How to find position of a word by using a counter? - perl

I am currently working on a code that changes certain words to Shakespearean words. I have to extract the sentences that contain the words and print them out into another file. I had to remove .START from the beginning of each file.
First I split the files with the text by spaces, so now I have the words. Next, I iterated the words through a hash. The hash keys and values are from a tab delimited file that is structured as so, OldEng/ModernEng (lc_Shakespeare_lexicon.txt). Right now, I'm trying to figure out how to find the exact position of each modern English word that is found, change it to the Shakespearean; then find the sentences with the change words and printing them out to a different file. Most of the code is finished except for this last part. Here is my code so far:
#!/usr/bin/perl -w
use diagnostics;
use strict;
#Declare variables
my $counter=();
my %hash=();
my $conv1=();
my $conv2=();
my $ssph=();
my #text=();
my $key=();
my $value=();
my $conversion=();
my #rmv=();
my $splits=();
my $words=();
my #word=();
my $vals=();
my $existingdir='/home/nelly/Desktop';
my #file='Sentences.txt';
my $eng_words=();
my $results=();
my $storage=();
#Open file to tab delimited words
open (FILE,"<", "lc_shakespeare_lexicon.txt") or die "could not open lc_shakespeare_lexicon.txt\n";
#split words by tabs
while (<FILE>){
chomp($_);
($value, $key)= (split(/\t/), $_);
$hash{$value}=$key;
}
#open directory to Shakespearean files
my $dir="/home/nelly/Desktop/input";
opendir(DIR,$dir) or die "can't opendir Shakespeare_input.tar.gz";
#Use grep to get WSJ file and store into an array
my #array= grep {/WSJ/} readdir(DIR);
#store file in a scalar
foreach my $file(#array){
#open files inside of input
open (DATA,"<", "/home/nelly/Desktop/input/$file") or die "could not open $file\n";
#loop through each file
while (<DATA>){
#text=$_;
chomp(#text);
#Remove .START
#rmv=grep(!/.START/, #text);
foreach $splits(#rmv){
#split data into separate words
#word=(split(/ /, $splits));
#Loop through each word and replace with Shakespearean word that exists
$counter=0;
foreach $words(#word){
if (exists $hash{$words}){
$eng_words= $hash{$words};
$results=$counter;
print "$counter\n";
$counter++;
#create a new directory and store senteces with Shakespearean words in new file called "Sentences.txt"
mkdir $existingdir unless -d $existingdir;
open my $FILE, ">>", "$existingdir/#file", or die "Can't open $existingdir/conversion.txt'\n";
#print $FILE "#words\n";
close ($FILE);
}
}
}
}
}
close (FILE);
close (DIR);

Natural language processing is very hard to get right except in trivial cases, for instance it is difficult to define exactly what is meant by a word or a sentence, and it is awkward to distinguish between a single quote and an apostrophe when they are both represented using the U+0027 "apostrophe" character '
Without any example data it is difficult to write a reliable solution, but the program below should be reasonably close
Please note the following
use warnings is preferable to -w on the shebang line
A program should contain as few comments as possible as long as it is comprehensible. Too many comments just make the program bigger and harder to grasp without adding any new information. The choice of identifiers should make the code mostly self documenting
I believe use diagnostics to be unnecessary. Most messages are fairly self-explanatory, and diagnostics can produce large amounts of unnecessary output
Because you are opening multiple files it is more concise to use autodie which will avoid the need to explicitly test every open call for success
It is much better to use lexical file handles, such as open my $fh ... instead of global ones, like open FH .... For one thing a lexical file handle will be implicitly closed when it goes out of scope, which helps to tidy up the program a lot by making explicit close calls unnecessary
I have removed all of the variable declarations from the top of the program except those that are non-empty. This approach is considered to be best practice as it aids debugging and assists the writing of clean code
The program lower-cases the original word using lc before checking to see if there is a matching entry in the hash. If a translation is found, then the new word is capitalised using ucfirst if the original word started with a capital letter
I have written a regular expression that will take the next sentence from the beginning of the string $content. But this is one of the things that I can't get right without sample data, and there may well be problems, for instance, with sentences that end with a closing quotation mark or a closing parenthesis
use strict;
use warnings;
use autodie;
my $lexicon = 'lc_shakespeare_lexicon.txt';
my $dir = '/home/nelly/Desktop/input';
my $existing_dir = '/home/nelly/Desktop';
my $sentences = 'Sentences.txt';
my %lexicon = do {
open my ($fh), '<', $lexicon;
local $/;
reverse(<$fh> =~ /[^\t\n\r]+/g);
};
my #files = do {
opendir my ($dh), $dir;
grep /WSJ/, readdir $dh;
};
for my $file (#files) {
my $contents = do {
open my $fh, '<', "$dir/$file";
join '', grep { not /\A\.START/ } <$fh>;
};
# Change any CR or LF to a space, and reduce multiple spaces to single spaces
$contents =~ tr/\r\n/ /;
$contents =~ s/ {2,}/ /g;
# Find and process each sentence
while ( $contents =~ / \s* (.+?[.?!]) (?= \s+ [A-Z] | \s* \z ) /gx ) {
my $sentence = $1;
my #words = split ' ', $sentence;
my $changed;
for my $word (#words) {
my $eng_word = $lexicon{lc $word};
$eng_word = ucfirst $eng_word if $word =~ /\A[A-Z]/;
if ($eng_word) {
$word = $eng_word;
++$changed;
}
}
if ($changed) {
mkdir $existing_dir unless -d $existing_dir;
open my $out_fh, '>>', "$existing_dir/$sentences";
print "#words\n";
}
}
}

Related

Search for multiple terms in perl

I have a file with more than hundred single column entries. I need to search for each of these entries into a file of multiple column and more than thousand entries and need a output file. I tried these codes:
#!/usr/bin/perl -w
use strict;
use warnings;
print "Enter the input file name:";
my $inputfile = <STDIN>;
chomp($inputfile);
print "\nEnter the search file name:";
my $searchfile=<STDIN>;
chomp($searchfile);
open (INPUTFILE, $inputfile) || die;
open (SEARCHFILE, $searchfile) || die;
open (OUT, ">write.txt") || die;
while (my $line=<SEARCHFILE>){
while (<INPUTFILE>) {
if (/$line/){
print OUT $_;
}
}
}
close (INPUTFILE) || die;
close (SEARCHFILE) || die;
close (OUT) || die;
The output file has only one line. It has searched the term from the search file into input file, but only for the first term, not for all. Please help!
When you read INPUTFILE in the inner loop, it's read to the end during the first round of SEARCHFILE. Because it's not reset, the filehandle is used up and will always return eof.
If there are hundreds of lines, but not several 100,000 you can easily read it into an array first and then use that for the lookup. The fact that it's single-column makes that very easy. Note that this is less efficient then the alternative solution below.
chomp( my #needles = <SEARCHFILE> );
while (<INPUTFILE>) {
foreach my $needle (#needles) {
print OUT $_ if m/\Q$needle\E/; # \Q end \E quote regex meta chars
}
}
Alternatively you can also build one large lookup regex that matches all the strings in one go. That is probably faster than iterating the array for each line.
# open ...
chomp( my #needles = <SEARCHFILE> );
my $lookup = join '|', map quotemeta, #needles;
my $lookup_regex = qr/$lookup/; # possibly with /i?
while (my $line = <INPUTFILE>) {
print OUT $line if $line =~ $lookup_regex;
}
The quotemeta takes care of strings that contain regex meta characters like / or | or even .. It's the same as using \Q and \E as above.
Please also use three-argument-open and named filehandles.
open my $fh_searchfile, '<', $searchfile or die $!;
open my $fh_inputfile, '<', $inputfile or die $!;
open my $fh_out, '>', 'write.txt' or die $!;
chomp( my #needles = <$fh_searchfile> );
# ...
The three-argument-open is important because you are taking user input and using it as the filename directly. A malicious user could enter something like | rm -rf *, which would open a pipe to a delete all my files without asking program. Oops. But if you specify the '<' read open method explicitly in its own parameter, the method characters are ignored in the third param.
The lexical filehandle $fh is, as the name says, lexical, while INPUTFILE is a GLOB, which makes it global. That's not so bad if you only have this one script and no modules, but as soon as you deal with different packages it becomes problematic because those are super-global and every part of the program sees them. That can lead to name collisions and weird stuff happening.

Match file names in if condition of perl

I've files with filenames such as lin.txt and lin1.txt along with other .txt files. I need to find only these files and print its content only by one. I've the below code, but its somehow not matching the files starting with lin*. What is the issue?
$te_dir= "/projects/xxx/";
opendir (DIR, $te_dir) or die $!;
while (my $file = readdir(DIR))
{
if ($file=~/\.txt/)
{
#// Doing some tasks.
if($file ~= 'lin*.txt')
{
$linfile=$te_dir/$file;
open(LINFILE, $linfile) or die "Couldn't open file $file:$!";
while(my $line = <LINFILE>)
{
print $line;
}
close LINFILE;
}
}
}
You are mixing globs (shell wildcards) with regular expressions. These are two different formalisms with different syntax and semantics. In regular expressions (which is what Perl matching uses), n* matches zero or more occurrences of the character n. You probably mean
if ($file =~ /lin.*\.txt/)
Notice also the syntax error in the operator. You correctly have =~ in the first conditional, but you misspelled it as ~= where you do this comparison. (Maybe it's just a transcription error; for me, this creates a clear syntax error, so the script would not run in the first place.)
As noted in #brianadams' answer, the proper regular expression for this is
if ($file =~ /^lin.*\.txt$/)
with beginning of line ^ and end of line $ anchors to prevent e.g. feline.txt.html from matching. The default behavior of Perl's regular expressions is to find a match anywhere in the input string.
Here's a quick (and minimal) rewrite of your code that might help:
use strict;
use warnings;
my $te_dir = "/projects/xxx/";
opendir( my $dirh, $te_dir ) or die "Could not open '$te_dir': $!";
while ( my $file = readdir($dirh) ) {
next unless $file =~ /\.txt$/;
#// Doing some tasks.
if ( $file =~ /^ lin \d* \.txt $/x ) {
my $linfile = "$te_dir/$file";
open( my $fh, $linfile ) or die "Couldn't open file $linfile: $!";
while ( my $line = <$fh> ) {
print $line;
}
close $fh or die "Could not close $linfile: $!";
}
}
First, note that we've put strict and warnings at the top of the code. That will tell you about all sorts of interesting issues, including misspelled variable names.
Next, we've switch to lexical handles (e.g., my $dirh instead of DIR). The "bareword" version of the handles you're using (DIR and LINFILE have been discouraged for a long time because those are effectively global constructs and generally global data is bad because when it gets broken, it's awfully hard to tell what broke it, so we much, much prefer the lexical versions (the handles declared with the my builtin).
Also, this line you had probably doesn't do what you're thinking:
$linfile=$te_dir/$file;
You're trying to smash together a directory and filename with a forward slash, but since you didn't use string interpolation, you're actually using division. Both your director and filename will, in this numeric context, probably evaluate to zero, giving you a divide by zero error when you're trying to open a file!
However, if you're willing to use a CPAN module, you can make this even easier:
use strict;
use warnings;
use File::Find::Rule;
my $te_dir = "/projects/xxx/";
my #files = File::Find::Rule->file->name('lin*.txt')->in($te_dir);
foreach my $linfile (#files) {
#// Doing some tasks.
open my $fh, $linfile or die "Couldn't open file $linfile: $!";
while ( my $line = <$fh> ) {
print $line;
}
}
No muss, no fuss. Get only the files you want in the first pass and already have the correct file names (note that I didn't close the filehandle because it will close automatically when $fh goes out of scope at the end of the foreach loop.)
To match files starting with lin
if ( $file =~ /^lin.*\.txt$/ )
Try changing your 2nd if condition from this,
if($file ~= 'lin*.txt')
to this,
if($file =~ /lin*\.txt/)
You could also try: if($file =~ /^lin*\.txt/) , as already pointed out in other answers, but you'll need to make sure that the file names stored in the $file variable contain only the file name and not the entire path as well.

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;

perl print only the last line of the array

I am trying to print the array but the out put contain only the last line of the array. the partial code is as follow.
open OUT, "> /myFile.txt"
or die "Couldn't open output file: $!";
foreach (#result) {
print OUT;
}
the out put is
List Z
which is the last line, but when I do print "#result" the out put is
List A
List B
List C so on...
I am little bit confuse why the results are different on the same array.
Working on a hunch, I tried adding \r to the end of your input lines, and sure enough, it creates the illusion that only the last line of your input is printed to the file. Here's the code to test it:
use strict;
use warnings;
my #result = map "$_\r", 'A' .. 'Z';
open (OUT, "> myFile.txt") or die("Couldn't open output file: $!");
foreach (#result) {
print OUT ;
}
What you have probably done is performed chomp on lines from a file from a different operating system (DOS, Windows), which does not strip the \r line endings. Hence, when the lines are printed, the lines overwrite each other.
If this is what is wrong, the solution is to use the dos2unix tool to fix your files, or to use:
s/\s+\z//;
to strip your newlines.
You may inspect your input by using the Data::Dumper module, using the option Useqq, e.g.:
use Data::Dumper;
$Data::Dumper::Useqq = 1;
print Dumper \#result;
If these whitespace characters are in your output, they will then be visible.
the problem is here
open OUT, "> /myFile.txt"
this should be
open OUT, ">>", "/myfile.txt"
What you wrote overwrites the entire file for each iteration of the foreach(#result) loop.
What you are intending to do is append to it (">>").
">>" appends, ">" overwrites.
Also take note of how i broke ">> /myfile.txt" into ">>", "/myfile.txt".
This is both more secure, and more robust for less specific applications of open.
Foreign line terminators from any platform can easily be fixed by clearing whitespace from the end of the line and adding it back when printing it
Like this
open my $out, '>', '/myFile.txt' or die "Couldn't open output file: $!";
foreach (#result) {
s/\s+$//;
print $out "$_\n";
}
or
foreach my $line (#result) {
$line =~ s/\s+$//;
print $out "$line\n";
}

Replace substring with string from second csv file

Earlier I was working on a loop within a loop and if a match was made it would replace the entire string from the second loop file. Now i have a slightly different situation. I'm trying to replace a substring from the first loop with a string from the second loop. They're both csv files and semicolon delimited. What i'm trying to replace are special characters: from the numerical code to the character itself The first file looks like:
1;2;bla&#322blabla &#261bla;7;8
3;4;bl&#261blabla;9;10
2;3;blablabla&#261ał8;9
and the second file has the numerical code and the corresponding character:
Ą;Ą
ą;ą
Ǟ;Ǟ
Á;Á
á;á
Â;Â
ł;ł
The first semicolon in the second file belongs to the numerical code of the corresponding character and should not be used to split the file. The result should be:
1;2;blałblabla ąbla;7;8
3;4;bląblabla;9;10
2;3;blablablaąał;8;9
This is the code I have. How can i fix this?
use strict;
use warnings;
my $inputfile1 = shift || die "input/output!\n";
my $inputfile2 = shift || die "input/output!\n";
my $outputfile = shift || die "output!\n";
open my $INFILE1, '<', $inputfile1 or die "Used/Not found :$!\n";
open my $INFILE2, '<', $inputfile2 or die "Used/Not found :$!\n";
open my $OUTFILE, '>', $outputfile or die "Used/Not found :$!\n";
my $infile2_pos = tell $INFILE2;
while (<$INFILE1>) {
s/"//g;
my #elements = split /;/, $_;
seek $INFILE2, $infile2_pos, 0;
while (<$INFILE2>) {
s/"//g;
my #loopelements = split /;/, $_;
#### The problem part ####
if (($elements[2] =~ /\&\#\d{3}\;/g) and (($elements[2]) eq ($loopelements[0]))){
$elements[2] =~ s/(\&\#\d{3}\;)/$loopelements[1]/g;
print "$2. elements[2]\n";
}
#### End problem part #####
}
my $output_line = join(";", #elements);
print $OUTFILE $output_line;
#print "\n"
}
close $INFILE1;
close $INFILE2;
close $OUTFILE;
exit 0;
Assuming your character codes are standard Unicode entities, you are better off using HTML::Entities to decode them.
This program processes the data you show in your first file and ignores the second file completely. The output seems to be what you want.
use strict;
use warnings;
use HTML::Entities 'decode_entities';
binmode STDOUT, ":utf8";
while (<DATA>) {
print decode_entities($_);
}
__DATA__
1;2;bla&#322blabla &#261bla;7;8
3;4;bl&#261blabla;9;10
2;3;blablabla&#261ał8;9
output
1;2;blałblabla ąbla;7;8
3;4;bląblabla;9;10
2;3;blablablaąał8;9
You split your #elements at every occurrence of ;, which is then removed. You will not find it in your data, the semicolon in your Regexp can never match, so no substitutions are done.
Anyway, using seek is somewhat disturbing for me. As you have a reasonable number of replacement codes (<5000), you might consider putting them into a hash:
my %subst;
while(<$INFILE2>){
/^&#(\d{3});;(.*)\n/;
$subst{$1} = $2;
}
Then we can do:
while(<$INFILE1>){
s| &# (\d{3}) | $subst{$1} // "&#$1" |egx;
# (don't try to concat undef
# when no substitution for our code is defined)
print $OUTFILE $_;
}
We do not have to split the files or view them as CSV data if replacement should occur everywhere in INFILE1. My solution should speed things up a bit (parsing INFILE2 only once). Here I assumed your input data is correct and the number codes are not terminated by a semicolon but by length. You might want to remove that from your Regexes.(i.e. m/&#\d{3}/)
If you have trouble with character encodings, you might want to open your files with :uft8 and/or use Encode or similar.