two loops simultaneous within the same thread, you'd have to fork, but that would not be guaranteed to run synchronously.