Push File contents into the array using perl - perl

Suppose this is the file I am reading
hey how are you
I am fine thank you
Here I want to store the contents of file into an array using one while loop so that I can easily use the array later and need not to open close file again.
Code
use warnings;
use strict;
my #point1;
my #point ;
my $log1= "log1.log";
open(IN1, "<$log1" ) or die "Could not open file $log1: $!";
while (my $line = <IN1>) {
#point = split " ",$line;
push(#point1,#point);
push(#point1,"\n");
}
print "$point1[0] 2nd\n";
close IN1;
Output
hey 2nd
I want output like below if I am printing outside while loop.
Output I want:
hey 2nd
I 2nd
What changes should I make here?

You are pushing all the words in the file onto the same list, which will make it difficult to tell them apart.
push(#point1,#point);
This is the same as doing
#point1 = qw(hey how are you I am fine thank you);
I suspect what you want is a two-dimensional array, so that you afterwards can supply line number and word number and print that word, like this:
print $point1[0][0]; # prints "hey"
To do that, you would do this:
push #point1, \#point; # the backslash makes us get the reference to the array
But then you also have to make sure that all the lines do not point to the same array, as they would when you declare my #point outside of the loop.
my #point; # outside the loop
while (my $line = <IN1>) {
#point = split " ",$line;
push(#point1, \#point); # wrong
}
You would have to declare it inside the loop
while (my $line = <IN1>) {
my #point = split " ",$line; # inside the loop
push(#point1, \#point); # correct
}
Because then it will be a new array reference each loop iteration, one for each new line. But you do not need to use a temporary variable, you can just push the values directly
while (my $line = <IN1>) {
push #point1, [ split " ",$line; ];
}
The square brackets creates a reference to an anonymous array, with the values that are inside it. Afterward you can solve your task like this:
for my $aref (#point1) {
print "$aref->[0] 2nd\n";
}
Or
for my $line_no (0 .. $#point1) {
print "$point1[$line_no][0] 2nd\n";
}

use strict;
use warnings;
use feature qw( say );
my $log1 = "log1.log";
open(my $fh, "<", $log1) # Don't use a global. Use 3-arg open.
or die("Can't open file \"$log1\": $!\n"); # No need for the line number.
my #first_words;
while (my $line = <$fh>) {
# chomp($line); # Not needed with C<< split " " >>, so that was ok.
my #words = split " ", $line; # Declare variable to the scope where they are needed.
push #first_words, $words[0]; # You want the first word of each line.
}
for my $first_word (#first_words) { # Need a loop to print stuff repeatedly.
say "$first_word 2nd";
}
or
use strict;
use warnings;
use feature qw( say );
my #first_words;
while (my $line = <>) {
my #words = split " ", $line;
push #first_words, $words[0];
}
for my $first_word (#first_words) {
say "$first_word 2nd";
}
The second is more flexible. Just pass the desired file name as an argument. It can also handle input via STDIN.

It's not really clear what data structure you're looking for. Here are a few possibilities.
You want each line of your file in an element in the array.
my #array = <$fh>;
You want each line of your file in an element in the array, but you also want the input split into individual words (so you end up with an array of arrays).
my #array = map { [ split ] } <$fh>;
You want the first word of each line in an element in the array.
my #array = map { (split)[0] } <$fh>;
I've mentioned before that you should switch to using the three-arg version of open() and lexical filehandles. So, assume that all of my code examples above are prefaced with:
open my $fh, '<', $log1 or die "Cannot open '$log1': $!\n";
Looking back over your last few questions, I can't help thinking that this is an X/Y question. You're asking for our help with tiny problems that make up part of your code, but actually, we could give far better help if we knew more about the bigger picture.

Related

Perl - Using an Array on a Config txt file

So I have a text file with four sets of data on a line, such as aa bb username password. So far I have been able to parse through the first line of the file using substrings and indices, and assigning each of the four to variables.
My goal is to use an array and chomp through each line and assign them to the four variables, and than to match an user inputted argument to the first variable, and use the four variables in that correct line.
For example, this would be the text file:
"aa bb cc dd"
"ee ff gg hh"
And depending on whether the user inputs "aa" or "ee" as the argument, it would use that line's set of arguments in the code.
I am trying to get up a basic array and chomp through it based on a condition for the first variable, essentially.
Here is my code for the four variables for the first line, but like I said, this only works for the first line in the text file:
local $/;
open(FILE, $configfile) or die "Can't read config file 'filename' [$!]\n";
my $document = <FILE>;
close (FILE);
my $string = $document;
my $substring = " ";
my $Index = index($string, $substring);
my $aa = substr($string, 0, $Index);
my $newstring = substr($string, $Index+1);
my $Index2 = index($newstring, $substring);
my $bb = substr($newstring, 0, $Index2);
my $newstring2 = substr($newstring, $Index2+1);
my $Index3 = index($newstring2, $substring);
my $cc = substr($newstring2, 0, $Index3);
my $newstring3 = substr($newstring2, $Index3+1);
my $Index4 = index($newstring3, $substring);
my $dd = substr($newstring3, 0, $Index4);
First of all, you can parse your whole line using split instead of running index and substring on them:
my ( $aa, $bb, $cc, $dd ) = split /\s+/, $line;
Even better, use an array:
my #array = split /\s+/, $line;
I think you're saying that you need to store each array of command parts into another array of lines. Is that correct? Take a look at this tutorial on references available in the Perl Documentation.
Perl has three different types of variables. The problem is that each of the types of variables of these stores only a single piece of data. Arrays and hashes may store lots of data, but only one piece of data can be stored in each element of a hash or array.
References allow you to get around this limitation. A reference is simply a pointer to another piece of data. For example, if $line = aa bb cc dd, doing this:
my #command_list = split /\s+/ $line;
Will give you the following:
$command_list[0] = "aa";
$command_list[1] = "bb";
$command_list[2] = "cc";
$command_list[3] = "dd";
You want to store #command_list into another structure. What you need is a reference to #command_list. To get a reference to it, you merely put a backslash in front of it:
my $reference = \#command_list;
This could be put into an array:
my #array;
$array[0] = $reference;
Now, I'm storing an entire array into a single element of an array.
To get back to the original structure from the reference, you put the correct sigil. Since this is an array, you put # in front of it:
my #new_array = #{ $reference };
If you want the first item in your reference without using having to transport it into another array, you could simply treat #{ $reference } as an array itself:
${ $reference }[0] = "aa";
Or, use the magic -> which makes the syntax a bit cleaner:
$reference->[0] = "aa";
Go through the tutorial. This will help you understand the full power of references, and how they can be used. Your program would look something like this:
use strict;
use warnings;
use feature qw(say); #Better print that print
use autodie; #Kills your program if the file can't be open
my $file = [...] #Somehow get the file you're reading in...
open my $file_fh, "<", $file;
my #command_list;
while ( my $line = <$file_fh> ) {
chomp $line;
my #line_list = split /\s+/, $line;
push #command_list, \#line_list;
}
Note that push #command_list, \#line_list; is pushing a reference to one array into another. How do you get it back out? Simple:
for my $cmd_line_ref ( #command_list ) {
my $command = $cmd_line_ref->[0]; #This is the first element in your command
next unless $command eq $user_desires; # However you figure out what the user wants
my $line = join " ", #{ $cmd_line_ref } #Rejoins your command line once again
??? #Profit
}
Read the tutorial on references, and learn about join and split.
You are reading the whole file in the my $document = <FILE> line.
Try something like:
my #lines;
open my $file, '<', $configfile or die 'xxx';
while( <$file> ) {
chomp;
push #lines, [ split ]
}
And now #lines has an array of arrays with the information you need.
(EDIT) don't forget to lose the local $/; -- it's what is making you read the whole file at once.
my $document = <FILE> is reading in only the first line. Try using a while loop.
If you want to read all lines of the file at once - assuming it's a small file - you may want to use File::Slurp module:
use File::Slurp;
my #lines = File::Slurp::read_file($configfile);
foreach my $line (#lines) {
# do whatever
Also, you can use CPAN modules to split the strings into fields.
If they are single-space separated, simply read the whole file using a standard CSV parser (you can configure Text::CSV_XS to use any characater as separator). Example here: How can I parse downloaded CSV data with Perl?
If they are separated by random amount of whitespace, use #massa's advice below and use split function.

I want to replace a sequence name in fasta file with another name

I have one fasta file and one text file fasta file contains sequences in fasta format and text file contains name of genes now I want to replace name of the sequences in fasta file after '>' sign with the gene names in text file
I am new to perl though I have written a script but I don't know why its not working can anyone help me on that please
following is my script:
print"Enter annotated file...";
$f1=<STDIN>;
print"Enter sequence file...";
$f2=<STDIN>;
open(FILE1,$f1) || die"Can't open $f1";
#annotfile=<FILE1>;
open(FILE2,$f2) || die"Can't open $f2";
#seqfile=<FILE2>;
#d=split('\t',#annotfile[0]);
for($i=0;$i<scalar(#annotfile);$i++)
{
#curr_all=split('\t',#annotfile[$i]);
#curr_id[$i]=#curr_all[0];
#gene_nm[$i]=#curr_all[1];
}
for($j=0;$j<scalar(#seqfile);$j++)
{
$id=#curr_id[$j];
$gene=#gene_nm[$j];
#seqfile[$j]=~s/$id[$j]/$gene[$j]/g;
print #seqfile[$j];
}
my files looks like following:
annot.txt
pool75_contig_389 ubiquitin ligase e3a
pool75_contig_704 tumor susceptibility
pool75_contig_1977 serine threonine-protein phosphatase 4 catalytic subunit
pool75_contig_3064 bardet-biedl syndrome 2 protein P
pool75_contig_2499 succinyl- ligase
goat300.fasta
goat300.fasta
>pool75_contig_704
CCCTTTCTCCCTTCCCAACATTCAGAGATACTGAATCGAAACTCTTACTGTCTGTTAGAT
GACAAAGAGTTATCCATCCTACATACTCCAATTTCCTTCCGCAACTTGTGATTTCGCCGC
TTGAATCTTGACGCCGTGCGTCCACAGTTTGTTGTGTTTTATCAATCAAGGTCATTATCA
ACCGAAGACGCTATCTATTTTCTTGGCGAAGCTCTCGGAAAGGAGCCATCGAAATGGAAG
TATTTCTCAAGAAAGTCCGCGAGTTATCCCGGAAGCAGTTC
>pool75_contig_389
GACCTATACCGGACCGTCACTGAAAGNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
ACGATCCAGGCATGGAGTTGTGGTGACGAGTAGGAGGGTCACCGTGGTGAGCGGGAAGCC
TCGGGCGTGAGCCTGGGTGGAGCCGCCACGGGTGCAGATCTTGGTGGTAGTAGCAAATAT
TCAAGTGAGAACCTTGAAGGCCGAGGTGGAGAAGGNNNNNNNNNNNNNNNNNNNNNNNNN
NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNTCATTTGTAT
CGCCCGGAAAACGTCACAAGAACGGGAGTTGCGTACAGAA
>pool75_contig_1977
AAGGGACACCGTTGGGTGAGGCGAGCTGCGTTCCTCGAACCATGGCTTCAAAAAGCGACT
TAGACCGTCAGATTGAACAGCTCAGGGCCTGCAAGCTCATTACAGAGGATGAGGTTAAGG
CACTCTGCGCTAAGGCGCGTGAGATTTTAATTGAAGAGAGTAATGTCCAGTGCGTGGACT
CACCTGTCACGGTTTGTGGCGATATCCACGGCCAGTTTTACGACTTGATTGAACTGTTTA
AAGTGGGCGGAGATGTTC
>pool75_contig_3064
TTACTATTTCTGGGCCTTAAGACTGGCTTAGTCGCTTACGACCCTTATAACAATGTAGAT
GTATATTATAAGGATCTTCCTGATGGTGCTAACGCTATGTTAATTTATTCAAACTCACCG
ACAAAGGAACAGAATATGCTTTGGCAGGTGGAAACTGTTCGATAATTGGATTGAACGACG
GCGGATGCGAGGTATTTTGGACAGTCACTGGCGACTCCGTTTGCTCTCTTTGCTCGATTA
AATCCGACAGCGATAAGTCAAGAGATTTTGTGGTTGGCTCTGAAGATTTTGACATCCGAA
TCTTCCATGGGGATGCCATAATATATGAAATCACGGAGTCTGATG
>pool75_contig_2499
AAGAGAAGAGGTGAGTTTGAGTATTGTTTGTGTGTGTGTGGTTGGGTGAGTGTGTGGTAT
GTGGTGTATGTGTGTGATGAATGTATGTGAAAGAGAGTGATGAATCTCATGGATATGTTC
GAGTTCGTGGTTTCCATTGATCGGTTATAGCCGAGATGATGGATGTGTTCCATGTGTCTG
ATTTCAGTTTAGGATTGTGTTGATGATGTTGATGATGAAAATTGTTGATGGTGATGACGA
TAGTGATGATGATGACGATGTTTCGGATAATGGTGATGATGATGATGGTTCCGACGATGA
TGTTTCGCTTGATGATGGTGATAATGATGACTCCGAAAATAACGTTGACTCGGATGAG
Consider using Bio::SeqIO to parse your Fasta dataset, instead of doing it yourself. Bio::SeqIO lives for this task, and is well developed for it. Additionally, if you're in bioinformatics, it would serve you well to get to know Bio::SeqIO. Given this, consider the following:
use strict;
use warnings;
use Bio::SeqIO;
open my $fh, '<', 'annot.txt' or die $!;
my %annot = map { /(\S+)\s+(.+)/; $1 => $2 } <$fh>;
close $fh;
my $in = Bio::SeqIO->new( -file => 'goat300.fasta', -format => 'Fasta' );
while ( my $seq = $in->next_seq() ) {
my $seqID = $annot{ $seq->id } // $seq->id;
print "$seqID\n" . $seq->seq . "\n";
}
Output on your datasets:
tumor susceptibility
CCCTTTCTCCCTTCCCAACATTCAGAGATACTGAATCGAAACTCTTACTGTCTGTTAGATGACAAAGAGTTATCCATCCTACATACTCCAATTTCCTTCCGCAACTTGTGATTTCGCCGCTTGAATCTTGACGCCGTGCGTCCACAGTTTGTTGTGTTTTATCAATCAAGGTCATTATCAACCGAAGACGCTATCTATTTTCTTGGCGAAGCTCTCGGAAAGGAGCCATCGAAATGGAAGTATTTCTCAAGAAAGTCCGCGAGTTATCCCGGAAGCAGTTC
ubiquitin ligase e3a
GACCTATACCGGACCGTCACTGAAAGNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNACGATCCAGGCATGGAGTTGTGGTGACGAGTAGGAGGGTCACCGTGGTGAGCGGGAAGCCTCGGGCGTGAGCCTGGGTGGAGCCGCCACGGGTGCAGATCTTGGTGGTAGTAGCAAATATTCAAGTGAGAACCTTGAAGGCCGAGGTGGAGAAGGNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNTCATTTGTATCGCCCGGAAAACGTCACAAGAACGGGAGTTGCGTACAGAA
serine threonine-protein phosphatase 4 catalytic subunit
AAGGGACACCGTTGGGTGAGGCGAGCTGCGTTCCTCGAACCATGGCTTCAAAAAGCGACTTAGACCGTCAGATTGAACAGCTCAGGGCCTGCAAGCTCATTACAGAGGATGAGGTTAAGGCACTCTGCGCTAAGGCGCGTGAGATTTTAATTGAAGAGAGTAATGTCCAGTGCGTGGACTCACCTGTCACGGTTTGTGGCGATATCCACGGCCAGTTTTACGACTTGATTGAACTGTTTAAAGTGGGCGGAGATGTTC
bardet-biedl syndrome 2 protein P
TTACTATTTCTGGGCCTTAAGACTGGCTTAGTCGCTTACGACCCTTATAACAATGTAGATGTATATTATAAGGATCTTCCTGATGGTGCTAACGCTATGTTAATTTATTCAAACTCACCGACAAAGGAACAGAATATGCTTTGGCAGGTGGAAACTGTTCGATAATTGGATTGAACGACGGCGGATGCGAGGTATTTTGGACAGTCACTGGCGACTCCGTTTGCTCTCTTTGCTCGATTAAATCCGACAGCGATAAGTCAAGAGATTTTGTGGTTGGCTCTGAAGATTTTGACATCCGAATCTTCCATGGGGATGCCATAATATATGAAATCACGGAGTCTGATG
succinyl- ligase
AAGAGAAGAGGTGAGTTTGAGTATTGTTTGTGTGTGTGTGGTTGGGTGAGTGTGTGGTATGTGGTGTATGTGTGTGATGAATGTATGTGAAAGAGAGTGATGAATCTCATGGATATGTTCGAGTTCGTGGTTTCCATTGATCGGTTATAGCCGAGATGATGGATGTGTTCCATGTGTCTGATTTCAGTTTAGGATTGTGTTGATGATGTTGATGATGAAAATTGTTGATGGTGATGACGATAGTGATGATGATGACGATGTTTCGGATAATGGTGATGATGATGATGGTTCCGACGATGATGTTTCGCTTGATGATGGTGATAATGATGACTCCGAAAATAACGTTGACTCGGATGAG
The hash %annot is initialized by reading and capturing the contents of your annot.txt data. A Bio::SeqIO object is created using your goat300.fasta file data. The while loop iterates through your fasta sequences. The variable $seqID either takes the associated value of the key in the %annot hash or it keeps the current sequence ID (the // notation means defined or, so that insures $seqID will be defined). Finally, the Fasta record is printed.
Hope this helps!
There were a lot of warnings in your code, and your approach was inefficient. Let me first show you a working Perl program. I'll explain afterwards.
#!/usr/bin/perl
use strict;
use warnings;
# Read the annotations file
print"Enter annotated file...\n";
# my $f1 = <STDIN>;
my $f1 = 'annot.txt';
open(my $fh_annotations, '<', $f1) or die "Can't open $f1";
my #annotfile = <$fh_annotations>;
close $fh_annotations;
# Read the sequence file
print"Enter sequence file...\n";
# my $f2 = <STDIN>;
my $f2 = 'goat300.fasta';
open(my $fh_genes, '<', $f2) or die "Can't open $f2";
my #seqfile = <$fh_genes>;
close $fh_genes;
# Process the annotations data
my %names; # this hash is going to hold the names
foreach my $line (#annotfile) {
chomp $line; # remove newline
my #fields = split /\t/, $line; # split into array
$names{$fields[0]} = $fields[1]; # save in the hash as key->value pair
}
# Process the sequence data
foreach my $line (#seqfile) {
# Look at each line
if ($line =~ m/>(.+)$/) {
# If there is a heading there, remember it...
if (exists $names{$1}) {
# ... check if we know a name for it and replace it in the line
$line =~ s/($1)/$names{$1}/;
}
}
# output the line (this would be done to another filehandle)
print $line;
}
This reads both files and saves them in memory, just like yours did. But instead of trying to build two arrays for the names, I went with a hash, which is a key/value pair. Think of it like an array with names instead of numbers and no particular sorting.
Once these names are set up, I can process the sequence file. I simply look at each line and check if there is a heading there, by looking for the > sign. If it's there (it goes into $1 because of the parenthesis), I look if we have a hash entry (with exists) in our %names hash. If we do, we can replace the heading with the proper name.
After that, we could write it out to a new file. I'm just printing it.
I've used a few other techniques. Unfortunately the literature people get in a BioPerl context is quite outdated. Please take this advice, it will make your live easier.
Always use strict and warnings. They will tell you about problems with your code.
Always declare your variables with my. This is not like other languages, where you need to set up a variable at the top of your problem. You can declare it where you need it. The vars only live in a certain scope, which means between the nearest enclosing { and } brackets, or block.
Use three-argument open and lexical file handles for security. Read more here.
Perl offers foreach as an alternative to the C for loop. In this case, it made things a lot easier.
One more thing about this program: While this example data was rather short, I believe your actual data might be a lot larger. Consider processing the sequence file while you read it so you do not run out of memory. There's no need to save all the lines, unless you want to do something else with them.
open my $fh_out, '>', $filename_out or die $!;
open my $fh_in, '<', $filename_in or die $!;
while (my $line = <$fh_in>) {
# do stuff with the line, like your regex
print $fh_out $line;
}
close $fh_in;
close $fh_out;

Using Perl to parse a CSV file from a particular row to the end of the file

am very new to Perl and need your help
I have a CSV file xyz.csv with contents:
here level1 and er values are strings names...not numbers...
level1,er
level2,er2
level3,er3
level4,er4
I parse this CSV file using the script below and pass the fields to an array in the first run
open(my $d, '<', $file) or die "Could not open '$file' $!\n";
while (my $line = <$d>) {
chomp $line;
my #data = split "," , $line;
#XYX = ( [ "$data[0]", "$data[1]" ], );
}
For the second run I take an input from a command prompt and store in variable $val. My program should parse the CSV file from the value stored in variable until it reaches the end of the file
For example
I input level2 so I need a script to parse from the second line to the end of the CSV file, ignoring the values before level2 in the file, and pass these values (level2 to level4) to the #XYX = (["$data[1]","$data[1]"],);}
level2,er2
level3,er3
level4,er4
I input level3 so I need a script to parse from the third line to the end of the CSV file, ignoring the values before level3 in the file, and pass these values (level3 and level4) to the #XYX = (["$data[0]","$data[1]"],);}
level3,er3
level4,er4
How do I achieve that? Please do give your valuable suggestions. I appreciate your help
As long as you are certain that there are never any commas in the data you should be OK using split. But even so it would be wise to limit the split to two fields, so that you get everything up to the first comma and everything after it
There are a few issues with your code. First of all I hope you are putting use strict and use warnings at the top of all your Perl programs. That simple measure will catch many trivial problems that you could otherwise overlook, and so it is especially important before you ask for help with your code
It isn't commonly known, but putting a newline "\n" at the end of your die string prevent Perl from giving file and line number details in the output of where the error occurred. While this may be what you want, it is usually more helpful to be given the extra information
Your variable names are verly unhelpful, and by convention Perl variables consist of lower-case alphanumerics and underscores. Names like #XYX and $W don't help me understand your code at all!
Rather than splitting to an array, it looks like you would be better off putting the two fields into two scalar variables to avoid all that indexing. And I am not sure what you intend by #XYX = (["$data[1]","$data[1]"],). First of all do you really mean to use $data[1] twice? Secondly, your should never put scalar variables inside double quotes, as it does something very specific, and unless you know what that is you should avoid it. Finally, did you mean to push an anonymous array onto #XYX each time around the loop? Otherwise the contents of the array will be overwritten each time a line is read from the file, and the earlier data will be lost
This program uses a regular expression to extract $level_num from the first field. All it does it find the first sequence of digits in the string, which can then be compared to the minimum required level $min_level to decide whether a line from the log is relevant
use strict;
use warnings;
my $file = 'xyz.csv';
my $min_level = 3;
my #list;
open my $fh, '<', $file or die "Could not open '$file' $!";
while (my $line = <$fh>) {
chomp $line;
my ($level, $error) = split ',', $line, 2;
my ($level_num) = $level =~ /(\d+)/;
next unless $level_num >= $min_level;
push #list, [ $level, $error ];
}
For deciding which records to process you can use the "flip-flop" operator (..) along these lines.
#!/usr/bin/perl
use strict;
use warnings;
use 5.010;
my $level = shift || 'level1';
while (<DATA>) {
if (/^\Q$level,/ .. 0) {
print;
}
}
__DATA__
level1,er
level2,er2
level3,er3
level4,er4
The flip-flop operator returns false until its first operand is true. At that point it returns false until its second operand is true; at which point it returns false again.
I'm assuming that your file is ordered so that once you start to process it, you never want to stop. That means that the first operand to the flip-flop can be /^\Q$level,/ (match the string $level at the start of the line) and the second operand can just be zero (as we never want it to stop processing).
I'd also strongly recommend not parsing CSV records using split /,/. That may work on your current data but, in general, the fields in a CSV file are allowed to contain embedded commas which will break this approach. Instead, have a look at Text::CSV or Text::ParseWords (which is included with the standard Perl distribution).
Update: I seem to have got a couple of downvotes on this. It would be great if people would take the time to explain why.
#!/usr/bin/perl
use strict;
use warnings;
use Text::CSV;
my #XYZ;
my $file = 'xyz.csv';
open my $fh, '<', $file or die "$file: $!\n";
my $level = shift; # get level from commandline
my $getall = not defined $level; # true if level not given on commandline
my $parser = Text::CSV->new({ binary => 1 }); # object for parsing lines of CSV
while (my $row = $parser->getline($fh)) # $row is an array reference containing cells from a line of CSV
{
if ($getall # if level was not given on commandline, then put all rows into #XYZ
or # if level *was* given on commandline, then...
$row->[0] eq $level .. 0 # ...wait until the first cell in a row equals $level, then put that row and all subsequent rows into #XYZ
)
{
push #XYZ, $row;
}
}
close $fh;
#!/usr/bin/perl
use strict;
use warnings;
open(my $data, '<', $file) or die "Could not open '$file' $!\n";
my $level = shift ||"level1";
while (my $line = <$data>) {
chomp $line;
my #fields = split "," , $line;
if($fields[0] eq $level .. 0){
print "\n$fields[0]\n";
print "$fields[1]\n";
}}
This worked....thanks ALL for your help...

In Perl, how can I read the contents of a file into an array? [duplicate]

This question already has answers here:
Closed 10 years ago.
Possible Duplicate:
Easiest way to open a text file and read it into an array with Perl
I'm new to Perl and want for each file push the contents of that file in one separate array, I managed to do so by the following, which uses if statements. But, I want something like $1 for my arrays. Is that possible?
#!/usr/bin/perl
use strict;
my #karray;
my #sarray;
my #testarr = (#sarray,#karray);
my $stemplate = "foo.txt";
my $ktemplate = "bar.txt";
sub pushf2a {
open(IN, "<$_[0]") || die;
while (<IN>) {
if ($_[0] eq $stemplate) {
push (#sarray,$_);
} else {
push (#karray,$_);
}
}
close(IN) || die $!;
}
&pushf2a($stemplate,#sarray);
&pushf2a($ktemplate,#karray);
print sort #sarray;
print sort #karray;
I want something like this:
#!/bin/sh
myfoo=(#s,#k)
barf() {
pushtoarray $1
}
barf #s
barf #k
If you are going to slurp a file, use File::Slurp:
use File::Slurp;
my #lines = read_file 'filename';
Firstly, you can't call an array $1 in Perl, as that (and all the other scalars with a number as their name) are used by the regex engine and so can get overwritten whenever a regex match is run.
Secondly, you can read a file into an array much more easily than that: just use the diamond operator in list context.
open my $file, '<', $filename or die $!;
my #array = <$file>;
close $file;
You then get an array of the lines of the file, as split by the current line separator which is by default what you might expect it to be i.e. your platform's newline.
Thirdly, your pushf2a sub is rather strange, especially passing in an array and then not using it. You could write a subroutine which takes a filename and returns an array, and thus avoid your issue with the internal if statements:
sub f2a {
open my $file, '<', $_[0] or die $!;
<$file>;
# $file closes here as it goes out of scope
}
my #sarray = f2a($stemplate);
my #karray = f2a($ktemplate);
Overall I'm unsure exactly what the best solution is as I can't quite make out exactly what you want to do, but maybe this will help you out.
don't understand, what you want like $1 for arrays, but good practice is this code:
i contain files and their content in HoA - hash of arrays
my $main_file = qq(container.txt); #contains all names of your files.
my $fh; #filehandler of main file
open $fh, "<", $main_file or die "something wrong with your main file! check it!\n";
my %hash; # this hash for containing all files
while(<$fh>){
my $tmp_fh; # will use it for files in main file
#$_ contain next name of file you want to push into array
open $tmp_fh, "<", $_ or next; #next? maybe die, don't bother about it
$hash{$_}=[<$tmp_fh>];
#close $tmp_fh; #it will close automatically
}
close $fh;

Perl nested loops

I have a text file with the following contents:
NW1 SN1 DEV1
NW2 SN1 DEV2
I wrote a Perl script to iterate over the file, but it is running only once. The code is:
open(INPUT1,"input.txt");
#input_array = <INPUT1>;
for($i=0;$i<#input_array;$i++)
{
my ($ser,$node,#dev)=split(/ +/,$input_array[$i]);
for($x=0;$x<#dev;$x++)
{
print("Hi");
}
}
The script is iterating for the first line but not iterating for second line.
The code you posted could be improved, and brought up to more modern standards.
It uses a bareword filehandle INPUT1.
It doesn't use 3-arg open.
It doesn't use strict or warnings (see this question).
It doesn't check the return value of open or close. ( That's what the autodie line is for in the following code )
It uses C-style for loops when it doesn't need to.
It loads the entire file into memory even though it only deals with the file one line at a time.
use strict;
use warnings;
use autodie; # checks return value of open and close for us
# 3 arg open
open( my $in_fh, '<', 'input.txt' );
# don't read the file into memory until needed
while( <$in_fh> ){
# using $_ simplified this line
my ($ser,$node,#dev) = split;
# no need to track the indices just loop over the array
for my $dev (#dev){
print "Hi\n";
}
}
close $in_fh;
If for some reason you really did need the indices of the #dev array it would be better to write it like this:
for my $x ( 0..$#dev ){
...
}
If you want to explicitly store the line into a variable of a different name, you would change the while loop to this:
while( my $line = <$in_fh> ){
my ($ser,$node,#dev) = split / +/ $line;
...
}
You forgot to enter to slurp mode of the '<>' operator. To suck in complete file you should do this:
open(INPUT1,"input.txt");
undef $/;
#input_array = split(/\r?\n/, <INPUT1>);
close INPUT1;
or better yet like this:
open(INPUT1,"input.txt");
while(<INPUT1>) {
chomp;
my ($ser,$node,#dev)=split(/ +/,$_);
for($x=0;$x<#dev;$x++)
{
print("Hi");
}
}
close INPUT1;