I would like to know how to append to a text file using Perl in this condition.
I have a text file, the content of it is:
apple,123,456,orange
cat,789,lion
I have a variable in a loop like this
for 1st loop:
my $text1 = "hi"
my $text2 = "go"
for 2nd loop:
my $text1 = "banana"
my $text2 = "car"
I would like to have the result in the text file
apple,123,456,orange,hi,banana
cat,789,lion,go,car
How can I do this?
You haven't described your problem very well and seem to be ignoring the requests for additional information. However, here's a program that matches your description and may help you
use strict;
use warnings;
my #extra = (
[qw/ hi go /],
[qw/ banana car /],
);
my #data = <DATA>;
chomp #data;
for ( #extra ) {
my ($text1, $text2) = #$_;
$data[0] .= ",$text1";
$data[1] .= ",$text2";
}
print "$_\n" for #data;
__DATA__
apple,123,456,orange
cat,789,lion
output
apple,123,456,orange,hi,banana
cat,789,lion,go,car
Related
I would like to check one of the file's values contains on another file. if one of the value contains it will show there is existing bin for that specific, if no, it will show there is no existing bin limit. the problem is I am not sure how to check all values at once.
first DID1 text file value contain :
L84A:D:O:M:
L84C:B:E:D:
second DID text file value contain :
L84A:B:E:Q:X:F:i:M:Y:
L84C:B:E:Q:X:F:i:M:Y:
L83A:B:E:Q:X:F:i:M:Y:
if first 4words value are match, need to check all value for that line.
for example L84A in first text file & second text file value has M . it should print out there is an existing M bin
below is my code :
use strict;
use warnings;
my $filename = 'DID.txt';
my $filename1 = 'DID1.txt';
my $count = 0;
open( FILE2, "<$filename1" )
or die("Could not open log file. $!\n");
while (<FILE2>) {
my ($number) = $_;
chomp($number);
my #values1 = split( ':', $number );
open( FILE, "<$filename" )
or die("Could not open log file. $!\n");
while (<FILE>) {
my ($line) = $_;
chomp($line);
my #values = split( ':', $line );
foreach my $val (#values) {
if ( $val =~ /$values1[0]/ ) {
$count++;
if ( $values[$count] =~ /$values1[$count]/ ) {
print
"Yes ,There is an existing bin & DID\n #values1\n";
}
else {
print "No, There is an existing bin & DID\n";
}
}
}
}
}
I cannot check all value. please help to give any advice on it since this is my first time learning for perl language. Thanks a lot :)
Based on my understanding I write this code:
use strict;
use warnings;
#use ReadWrite;
use Array::Utils qw(:all);
use vars qw($my1file $myfile1cnt $my2file $myfile2cnt #output);
$my1file = "did1.txt"; $my2file = "did2.txt";
We are going to read both first and second files (DID1 and DID2).
readFileinString($my1file, \$myfile1cnt); readFileinString($my2file, \$myfile2cnt);
In first file, as per the OP's request the first four characters should be matched with second file and then if they matched we need to check rest of the characters in the first file with the second one.
while($myfile1cnt=~m/^((\w){4})\:([^\n]+)$/mig)
{
print "<LineStart>";
my $lineChk = $1; my $full_Line = $3; #print ": $full_Line\n";
my #First_values = split /\:/, $full_Line; #print join "\n", #First_values;
If the first four digit matched then,
if($myfile2cnt=~m/^$lineChk\:([^\n]+)$/m)
{
Storing the rest of the content in the same and to be split with colon and getting the characters to be matched with first file contents.
my $FullLine = $1; my #second_values = split /:/, $FullLine;
Then search each letter first and second content which matched line...
foreach my $sngletter(#First_values)
{
If the letters are matched with first and second file its going to be printed.
if( grep {$_ eq "$sngletter"} #second_values)
{
print "Matched: $sngletter\t";
}
}
}
else { print "Not Matched..."; }
This is just information that the line end.
print "<LineEnd>\n"
}
#------------------>Reading a file
sub readFileinString
#------------------>
{
my $File = shift;
my $string = shift;
use File::Basename;
my $filenames = basename($File);
open(FILE1, "<$File") or die "\nFailed Reading File: [$File]\n\tReason: $!";
read(FILE1, $$string, -s $File, 0);
close(FILE1);
}
Read search pattern and data into hash (first field is a key), then go through data and select only field included into pattern for this key.
use strict;
use warnings;
use feature 'say';
my $input1 = 'DID1.txt'; # look for key,pattern(array)
my $input2 = 'DID.txt'; # data - key,elements(array)
my $pattern;
my $data;
my %result;
$pattern = file2hash($input1); # read pattern into hash
$data = file2hash($input2); # read data into hash
while( my($k,$v) = each %{$data} ) { # walk through data
next unless defined $pattern->{$k}; # skip those which is not in pattern hash
my $find = join '|', #{ $pattern->{$k} }; # form search pattern for grep
my #found = grep {/$find/} #{ $v }; # extract only those of interest
$result{$k} = \#found; # store in result hash
}
while( my($k,$v) = each %result ) { # walk through result hash
say "$k has " . join ':', #{ $v }; # output final result
}
sub file2hash {
my $filename = shift;
my %hash;
my $fh;
open $fh, '<', $filename
or die "Couldn't open $filename";
while(<$fh>) {
chomp;
next if /^\s*$/; # skip empty lines
my($key,#data) = split ':';
$hash{$key} = \#data;
}
close $fh;
return \%hash;
}
Output
L84C has B:E
L84A has M
I am trying to write a big script but I am stuck on a part. I want to sprit an array based on ".."
From the script I got this:
print #coordinates;
gene complement(872..1288)
my desired output:
complement 872 1288
I tried:
1) my #answer = split(.., #coordinates)
print("#answer\n");
2) my #answer = split /../, #coordinates;
3) print +(split /\../)[-1],[-2],[-3] while <#coordinates>
4) foreach my $anwser ( #coordinates )
{$anwser =~ s/../"\t"/;
print $anwser;}
5) my #answer = split(/../, "complement(872..1288)"); #to see if the printed array is problematic.
which prints:
) ) ) ) ) ) ) ) )
6) my #answer = split /"gene "/, #coordinates; # I tried to "catch" the entire output's spaces and tabs
which prints
0000000000000000000000000000000001000000000100000000
But none of them works. Does anyone has any idea how to step over this issue?
Ps, unfortunately, I can't run my script right now on Linux so I used this website to run my script. I hope this is not the reason why I didn't get my desired output.
my $RE_COMPLEMENT = qr{(complement)\((\d+)\.\.(\d+)\)}msx;
for my $item (#coordinates) {
my ($head, $i, $j) = $item =~ $RE_COMPLEMENT;
if (defined($head) && defined($i) && defined($j)) {
print("$head\t$i\t$j\n");
}
}
split operates on a scalar, not on an array.
my $string = 'gene complement(872..1288)';
my #parts = split /\.\./, $string;
print $parts[0]; # gene complement(872
print $parts[1]; # 1288)
To get the desired output, you can use a substitution:
my $string = 'gene complement(872..1288)';
$string =~ s/gene +|\)//g;
$string =~ s/\.\./ /;
$string =~ s/\(/ /;
Desired effect can be achieved with
use of tr operator to replace '(.)' => ' '
then splitting data string into element on space
storing only required part of array
output elements of array joined with tabulation
use strict;
use warnings;
use feature 'say';
my $data = <DATA>;
chomp $data;
$data =~ tr/(.)/ /;
my #elements = (split ' ', $data)[1..3];
say join "\t", #elements;
__DATA__
gene complement(872..1288)
Or as an alternative solution with only substitutions (without splitting data string into array)
use strict;
use warnings;
use feature 'say';
my $data = <DATA>;
chomp $data;
$data =~ s/gene\s+//;
$data =~ s/\)//;
$data =~ s/[(.]+/\t/g;
say $data;
__DATA__
gene complement(872..1288)
Output
complement 872 1288
I trying to parse a GenBank file so I could get the accession number, the definition, the size of the file and the DNA sequence
Is there a way to modify my code and make it shorter and just declare all the variables at once like they do in the book and parse the file in one or two blocks of code?
If you have access to Bio Perl, you might find a solution such as the following.
#!/usr/bin/perl
use strict;
use warnings;
use Bio::SeqIO;
my $in = Bio::SeqIO->new( -file => "input.txt",
-format => 'GenBank');
while ( my $seq = $in->next_seq ) {
my $acc = $seq->accession;
my $length = $seq->length;
my $definition = $seq->desc;
my $type = $seq->molecule;
my $organism = $seq->species->binomial;
if ($type eq 'mRNA' &&
$organism =~ /homo sapiens/i &&
$acc =~ /[A-Za-z]{2}_[0-9]{6,}/ )
{
print "$acc | $definition | $length\n";
print $seq->seq, "\n";
print "\n";
}
}
I was able to capture the 5 variables from a sample GenBank file I have (input.txt). It should simplify your code.
I've initialized a hash with Names and their class ranking as follows
a=>5,b=>2,c=>1,d=>3,e=>5
I've this code so far
my %Ranks = reverse %Class; #As I need to find out who's ranked first
print "\nFirst place goes to.... ", $Ranks{1};
The code only prints out
"First place goes to...."
I want it to print out
First place goes to....c
Could you tell me where' I'm going wrong here?
The class hash prints correctly
but If I try to print the reversed hash using
foreach $t (keys %Ranks) {
print "\n $t $Ranks{$t}"; }
It prints
5
abc23
cab2
ord
If this helps in any way
FULL CODE
#Script to read from the data file and initialize it into a hash
my %Code;
my %Ranks;
#Check whether the file exists
open(fh, "Task1.txt") or die "The File Does Not Exist!\n", $!;
while (my $line = <fh>) {
chomp $line;
my #fields = split /,/, $line;
$Code{$fields[0]} = $fields[1];
$Class{$fields[0]} = $fields[2];
}
close(fh);
#Prints the dataset
print "Code \t Name\n";
foreach $code ( keys %Code) {
print "$code \t $Code{$code}\n";
}
#Find out who comes first
my %Ranks = reverse %Class;
foreach $t (keys %Ranks)
{
print "\n $t $Ranks{$t}";
}
print "\nFirst place goes to.... ", $Ranks{1}, "\n";
When you want to check what your data structures actually contain, use Data::Dumper. use Data::Dumper; local $Data::Dumper::Useqq = 1; print(Dumper(\%Class));. You'll find un-chomped newlines.
You need to use chomp. At present your $fields[2] value has a trailing newline.
Change your file read loop to this
while (my $line = <fh>) {
chomp $line;
my #fields = split /,/, $line;
$Code{$fields[0]} = $fields[1];
$Class{$fields[0]} = $fields[2];
}
I have created an array as follows
while (defined ($line = `<STDIN>`))
{
chomp ($line);
push #stack,($line);
}
each line has two numbers.
15 6
2 8
how do iterate over each item in each line?
i.e. I want to print
15
6
2
8
I understand it's something like
foreach (#{stack}) (#stack){
print "?????
}
This is where I am stuck.
See the perldsc documentation. That's the Perl Data Structures Cookbook, which has examples for dealing with arrays of arrays. From what you're doing though, it doesn't look like you need an array of arrays.
For your problem of taking two numbers per line and outputting one number per line, just turn the whitespace into newlines:
while( <> ) {
s/\s+/\n/; # turn all whitespace runs into newlines
print; # it's ready to print
}
With Perl 5.10, you can use the new \h character class that matches only horizontal whitespace:
while( <> ) {
s/\h+/\n/; # turn all horizontal whitespace runs into newlines
print; # it's ready to print
}
As a Perl one-liner, that's just:
% perl -pe 's/\h+/\n/' file.txt
#!/usr/bin/perl
use strict;
use warnings;
while ( my $data = <DATA> ) {
my #values = split ' ', $data;
print $_, "\n" for #values;
}
__DATA__
15 6
2 8
Output:
C:\Temp> h
15
6
2
8
Alternatively, if you want to store each line in #stack and print out later:
my #stack = map { [ split ] } grep { chomp; length } <DATA>;
The line above slurps everything coming from the DATA filehandle into a list of lines (because <DATA> happens in list context). The grep chomps each line and filters by length after chomping (to avoid getting any trailing empty lines in the data file -- you can avoid it if there are none). The map then splits each line along spaces, and then creates an anonymous array reference for each line. Finally, such array references are stored in each element of #stack. You might want to use Data::Dumper to look at #stack to understand what's going on.
print join("\n", #$_), "\n" for #stack;
Now, we look over each entry in stack, dereferencing each array in turn, then joining the elements of each array with newlines to print one element per line.
Output:
C:\Temp> h
15
6
2
8
The long way of writing essentially the same thing (with less memory consumption) would be:
my #stack;
while ( my $line = <DATA> ) {
last unless $line =~ /\S/;
my #values = split ' ', $line;
push #stack, \#values;
}
for my $ref ( #stack ) {
print join("\n", #$ref), "\n";
}
Finally, if you wanted do something other than printing all values, say, sum all the numbers, you should store one value per element of #stack:
use List::Util qw( sum );
my #stack;
while ( my $line = <DATA> ) {
last unless $line =~ /\S/;
my #values = split ' ', $line;
push #stack, #values;
}
printf "The sum is %d\n", sum #stack;
#!/usr/bin/perl
while ($line = <STDIN>) {
chomp ($line);
push #stack, $line;
}
# prints each line
foreach $line (#stack) {
print "$line\n";
}
# splits each line into items using ' ' as separator
# and prints the items
foreach $line (#stack) {
#items = split / /, $line;
foreach $item (#items) {
print $item . "\n";
}
}
I use 'for' for "C" style loops, and 'foreach' for iterating over lists.
#!/usr/bin/perl
use strict;
use warnings;
open IN, "< read.txt" or
die "Can't read in 'read.txt'!";
my $content = join '', <IN>;
while ($content =~ m`(\d+)`g) {
print "$1\n";
}