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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 ( #1001482=note: print w/ replies, xml ) Need Help??


in reply to Re^2: 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

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

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

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
There does appear to be a stray carriage return in the output - the code may needs a chomp somewhere...


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Re^4: Replacement of data in a column of a file using Hashes created from another file
by choroba (Abbot) on Oct 30, 2012 at 11:23 UTC
    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
Re^4: Replacement of data in a column of a file using Hashes created from another file
by rohitmonk (Initiate) on Oct 30, 2012 at 12:47 UTC

    Thanks a ton Choroba

Re^4: Replacement of data in a column of a file using Hashes created from another file
by perl_walker (Novice) on Oct 30, 2012 at 14:49 UTC

    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;
      Why don't you do error checking?

        He's obviously from the Klingon school of programming; error checking is for the weak! ;-)

        More seriously programs on here are to demonstrate general principles and outline solutions to the problem raised, not full solutions with complete error checking, unless error checking is the specific issue raised.

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

Re^4: Replacement of data in a column of a file using Hashes created from another file
by rohitmonk (Initiate) on Oct 31, 2012 at 05:44 UTC

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

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