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in reply to Re: Replacement of data in a column of a file using Hashes created from another file
in thread Replacement of data in a column of a file using Hashes created from another file

Thank you for the reply. But I need to get an output file, I am pretty new to this syntax.

And this output which gets printed does not have any replacements in it when i run it. Where is it searching for the hash-key and replacing it with the value?

  • Comment on Re^2: Replacement of data in a column of a file using Hashes created from another file

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Re^3: Replacement of data in a column of a file using Hashes created from another file
by space_monk (Chaplain) on Oct 30, 2012 at 10:44 UTC

    Not sure what you mean:

    Input:

    10_25_res.txt:Locus3034v1rpkm4.98 gi|315134697|dbj|AP012030.1| 100.00 
+280 0 0 1 280 3402569 3402290 4e-140 506
10_25_res.txt:Locus3034v1rpkm4.98 gi|315134697|dbj|AP012030.1| 99.64 2
+80 1 0 1 280 227880 228159 2e-138 500
10_25_res.txt:Locus3034v1rpkm4.98 gi|315134697|dbj|AP012030.1| 99.64 2
+80 1 0 1 280 2704973 2704694 2e-138 500
10_25_res.txt:Locus3034v1rpkm4.98 gi|315134697|dbj|AP012030.1| 99.64 2
+80 1 0 1 280 4018745 4019024 2e-138 500
10_25_res.txt:Locus3034v1rpkm4.98 gi|315134697|dbj|AP012030.1| 99.64 2
+80 1 0 1 280 4149866 4150145 2e-138 500
10_25_res.txt:Locus3034v1rpkm4.98 gi|315134697|dbj|AP012030.1| 99.64 2
+80 1 0 1 280 4191268 4191547 2e-138 500
10_25_res.txt:Locus3034v1rpkm4.98 gi|315134697|dbj|AP012030.1| 98.93 2
+80 3 0 1 280 3924929 3925208 9e-136 491
10_25_res.txt:Locus3034v1rpkm4.98 gi|260447279|gb|CP001637.1| 100.00 2
+80 0 0 1 280 459101 459380 4e-140 506
10_25_res.txt:Locus3034v1rpkm4.98 gi|260447279|gb|CP001637.1| 99.64 28
+0 1 0 1 280 1156698 1156977 2e-138 500
10_25_res.txt:Locus3034v1rpkm4.98 gi|260447279|gb|CP001637.1| 99.64 28
+0 1 0 1 280 3643499 3643220 2e-138 500
10_25_res.txt:Locus3034v1rpkm4.98 gi|260447279|gb|CP001637.1| 99.64 28
+0 1 0 1 280 4302307 4302028 2e-138 500
10_25_res.txt:Locus3034v1rpkm4.98 gi|260447279|gb|CP001637.1| 99.64 28
+0 1 0 1 280 4343709 4343430 2e-138 500
10_25_res.txt:Locus3034v1rpkm4.98 gi|260447279|gb|CP001637.1| 99.64 28
+0 1 0 1 280 4474830 4474551 2e-138 500
10_25_res.txt:Locus3034v1rpkm4.98 gi|260447279|gb|CP001637.1| 98.93 28
+0 3 0 1 280 4568646 4568367 9e-136 491

    [download]

    Output:

    10_25_res.txt:Locus3034v1rpkm4.98 gi|315134697|dbj|AP012030.1| Escheri
+chia coli DH1 (ME8569) DNA,...
 100.00 280 0 0 1 280 3402569 3402290 4e-140 506
10_25_res.txt:Locus3034v1rpkm4.98 gi|315134697|dbj|AP012030.1| Escheri
+chia coli DH1 (ME8569) DNA,...
 99.64 280 1 0 1 280 227880 228159 2e-138 500
10_25_res.txt:Locus3034v1rpkm4.98 gi|315134697|dbj|AP012030.1| Escheri
+chia coli DH1 (ME8569) DNA,...
 99.64 280 1 0 1 280 2704973 2704694 2e-138 500
10_25_res.txt:Locus3034v1rpkm4.98 gi|315134697|dbj|AP012030.1| Escheri
+chia coli DH1 (ME8569) DNA,...
 99.64 280 1 0 1 280 4018745 4019024 2e-138 500
10_25_res.txt:Locus3034v1rpkm4.98 gi|315134697|dbj|AP012030.1| Escheri
+chia coli DH1 (ME8569) DNA,...
 99.64 280 1 0 1 280 4149866 4150145 2e-138 500
10_25_res.txt:Locus3034v1rpkm4.98 gi|315134697|dbj|AP012030.1| Escheri
+chia coli DH1 (ME8569) DNA,...
 99.64 280 1 0 1 280 4191268 4191547 2e-138 500
10_25_res.txt:Locus3034v1rpkm4.98 gi|315134697|dbj|AP012030.1| Escheri
+chia coli DH1 (ME8569) DNA,...
 98.93 280 3 0 1 280 3924929 3925208 9e-136 491
10_25_res.txt:Locus3034v1rpkm4.98 gi|260447279|gb|CP001637.1| Escheric
+hia coli DH1, complete genome
 100.00 280 0 0 1 280 459101 459380 4e-140 506
10_25_res.txt:Locus3034v1rpkm4.98 gi|260447279|gb|CP001637.1| Escheric
+hia coli DH1, complete genome
 99.64 280 1 0 1 280 1156698 1156977 2e-138 500
10_25_res.txt:Locus3034v1rpkm4.98 gi|260447279|gb|CP001637.1| Escheric
+hia coli DH1, complete genome
 99.64 280 1 0 1 280 3643499 3643220 2e-138 500
10_25_res.txt:Locus3034v1rpkm4.98 gi|260447279|gb|CP001637.1| Escheric
+hia coli DH1, complete genome
 99.64 280 1 0 1 280 4302307 4302028 2e-138 500
10_25_res.txt:Locus3034v1rpkm4.98 gi|260447279|gb|CP001637.1| Escheric
+hia coli DH1, complete genome
 99.64 280 1 0 1 280 4343709 4343430 2e-138 500
10_25_res.txt:Locus3034v1rpkm4.98 gi|260447279|gb|CP001637.1| Escheric
+hia coli DH1, complete genome
 99.64 280 1 0 1 280 4474830 4474551 2e-138 500
10_25_res.txt:Locus3034v1rpkm4.98 gi|260447279|gb|CP001637.1| Escheric
+hia coli DH1, complete genome
 98.93 280 3 0 1 280 4568646 4568367 9e-136 491

    [download]

    The replacement is done in the s/($regex)/$subst{$1}/ statement, and you can direct the output to a file by: 

    ./program.pl > output_file.txt

    [download]
    There does appear to be a stray carriage return in the output - the code may needs a chomp somewhere...
[reply]
[d/l]
[select]
      True, thank you. chomp added to the code. I did not notice because the format is not familiar to me and the expected output was not included to diff against.
      لսႽ† ᥲᥒ⚪⟊Ⴙᘓᖇ Ꮅᘓᖇ⎱ Ⴙᥲ𝇋ƙᘓᖇ
[reply]

      Hi, Try this one

      use strict;
use warnings;

my ($a, $b, $c) = @ARGV;

open(FILE, "$a");
my $text=do {local $/; <FILE>};
close FILE;

my %mymatch = $text =~ m/^\s*(.*?)\s*\=\s*(.*?)\s*$/igm;

open(FILE, "$b");
my $maintext=do {local $/; <FILE>};
close FILE;

foreach my $myfnd (sort {length($b) <=> length($a)} keys %mymatch) {
    $maintext =~ s/\Q$myfnd\E/$mymatch{$myfnd}/ig;
}

open(FILE,">$c");
print FILE $maintext;
close FILE;

      [download]
[reply]
[d/l]
        Why don't you do error checking?
[reply]

        Thanks a ton perl walker, keep walking ;) <\p>

[reply]

      Thanks a ton Choroba

[reply]

      Thank you so much for looking into the problem and helping me out. Cheers... <\p>

[reply]

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