I have 2 files:
1. a.txt
2. b.txt
a.txt:
UP_00292229 191
Xa_09833888 199
b.txt
UP_00292229 191
Xa_09833888 188
I want to compare this 2 files with the first column.
result:
UP_00292229 is same
Xa_09833888 is not same
How can I do it in perl?
How can I input 2 files at the same times?
How can I check the file format is xxxxx dddd (there is a space between xxxxx dddd)?
This code will compare first column of both files and if value matches it will print same otherwise not same:
use strict;
use warnings;
my %seen;
open ( my $file2,"<", "b.txt" ) or die $!;
while ( my $line = <$file2> )
{
chomp ( $line );
my ($column3, $column4) = split ' ', $line;
$seen{$column3}++;
}
close ( $file2 );
open ( my $file1, "<", "a.txt" ) or die $!;
while ( my $line1 = <$file1> )
{
chomp $line1;
my ($column1, $column2) = split ' ', $line1;
print $column1, " ", $seen{$column1} ? "is same" : "is not same", "\n";
}
close ( $file1 );
Try this:
use warnings;
use strict;
open my $handle_file1,"<","file1";
open my $handle_file2,"<","file2";
my #ar = <$handle_file1>;
my #br = <$handle_file2>;
for my $i(0..$#ar){
if($ar[$i] eq $br[$i]){
chomp $ar[$i];
print "$ar[$i] is same\n";
}
else{
chomp $ar[$i];
print "$ar[$i] is not same\n";
}
}
Related
I have a original file which has following columns,
02-May-2018,AAPL,Sell,0.25,1000
02-May-2018,C,Sell,0.25,2000
02-May-2018,JPM,Sell,0.25,3000
02-May-2018,WFC,Sell,0.25,5000
02-May-2018,AAPL,Sell,0.25,7000
02-May-2018,GOOG,Sell,0.25,8000
02-May-2018,GOOG,Sell,0.25,9000
02-May-2018,C,Sell,0.25,2000
02-May-2018,AAPL,Sell,0.25,3000
I am trying to print this original line if I see value in the second column more then 2 times.. for example, if I see AAPL more then 2 times desired result should print
02-May-2018,AAPL,Sell,0.25,1000
02-May-2018,AAPL,Sell,0.25,7000
02-May-2018,AAPL,Sell,0.25,3000
So Far, I have written the following which prints results multiple times which is wrong.. can you please help on what I am doing wrong?
open (FILE, "<$TMPFILE") or die "Could not open $TMPFILE";
open (OUT, ">$TMPFILE1") or die "Could not open $TMPFILE1";
%count = ();
#symbol = ();
while ($line = <FILE>)
{
chomp $line;
(#data) = split(/,/,$line);
$count{$data[1]}++;
#keys = sort {$count{$a} cmp $count{$b}} keys %count;
for my $key (#keys)
{
if ( $count{$key} > 2 )
{
print "$line\n";
}
}
}
I'd do it something like this - store lines you've seen in a 'buffer' and print them out again if the condition is hit (before continuing to print as you go):
#!/usr/bin/env perl
use strict;
use warnings;
my %buffer;
my %count_of;
while ( my $line = <> ) {
my ( $date, $ticker, #values ) = split /,/, $line;
#increment the count
$count_of{$ticker}++;
if ( $count_of{$ticker} < 3 ) {
#count limit not hit, so stash the current line in the buffer.
$buffer{$ticker} .= $line;
next;
}
#print the buffer if the count has been hit
if ( $count_of{$ticker} == 3 ) {
print $buffer{$ticker};
}
#only gets to here once the limit is hit, so just print normally.
print $line;
}
With your input data, this outputs:
02-May-2018,AAPL,Sell,0.25,1000
02-May-2018,AAPL,Sell,0.25,7000
02-May-2018,AAPL,Sell,0.25,3000
Simple answer:
push #{ $lines{(split",")[1]} }, $_ while <>;
print #{ $lines{$_} } for grep #{ $lines{$_} } > 2, sort keys %lines;
perl program.pl inputfile > outputfile
You need to read the input file twice, because you don't know the final counts until you get to the end of the file
use strict;
use warnings 'all';
my ($TMPFILE, $TMPFILE1) = qw/ infile outfile /;
my %counts;
{
open my $fh, '<', $TMPFILE or die "Could not open $TMPFILE: $!";
while ( <$fh> ) {
my #fields = split /,/;
++$counts{$fields[1]};
}
}
open my $fh, '<', $TMPFILE or die "Could not open $TMPFILE: $!";
open my $out_fh, '>', $TMPFILE1 or die "Could not open $TMPFILE1: $!";
while ( <$fh> ) {
my #fields = split /,/;
print $out_fh $_ if $counts{$fields[1]} > 2;
}
output
02-May-2018,AAPL,Sell,0.25,1000
02-May-2018,AAPL,Sell,0.25,7000
02-May-2018,AAPL,Sell,0.25,3000
This should work:
use strict;
use warnings;
open (FILE, "<$TMPFILE") or die "Could not open $TMPFILE";
open (OUT, ">$TMPFILE1") or die "Could not open $TMPFILE1";
my %data;
while ( my $line = <FILE> ) {
chomp $line;
my #line = split /,/, $line;
push(#{$data{$line[1]}}, $line);
}
foreach my $key (keys %data) {
if(#{$data{$key}} > 2) {
print "$_\n" foreach #{$data{$key}};
}
}
I have a input and list file like this:
input.txt file:
>gi|NP_415931.4
MTEQQKLTFTALQQRLDSLMLRDRLRFSRRLHGVKKVKNPDAQQAIFQEMAKEIDQAAGKVLLREAARPEITYPD
>gi|NP_418770.2
MMNKSNFEFLKGVNDFTYAIACAAENNYPDDPNTTLIKMRMFGEATAKHLGLL
>gi|YP_026226.4
MRKFTLNIFTLSLGLAVMPMVEAAPTAQQQLLEQVRLGEATHREDLVQQSLYRLELIDPNNPDVVAARFRSLLRQGDIDGAQKQ
list.txt file:
NP_415931.4: 1-5, 6-8
YP_026226.4: 3-7, 9-9, 10, 12-15
Now, for this time, I want a csv formatted output.csv (with certain added header) as (for the above inputs):
ID,Regions,Length,Sequences
NP_415931.4,1-5,5,MTEQQ
,6-8,3,KLT
YP_026226.4,3-7,5,KFTLN
,9-9,1,F
,10,1,T
,12-15,4,SLGL
that is, it first match the list file headers with those of input files and the matched once's sequences are taken and then it gives the output arranging in the above format.
the excel view of the output.csv would be:
How can I generate the above output.csv file from those inputs?
Thanks
Here is an approach. To summarize: We have a master database file input.txt with all defined sequences. Our job is to extract certain information from this database and write it to a CSV file. The information about what to extract is given in file list.txt.
use feature qw(say);
use strict;
use warnings;
my $input_fn = 'input.txt';
open ( my $fh1, '<', $input_fn ) or die "Could not open file '$input_fn': $!";
my %seqs;
while( my $line = <$fh1> ) {
my ($id ) = $line =~ /gi\|(.*)$/;
chomp( my $seq = <$fh1> );
$seqs{$id} = $seq;
}
close $fh1;
say join ',', qw(ID Regions Length Sequences);
my $list_fn = 'list.txt';
open ( my $fh2, '<', $list_fn ) or die "Could not open file '$list_fn': $!";
while( my $line = <$fh2> ) {
chomp $line;
my ( $id, #regions ) = split /[:,]\s?/, $line;
for my $i (0..$#regions) {
my $region = $regions[$i];
my $start = my $end = $region;
if ( $region =~ /(\d+)-(\d+)/ ) {
$start = $1;
$end = $2;
}
my $name = ($i == 0) ? $id : "";
my $seq = substr( $seqs{$id}, $start - 1, $end - $start + 1);
say join ',', $name, $region, length( $seq ), $seq;
}
}
close $fh2;
Output:
ID,Regions,Length,Sequences
NP_415931.4,1-5,5,MTEQQ
,6-8,3,KLT
YP_026226.4,3-7,5,KFTLN
,9-9,1,F
,10,1,T
,12-15,4,SLGL
I couldn't figure it out how to escape this.
I would like to print the variable $rfam_column, which is inside two loops. But I cannot just write the print command right after the place where $rfam_column appears, because I would like to print other things which will be outside the loop and combine them to the printed content.
I would appreciate any advice as to what I'm doing wrong here.
use warnings;
use strict;
my $in;
GetOptions('input' => \$in) or die;
if ( $in ) {
my $input = $ARGV[0] or die;
open (my $fh, '<', $input) or die "Can't open $input $!\n";
chomp (my #db_file = <$fh>);
close $fh;
my #list = grep /RNA/, #db_file;
my $column;
my #column = ();
foreach $column ( #list ) {
my #all_columns = split (/\t/, $column);
my $rfam_column = $all_columns[0];
# insert "|" between RFs
foreach $_ ( $rfam_column ) {
s/^/|/;
}
}
}
print "$rfam_column";
Global symbol "$rfam_column" requires explicit package name at script_vbeta.pl line 90.
Execution of script_vbeta.pl aborted due to compilation errors.
EDITED to include all the code and information of the input--output as suggested:
Input file is a table with n lines vs n columns like this (I extracted a few columns otherwise it would be much long to represent in a line):
RF00001 1302 5S ribosomal RNA
RF00006 1307 Vault RNA
RF00007 1308 U12 minor spliceosomal RNA
RF00008 1309 Hammerhead ribozyme (type III)
Output should be like this:
|RF00001|RF00006|RF00007
And the code (usage: script.pl -i input_file):
use warnings;
use strict;
use Getopt::Long;
Getopt::Long::Configure("pass_through");
my $in;
GetOptions('input' => \$in) or die;
if ( $in ) {
my $input = $ARGV[0] or die;
open (my $fh, '<', $input) or die "Can't open $input $!\n";
chomp (my #db_file = <$fh>);
close $fh;
my #list = grep /RNA/, #db_file;
my $column;
my #column = ();
foreach $column ( #list ) {
my #all_columns = split (/\t/, $column);
my $rfam_column = $all_columns[0];
# insert "|" between RFs
foreach $_ ( $rfam_column ) {
s/^/|/;
}
}
}
print "$rfam_column";
I think you want
if ($in) {
...
my #rfams;
for my $row (#list) {
my #fields = split(/\t/, $row);
my $rfam = $fields[0];
push #rfams, $rfam;
}
my $rfams = join('|', #rfams);
print("$rfams\n");
}
I would like to print other things which will be outside the loop and combine them to the $rfam_column content
You can include anything that is in an outer scope in print. You can just put your print statement inside the inner loop
By the way, I don't know what you mean by
# insert "|" between RFs
foreach $_ ($rfam_column) {
s/^/|/;
}
That is the same as
$rfam_column =~ s/^/|/;
which just adds a pipe | character to the beginning of the string
What is an RF?
The script is printing the amount of input lines, I want it to print the amount of input lines that are present in another file
#!/usr/bin/perl -w
open("file", "text.txt");
#todd = <file>;
close "file";
while(<>){
if( grep( /^$_$/, #todd)){
#if( grep #todd, /^$_$/){
print $_;
}
print "\n";
}
if for example file contains
1
3
4
5
7
and the input file that will be read from contains
1
2
3
4
5
6
7
8
9
I would want it to print 1,3,4,5 and 7
but 1-9 are being printed instead
UPDATE******
This is my code now and I am getting this error
readline() on closed filehandle todd at ./may6test.pl line 3.
#!/usr/bin/perl -w
open("todd", "<text.txt");
#files = <todd>; #file looking into
close "todd";
while( my $line = <> ){
chomp $line;
if ( grep( /^$line$/, #files) ) {
print $_;
}
print "\n";
}
which makes no sense to me because I have this other script that is basically doing the same thing
#!/usr/bin/perl -w
open("file", "<text2.txt"); #
#file = <file>; #file looking into
close "file"; #
while(<>){
$temp = $_;
$temp =~ tr/|/\t/; #puts tab between name and id
my ($name, $number1, $number2) = split("\t", $temp);
if ( grep( /^$number1$/, #file) ) {
print $_;
}
}
print "\n";
OK, the problem here is - grep sets $_ too. So grep { $_ } #array will always give you every element in the array.
At a basic level - you need to:
while ( my $line = <> ) {
chomp $line;
if ( grep { /^$line$/ } #todd ) {
#do something
}
}
But I'd suggest instead that you might want to consider building a hash of your lines instead:
open( my $input, '<', "text.txt" ) or die $!;
my %in_todd = map { $_ => 1 } <$input>;
close $input;
while (<>) {
print if $in_todd{$_};
}
Note - you might want to watch for trailing linefeeds.
I am trying to solve below issues.
I have 2 files. Address.txt and File.txt. I want to replace all A/B/C/D (File.txt) with corresponding string value (Read from Address.txt file) using perl script. It's not replacing in my output file. I am getting same content of File.txt.
I tried below codes.
Here is Address.txt file
A,APPLE
B,BAL
C,CAT
D,DOG
E,ELEPHANT
F,FROG
G,GOD
H,HORCE
Here is File.txt
A B C
X Y X
M N O
D E F
F G H
Here is my code :
use strict;
use warnings;
open (MYFILE, 'Address.txt');
foreach (<MYFILE>){
chomp;
my #data_new = split/,/sm;
open INPUTFILE, "<", $ARGV[0] or die $!;
open OUT, '>ariout.txt' or die $!;
my $src = $data_new[0];
my $des = $data_new[1];
while (<INPUTFILE>) {
# print "In while :$src \t$des\n";
$_ =~ s/$src/$des/g;
print OUT $_;
}
close INPUTFILE;
close OUT;
# /usr/bin/perl -p -i -e "s/A/APPLE/g" ARGV[0];
}
close (MYFILE);
If i Write $_ =~ s/A/Apple/g;
Then output file is fine and A is replacing with "Apple". But when dynamically coming it's not getting replaced.
Thanks in advance. I am new in perl scripting language . Correct me if I am wrong any where.
Update 1: I updated below code . It's working fine now. My questions Big O of this algo.
Code :
#!/usr/bin/perl
use warnings;
use strict;
open( my $out_fh, ">", "output.txt" ) || die "Can't open the output file for writing: $!";
open( my $address_fh, "<", "Address.txt" ) || die "Can't open the address file: $!";
my %lookup = map { chomp; split( /,/, $_, 2 ) } <$address_fh>;
open( my $file_fh, "<", "File1.txt" ) || die "Can't open the file.txt file: $!";
while (<$file_fh>) {
my #line = split;
for my $char ( #line ) {
( exists $lookup{$char} ) ? print $out_fh " $lookup{$char} " : print $out_fh " $char ";
}
print $out_fh "\n";
}
Not entirely sure how you want your output formatted. Do you want to keep the rows and columns as is?
I took a similar approach as above but kept the formatting the same as in your 'file.txt' file:
#!/usr/bin/perl
use warnings;
use strict;
open( my $out_fh, ">", "output.txt" ) || die "Can't open the output file for writing: $!";
open( my $address_fh, "<", "address.txt" ) || die "Can't open the address file: $!";
my %lookup = map { chomp; split( /,/, $_, 2 ) } <$address_fh>;
open( my $file_fh, "<", "file.txt" ) || die "Can't open the file.txt file: $!";
while (<$file_fh>) {
my #line = split;
for my $char ( #line ) {
( exists $lookup{$char} ) ? print $out_fh " $lookup{$char} " : print $out_fh " $char ";
}
print $out_fh "\n";
}
That will give you the output:
APPLE BAL CAT
X Y X
M N O
DOG ELEPHANT FROG
FROG GOD HORCE
Here's another option that lets Perl handle the opening and closing of files:
use strict;
use warnings;
my $addresses_txt = pop;
my %hash = map { $1 => $2 if /(.+?),(.+)/ } <>;
push #ARGV, $addresses_txt;
while (<>) {
my #array;
push #array, $hash{$_} // $_ for split;
print "#array\n";
}
Usage: perl File.txt Addresses.txt [>outFile.txt]
The last, optional parameter directs output to a file.
Output on your dataset:
APPLE BAL CAT
X Y X
M N O
DOG ELEPHANT FROG
FROG GOD HORCE
The name of the addresses' file is implicitly popped off of #ARGV for use later. Then, a hash is built, using the key/value pairs in File.txt.
The addresses' file is read, splitting each line into its single elements, and the defined-or (//) operator is used to returned the defined hash item or the single element, which is then pushed onto #array. Finally, the array is interpolated in a print statement.
Hope this helps!
First, here is your existing program, rewritten slightly
open the address file
convert the address file to a hash so that the letters are the keys and the strings the values
open the other file
read in the single line in it
split the line into single letters
use the letters to lookup in the hash
use strict;
use warnings;
open(my $a,"Address.txt")||die $!;
my %address=map {split(/,/) } map {split(' ')} <$a>;
open(my $f,"File.txt")||die $!;
my $list=<$f>;
for my $letter (split(' ',$list)) {
print $address{$letter}."\n" if (exists $address{$letter});
}
to make another file with the substitutions in place alter the loop that processes $list
for my $letter (split(' ',$list)) {
if (exists $address{$letter}) {
push #output, $address{$letter};
}
else {
push #output, $letter;
}
}
open(my $o,">newFile.txt")||die $!;
print $o "#output";
Your problem is that in every iteration of your foreach loop you overwrite any changes made earlier to output file.
My solution:
use strict;
use warnings;
open my $replacements, 'Address.txt' or die $!;
my %r;
foreach (<$replacements>) {
chomp;
my ($k, $v) = split/,/sm;
$r{$k} = $v;
}
my $re = '(' . join('|', keys %r) . ')';
open my $input, "<", $ARGV[0] or die $!;
while (<$input>) {
s/$re/$r{$1}/g;
print;
}
#!/usr/bin/perl -w
# to replace multiple text strings in a file with text from another file
#select text from 1st file, replace in 2nd file
$file1 = 'Address.txt'; $file2 = 'File.txt';
# save the strings by which to replace
%replacement = ();
open IN,"$file1" or die "cant open $file1\n";
while(<IN>)
{chomp $_;
#a = split ',',$_;
$replacement{$a[0]} = $a[1];}
close IN;
open OUT,">replaced_file";
open REPL,"$file2" or die "cant open $file2\n";
while(<REPL>)
{chomp $_;
#a = split ' ',$_; #replaced_data = ();
# replace strings wherever possible
foreach $i(#a)
{if(exists $replacement{$i}) {push #replaced_data,$replacement{$i};}
else {push #replaced_data,$i;}
}
print OUT trim(join " ",#replaced_data),"\n";
}
close REPL; close OUT;
########################################
sub trim
{
my $str = $_[0];
$str=~s/^\s*(.*)/$1/;
$str=~s/\s*$//;
return $str;
}