I need to parse my text file (my output) to csv format, which contains just Names and Ips from devices. Somthing like:
Name, ip
LAB-W, 10.66.1.12
LAB-D, 10.66.1.13
I do not have experience with parsing in perl, maybe somebody can help me with this question.
use Net::Cisco::ISE;
use Data::Dumper;
use Text::CSV;
my $ise = Net::Cisco::ISE->new(hostname=>'hostname', username=>'user', password=>'user');
for my $name (keys %{$networkdevices}){
my $device = $ise->networkdevices("id" => $networkdevices->{$name}->id);
print Dumper $device->name;
print Dumper $device->NetworkDeviceIPList;
}
And I have this output:
$VAR1 = 'LAB-W';
$VAR1 = {
'NetworkDeviceIP' => {
'mask' => '32',
'ipaddress' => '10.66.1.12'
}
};
$VAR1 = 'LAB-D';
$VAR1 = {
'NetworkDeviceIP' => {
'mask' => '24',
'ipaddress' => '10.66.1.13'
}
};
I tried this script (from this post), but I do not see output, also no mistakes :
use DBI;
use strict;
use Data::Dumper;
use File::Slurp;
open (FILE, "<./my_output") or die "could not open file: $!";
undef $/;
my $contents = <FILE>;
close(FILE);
my $hash_of_arrays = eval $contents;
for my $key (keys %$hash_of_arrays) {
my $hash = $hash_of_arrays->{$key};
for my $key2 (keys %$hash) {
my $array = $hash->{$key2};
for my $i (0..$#$array) {
print "$i: $$array[$i]\n";
}
}
}
Since the data are just in a hash, you can access them directly inside your loop:
for my $name (keys %{$networkdevices}){
my $device = $ise->networkdevices("id" => $networkdevices->{$name}->id);
print join(',',
$device->name
$device->NetworkDeviceIPList->{NetworkDeviceIP}->{ipaddress}
) . "\n";
}
Related
I am trying to read text file content into hash but having some problem reading as well as accessing it.
resctrl_top
/path/to/a/
vdm05top
/path/to/b/
/path/to/c/
/path/to/d/
/path/to/e/
/path/to/f/
The file format will be as above. My desired output is a hash with the non spacing line as key, and the path lines as values. I would like to know also how to access each values for different keys.
resctrl_top => /path/to/a/
vdm05top => /path/to/b/,/path/to/c/,...
Below are the effort I tried:
use strict;
use warnings;
my %hash;
open FILE, "filename.txt" or die $!;
my $key;
while (my $line = <FILE>) {
chomp($line);
if ($line !~ /^\s/) {
($key) = $line =~ /^\S+/g;
$hash{$key} = [];
} else {
$line =~ s/^\s+//;
push #{ $hash{$key} }, $line;
}
}
close FILE;
foreach (keys %hash){
print "$key => $hash{$key}\n";
}
Try this way:
use strict;
use warnings;
use Data::Dumper;
my %hash;
my $key;
while (my $line = <DATA>) {
chomp($line);
if ($line !~ /^\s/) {
$key = $line;
} else {
$line =~ s/\s//g;
push (#{$hash{$key}} , $line);
}
}
my %final;
foreach my $k (keys %hash){
my $val = join(",", #{$hash{$k}});
$final{$k} = $val; #New hash will have key and respective values
}
print Dumper(\%final);
__DATA__
resctrl_top
/path/to/a/
vdm05top
/path/to/b/
/path/to/c/
/path/to/d/
/path/to/e/
/path/to/f/
Result:
$VAR1 = {
'vdm05top' => '/path/to/b/,/path/to/c/,/path/to/d/,/path/to/e/,/path/to/f/',
'resctrl_top' => '/path/to/a/'
};
Hope this solves your problem.
Here's a pretty simple solution.
#!/usr/bin/perl
use strict;
use warnings;
use feature 'say';
use Data::Dumper; # Just for output
my ($key, %hash); # Declare globals
while (<DATA>) { # Quick hack - read from DATA
chomp;
if (/^\s/) { # If the line starts with a space
s/^\s+//;
push #{$hash{$key}}, $_;
} else { # The line is a key
$key = $_;
}
}
say Dumper \%hash;
__DATA__
resctrl_top
/path/to/a/
vdm05top
/path/to/b/
/path/to/c/
/path/to/d/
/path/to/e/
/path/to/f/
I know it is not possible to have duplicate keys in a hash, but this is what my data looks like:
Key Value
SETUP_FACE_PROT great
SETUP_FACE_PROT great2
SETUP_FACE_PROT great3
SETUP_FACE_PROT great3
SETUP_ARM_PROT arm
SETUP_FOOT_PROT foot
SETUP_FOOT_PROT foot2
SETUP_HEAD_PROT goggle
I would like to concatenate values for repeated keys, separated by a * character. For example, this is what I want the output to look like:
SETUP_FACE_PROT'=great*great2*great3',
SETUP_ARM_PROT='arm',
SETUP_FOOT_PROT='foot*foot2',
SETUP_HEAD_PROT='google'
This is how I've tried to solve the problem so far:
foreach my $key ( sort keys %stuff )
{
print "$key=\'", join( "*", #{ $stuff{$key} } ), "\'\n";
}
But instead of printing the result, how can I store it in a variable so that I can pass it to another subroutine? I'm trying to create a new string that looks like this:
$newstring="
SETUP_FACE_PROT='great*great2*great3',
SETUP_ARM_PROT='arm',
SETUP_FOOT_PROT='foot*foot2',
SETUP_HEAD_PROT='google' "
You can't duplicate keys, you can create a hash of arrays.
#!/usr/bin/env perl
use strict;
use warnings;
use Data::Dumper;
my %stuff;
while (<DATA>) {
my ( $key, $value ) = split;
push( #{ $stuff{$key} }, $value );
}
print Dumper \%stuff;
foreach my $key ( sort keys %stuff ) {
print "$key=\'", join( "*", #{ $stuff{$key} } ), "\'\n";
}
__DATA__
SETUP_FACE_PROT great
SETUP_FACE_PROT great2
SETUP_FACE_PROT great3
SETUP_FACE_PROT great3
SETUP_ARM_PROT arm
SETUP_FOOT_PROT foot
SETUP_FOOT_PROT foot2
SETUP_HEAD_PROT goggle
Edit:
Turning it into a string as requested:
my $results;
foreach my $key ( sort keys %stuff ) {
$results .= "$key=\'". join( "*", #{ $stuff{$key} } ). "\'\n";
}
print $results;
Or perhaps using print still with a filehandle:
my $results;
open ( my $output, '>', \$results );
foreach my $key ( sort keys %stuff ) {
print {$output} "$key=\'", join( "*", #{ $stuff{$key} } ), "\'\n";
}
close ( $output );
print $results;
At last i got an answer doing this.
use Data::Dumper;
my %stuff;
use Text::CSV;
my $csv = Text::CSV_XS->new ({ binary => 1, eol => $/ });
my $filenamex = 'duplicate2.csv';
$checkstring ='';
open(my $datab, '<', $filenamex) or die "Could not open '$filename' $!\n";
$i=1;
my %datan;
while (my $linea = <$datab>)
{
chomp $linea;
#fieldsx = split ",",$linea;
$key = $fieldsx[0];
$value = $fieldsx[1];
# print $key;
push( #{ $stuff{$key} }, $value );
}
foreach my $key ( sort keys %stuff )
{
$checkstring = $checkstring.','.$key.'='. join( "*", #{ $stuff{$key} } );
}
print $checkstring;
Here is the code:
my #col= sort keys %colnames;
print "mRNA,".join(",",#col)."\n";
foreach my $row(keys %rownames){
print "$row";
foreach my $col(#col){
my $num=$mat{$col}->{$row};
$num=~s/(\.\d\d)\d+/$1/;
print ",$num";
}
print "\n";
}
Output:
mRNA,Benzopyrene12h_replica1,Benzopyrene12h_replica2
E2F1,5.01,4.72
REV1,2.76,2.67
POLK,1.21,1.87
POLH,1.49,1.56
POLI,1.94,2.45
Please help me write this output to .csv file.
Something like this might work... Combining with Miller's answer. I didn't test it, just giving you an idea. And it's defiantly could be written more cleanly and less redundant.
use strict;
use warnings;
use autodie;
my $csvFile = Text::CSV->new ( { binary => 1, eol => "\n" } )
or die "Cannot use CSV: ".Text::CSV->error_diag ();
my #col= sort keys %colnames;
my #csv;
$csv[0][0] = "mRNA,";
my #joinCol = join(",",#col);
my $i =1;
foreach (#joinCol) {
$csv[0][$i] = $_;
$i++;
}
my $k = 1;
foreach my $row(keys %rownames){
my $j = 0;
print "$row";
$csv[$k][$j] = $row;
foreach my $col(#col){
my $num=$mat{$col}->{$row};
$num=~s/(\.\d\d)\d+/$1/;
print ",$num";
$csv[$k][$j] = $num;
$j++;
}
print "\n";
$k++;
}
open $fh, '>', "new.csv" or die "Couldn't open csv file: $! \n";
for (#csv) {
$csvFile->print($fh, $_);
}
close $fh;
To write to a CSV file, use Text::CSV
use strict;
use warnings;
use autodie;
# Your Data Initialization
my %colnames; # = Something
my %rownames; # = Something else
my %mat; # = a hash of hash
# Prepare CSV
my $csv = Text::CSV->new ( { binary => 1, eol => "\n" } )
or die "Cannot use CSV: ".Text::CSV->error_diag ();
open $fh, '>', "new.csv";
my #col = sort keys %colnames;
# Output Header
$csv->print($fh, ['mRNA', #col]);
# Output Rows
for my $row (keys %rownames){
my #data = ($row);
for my $col (#col){
my $num = $mat{$col}{$row};
$num =~ s/(\.\d\d)\d+/$1/;
push #data, $num;
}
$csv->print($fh, \#data);
}
close $fh;
I feel like I'm missing something rather obvious, but can't find any answers in the documentation. Still new to OOP with Perl, but I'm using Text::CSV to parse a CSV for later use.
How would I go about extracting the first row and pushing the values to array #headers?
Here's what I have so far:
#!/usr/bin/perl
use warnings;
use diagnostics;
use strict;
use Fcntl ':flock';
use Text::CSV;
my $csv = Text::CSV->new({ sep_char => ',' });
my $file = "sample.csv";
my #headers; # Column names
open(my $data, '<:encoding(utf8)', $file) or die "Could not open '$file' $!\n";
while (my $line = <$data>) {
chomp $line;
if ($csv->parse($line)) {
my $r = 0; # Increment row counter
my $field_count = $csv->fields(); # Number of fields in row
# While data exists...
while (my $fields = $csv->getline( $data )) {
# Parse row into columns
print "Row ".$r.": \n";
# If row zero, process headers
if($r==0) {
# Add value to #columns array
push(#headers,$fields->[$c]);
} else {
# do stuff with records...
}
}
$r++
}
close $data;
You'd think that there would be a way to reference the existing fields in the first row.
Pretty much straight from the documentation, for example.
#!/usr/bin/perl
use strict;
use warnings;
use Text::CSV_XS;
my $csv = Text::CSV_XS->new ({ binary => 1, eol => $/ });
my $file = 'o33.txt';
open my $io, "<", $file or die "$file: $!";
my $header = $csv->getline ($io);
print join("-", #$header), "\n\n";
while (my $row = $csv->getline ($io)) {
print join("-", #$row), "\n";
}
__END__
***contents of o33.txt
lastname,firstname,age,gender,phone
mcgee,bobby,27,M,555-555-5555
kincaid,marl,67,M,555-666-6666
hofhazards,duke,22,M,555-696-6969
Prints:
lastname-firstname-age-gender-phone
mcgee-bobby-27-M-555-555-5555
kincaid-marl-67-M-555-666-6666
hofhazards-duke-22-M-555-696-6969
Update: Thinking about your problem, it may be that you want to address the data by its column name. For that, you might be able to use something (also from the docs), like this:
$csv->column_names ($csv->getline ($io));
while (my $href = $csv->getline_hr ($io)) {
print "lastname is: ", $href->{lastname},
" and gender is: ", $href->{gender}, "\n"
}
Note: You can use Text::CSV instead of Text::CSV_XS, as the former is a wrapper around the latter.
Thought I'd post my results for others.
#!/usr/bin/perl
use warnings;
use diagnostics;
use strict;
use Text::CSV;
sub read_csv {
my $csv = Text::CSV->new({ sep_char => ',' });
my $file = shift;
open(my $data, '<:encoding(utf8)', $file) or die "Could not open '$file' $!\n";
# Process Row Zero
my $header = $csv->getline ($data);
my $field_count = $csv->fields();
# Read the rest of the file
while (my $line = <$data>) {
chomp $line;
# Read line if possible
if ($csv->parse($line)) {
my $r = 0;
# While data exists...
while (my $fields = $csv->getline( $data )) {
# Parse row into columns
print Display->H2;
print "Row ".$r.": ".#$fields." columns. \n";
# Print column values
for(my $c=0; $c<#$fields; $c++) {
print #$header[$c]." : ".#$fields[$c]."\n";
}
$r++
}
}
close $data;
}
}
Cheers
I am trying to see the values in the the hash %pc are in the keys in the hash %fasta and then print the key and value of % fasta if it is.
So far I have the script:
#!/usr/bin/perl
use warnings;
use strict;
use Bio::SearchIO;
use Bio::SeqIO;
my %pc;
my %fasta;
#get list of core protein clusters
my $file1 = $ARGV[0];
open (INPUT1, $file1) or die "Could not open $file1\n";
while (my $line1 = <INPUT1>) {
chomp $line1;
my #spl = split (/\|/, $line1);
my $id = $spl[0];
my $gene = $spl[1];
$pc{$id}=$gene;
}
my #files = glob("*_PC.fa");
foreach my $fil (#files) {
my $seqio = Bio::SeqIO->new(-format => 'fasta', -file => $fil);
my $file = $fil;
$file =~ /^(.+)_PC.fa/;
my $outfile = $1."_core.fa";
open (OUTFILE,'>', $outfile) or die "Could not open $outfile \n";
while (my $seqobj = $seqio->next_seq) {
my $seqid = $seqobj->display_id;
my $nuc = $seqobj->seq();
$fasta{$seqid}=$nuc;
foreach my $key (keys %fasta) {
my #spl2 = split (/\|/,$key);
my $fasta_gene = $spl2[1];
if ($fasta_gene eq (keys %fasta)) {
print OUTFILE ">$key\n$fasta{$key}\n";
}
}
}
close OUTFILE;
}
Thanks in advance!
%fasta gets printed if all values from %pc exists as keys in %fasta
my $some_values_missing = grep { ! exists $fasta{$_} } values %pc;
unless ($some_values_missing) {
print "key:$_; value:$fasta{$_}\n" for keys %fasta;
}