Greeting I try to read a file into hash of hash following this tutorial.
http://docstore.mik.ua/orelly/perl/prog3/ch09_04.htm
My text input file is
event_a1_x1: email1=xxx#gmail.com email2=yyy#gmail.com email1_cnt=3
event_a1_x2: email1=xxx#gmail.com email2=yyy#gmail.com email1_cnt=3
event_b2_y1: email1=xxx#gmail.com email2=yyy#gmail.com email1_cnt=3
event_b2_y2: email1=xxx#gmail.com email2=yyy#gmail.com email1_cnt=3
event_c3_z1: email1=xxx#gmail.com email2=yyy#gmail.com email1_cnt=3
event_c3_z2: email1=xxx#gmail.com email2=yyy#gmail.com email1_cnt=3
My code is
#!/usr/bin/perl
use strict;
use warnings;
my $file = $ARGV[0] or die "Need to get config file on the command line\n";
open(my $data, '<', $file) or die "Could not open '$file' $!\n";
my %HoH;
#open FILE, "filename.txt" or die $!;
my $key;
my $value;
my $who;
my $rec;
my $field;
while ( my $line = <$data>) {
print $line;
next unless (s/^(.*?):\s*//);
$who = $1;
#print $who;
$rec = {};
$HoH{$who} = $rec;
for $field ( split ) {
($key, $value) = split /=/, $field;
$rec->{$key} = $value;
}
}
I keep getting this error...
Use of uninitialized value $_ in substitution (s///) at ./read_config.pl line 18, <$data> line 1.
This is about when $_, "the default input and pattern-searching space", is set and used.
In while (<$fh>), what is read from the filehandle is assigned to $_. Then your regex s/// and print and split can use it. See General Variables in perlvar.
However, once we specifically assign to a variable, while (my $line = <$fh>), this deal is off and $_ is not set. So when you later use the regex substitution in a way that relies on $_ the variable is found uninitialized.
Either consistently use the default $_, or (consistently) don't. So, either
while (<$fh>) {
print;
# same as posted
}
or
while (my $line = <$fh>) {
# ...
next unless $line =~ s/^(.*?):\s*//;
# ...
foreach my $field (split ' ', $line) {
# ...
}
}
There is quite a bit more that can be improved in the code, but that would take us elsewhere.
Related
I have a text file where is lot of lines, I need search in this file keywords and if exist write to log file line where is keywords and line one line below and one above the keyword. Now search or write keyword not function if find write all and I dont known how can I write line below and above. Thanks for some advice.
my $vstup = "C:/Users/Omega/Documents/Kontroly/testkontroly/kontroly20220513_154743.txt";
my $log = "C:/Users/Omega/Documents/Kontroly/testkontroly/kontroly.log";
open( my $default_fh, "<", $vstup ) or die $!;
open( my $main_fh, ">", $log ) or die $!;
my $var = 0;
while ( <$default_fh> ) {
if (/\Volat\b/)
$var = 1;
}
if ( $var )
print $main_fh $_;
}
}
close $default_fh;
close $main_fh;
The approach below use one semaphore variable and a buffer variable to enable the desired behavior.
Notice that the pattern used was replaced by 'A` for simplicity testing.
#!/usr/bin/perl
use strict;
use warnings;
my ($in_fh, $out_fh);
my ($in, $out);
$in = 'input.txt';
$out = 'output.txt';
open($in_fh, "< ", $in) || die $!."\n";
open($out_fh, "> ", $out) || die $!;
my $p_next = 0;
my $p_line;
while (my $line = <$in_fh>) {
# print line after occurrence
print $out_fh $line if ($p_next);
if ($line =~ /A/) {
if (defined($p_line)) {
# print previous line
print $out_fh $p_line;
# once printed undefine variable to avoid printing it again in the next loop
undef($p_line);
}
# Print current line if not already printed as the line follows a pattern
print $out_fh $line if (!$p_next);
# toggle semaphore to print the next line
$p_next = 1;
} else {
# pattern not found.
# if pattern was not detected in both current and previous line.
$p_line = $line if (!$p_next);
$p_next = 0;
}
}
close($in_fh);
close($out_fh);
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;
I am trying to send a variable that is defined in an if statement $abc to a new file. The code seems correct but, I know that it is not working because the file is not being created.
Data File Sample:
bos,control,x1,x2,29AUG2016,y1,y2,76.4
bos,control,x2,x3,30AUG2016,y2,y3,78.9
bos,control,x3,x4,01SEP2016,y3,y4,72.5
bos,control,x4,x5,02SEP2016,y4,y5,80.5
Perl Code:
#!/usr/bin/perl
use strict;
use warnings 'all';
use POSIX qw(strftime); #Pull in date
my $currdate = strftime( "%Y%m%d", localtime ); #Date in YYYYMMDD format
my $modded = strftime( "%d%b%Y", localtime ); #Date in DDMONYYYY format
my $newdate = uc $modded; #converts lowercase to uppercase
my $filename = '/home/.../.../text_file'; #Define full file path before opening
open(FILE, '<', $filename) or die "Uh, where's the file again?\n"; #Open file else give up and relay snarky error
while(<FILE>) #Open While Loop
{
chomp;
my #fields = split(',' , $_); #Identify columns
my $site = $fields[0];
my $var1 = $fields[1];
my $var2 = $fields[4];
my $var3 = $fields[7];
my $abc = print "$var1,$var2,$var3\n" if ($var1 =~ "control" && $var2 =~ "$newdate");
open my $abc, '>', '/home/.../.../newfile.txt';
close $abc;
}
close FILE;
In your code you have a few odd things that are likely mistakes.
my $abc = print "$var1,$var2,$var3\n" if ($var1 =~ "c01" && $var2 =~ "$newdate");
print will return success, which it does as 1. So you will print out the string to STDOUT, and then assign 1 to a new lexical variable $abc. $abc is now 1.
All of that only happens if that condition is met. Don't do conditional assignments. The behavior for this is undefined. So if the condition is false, your $abc might be undef. Or something else. Who knows?
open my $abc, '>', '/home/.../.../newfile.txt';
close $abc;
You are opening a new filehandle called $abc. The my will redeclare it. That's a warning that you would get if you had use warnings in your code. It also overwrites your old $abc with a new file handle object.
You don't write anything to the file
... are weird foldernames, but that's probably just obfuscation for your example
I think what you actually want to do is this:
use strict;
use warnings 'all';
# ...
open my $fh, '<', $filename or die $!;
while ( my $line = <$fh> ) {
chomp $line;
my #fields = split( ',', $line );
my $site = $fields[0];
my $var1 = $fields[1];
my $var2 = $fields[4];
my $var3 = $fields[7];
open my $fh_out, '>', '/home/.../.../newfile.txt';
print $fh_out "$var1,$var2,$var3\n" if ( $var1 =~ "c01" && $var2 =~ "$newdate" );
close $fh_out;
}
close $fh;
You don't need the $abc variable in between at all. You can just print to your new file handle $fh_out that's open for writing.
Note that you will overwrite the newfile.txt file every time you have a match in a line inside $filename.
Your current code:
Prints the string
Assigns the result of printing it to a variable
Immediately overwrites that variable with a file handle (assuming open succeeded)
Closes that file handle without using it
Your logic should look more like this:
if ( $var1 =~ "c01" && $var2 =~ "$newdate" ) {
my $abc = "$var1,$var2,$var3\n"
open (my $file, '>', '/home/.../.../newfile.txt') || die("Could not open file: " . $!);
print $file $abc;
close $file;
}
You have a number of problems with your code. In addition to what others have mentioned
You create a new output file every time you find a matching input line. That will leave the file containing only the last printed string
Your test checks whether the text in the second column contains c01, but all of the lines in your sample input have control in the second column, so nothing will be printed
I'm guessing that you want to test for string equality, in which case you need eq instead of =~ which does a regular expression pattern match
I think it should look something more like this
use strict;
use warnings 'all';
use POSIX 'strftime';
my $currdate = uc strftime '%d%b%Y', localtime;
my ($input, $output) = qw/ data.txt newfile.txt /;
open my $fh, '<', $input or die qq{Unable to open "$input" for input: $!};
open my $out_fh, '>', $output or die qq{Unable to open "$output" for output: $!};
while ( <$fh> ) {
chomp;
my #fields = split /,/;
my ($site, $var1, $var2, $var3) = #fields[0,1,4,7];
next unless $var1 eq 'c01' and $var2 eq $currdate;
print $out_fh "$var1,$var2,$var3\n";
}
close $out_fh or die $!;
Here I have a abc.txt file:
aaa,1000,kevin
bbb,2000,john
ccc,3000,jane
ddd,4000,kevin
Then I want to print out:
kevin
john
jane
my Perl script is:
open (INFILE, $ARGV[1]) or die "An input file is required as argument\n";
#store=();
while(<INFILE>)
{
chomp();
#data=split(/,/);
#
#
#
if (%store ne "0")
{
print "Printing users:\n";
foreach $key (keys %store)
{print $key."\n";}
}
print "Printing users:\n";
foreach $key (keys %store)
{print $key."\n";}
}
My idea is to store the value into hash and create key to each value. How can I do in the ### line?
You have declared #store and then using %store. I didn't understand that why you doing that, but the below code will give you desire output. First read the input file, split the data and then remove the duplicates.
use strict;
use warnings;
my $infile = $ARGV[0];
open my $fh, "<", $infile or die "An input file is required as argument: $!";
my %store;
while(my $line = <$fh>)
{
chomp($line);
my #data = split /,/, $line;
my #removeduplicate = (grep { !$store{$_}++ } #data)[2];
foreach(#removeduplicate){
if( $_ ne ''){
print "$_\n";
}
}
}
close $fh;
Output:
kevin
john
jane
hmmm. it depends what do you want. maybe this example will help you:
#!/usr/bin/perl
use strict;
use warnings;
use Data::Dumper; #for debug if you want
my $infile='abc.txt'; #or ARGV[0] whatever it is
my $fh;
open $fh,'<',$infile or die "problem with $infile $# $!";
my $inputline;
my %Storage;
my #Values;
while (defined($inputline=<$fh>)) {
chomp $inputline;
#Values=split ',',$inputline;
if (#Values != 3) {
warn "$inputline has formatted badly";
next;
}
#warn if exists $Storage{$Values[1]}; #optional warning for detected duplicates
$Storage{$Values[1]}=#Values[0,2]; #create hash data
#duplicates will be removed automaticly
}
close $fh;
print Dumper \%Storage; #print how perl it stores
foreach my $Key (keys %Storage) { #example loop
print #{Storage->{$Key}},"\n"; #do anything
}
I hope this template will be enough for you.
I want to add random string to existing identifier line in fasta file.
So I get:
MMETSP0259|AmphidiniumcarteCMP1314aaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaa
Then the sequence on the next lines as normal. I am have problem with i think in the format output. This is what I get:
MMETSP0259|AmphidiniumCMP1314aaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaa
CTTCATCGCACATGGATAACTGTGTACCTGACTaaaaaaaaaaaaaaaaaaaaaaaaaaaaaab
TCTGGGAAAGGTTGCTATCATGAGTCATAGAATaaaaaaaaaaaaaaaaaaaaaaaaaaaaaac
It's added to every line. (I altered length to fit here.) I want just to add to the identifier line.
This is what i have so far:
use strict;
use warnings;
my $currentId = "aaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaa";
my $header_line;
my $seq;
my $uniqueID;
open (my $fh,"$ARGV[0]") or die "Failed to open file: $!\n";
open (my $out_fh, ">$ARGV[0]_longer_ID_MMETSP.fasta");
while( <$fh> ){
if ($_ =~ m/^(\S+)\s+(.*)/) {
$header_line = $1;
$seq = $2;
$uniqueID = $currentId++;
print $out_fh "$header_line$uniqueID\n$seq";
} # if
} # while
close $fh;
close $out_fh;
Thanks very much, any ideas will be greatly appreciated.
Your program isn't working because the regex ^(\S+)\s+(.*) matches every line in the input file. For instance, \S+ matches CTTCATCGCACATGGATAACTGTGTACCTGACT; the newline at the end of the line matches \s+; and nothing matches .*.
Here's how I would encode your solution. It simply appends $current_id to the end of any line that contains a pipe | character
use strict;
use warnings;
use 5.010;
use autodie;
my ($filename) = #ARGV;
my $current_id = 'a' x 57;
open my $in_fh, '<', $filename;
open my $out_fh, '>', "${filename}_longer_ID_MMETSP.fasta";
while ( my $line = <$in_fh> ) {
chomp $line;
$line .= $current_id if $line =~ tr/|//;
print $line, "\n";
}
close $out_fh;
output
MMETSP0259|AmphidiniumCMP1314aaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaa
CTTCATCGCACATGGATAACTGTGTACCTGACT
TCTGGGAAAGGTTGCTATCATGAGTCATAGAAT