reading and working with grow.out files

rmgzsm9 has asked for the wisdom of the Perl Monks concerning the following question:

I have a grow.out file showing protein ligand interaction. I converted that file into text file. It looks like:

H P L A   143 TYR   202  OH  -->  O2   2014 MC9   500 A
H P L A   143 TYR   202  OH  <--  O2   2014 ASH   500 A
H P L A   237 SER   532  OG  -->  O1   2015 MC9   500 A
H P L A   237 SER   532  OG  <--  O1   2015 AGM   500 A
H P L A   274 ARG   821  NH1 -->  O1   2015 MC9   500 A
H P L A   278 SER   851  OG  -->  O2   2014 VIA   500 A
[download]

Now what I want is that the program should search for a particular ligand code (Say MC9 here). After searching for MC9 the program should print each line (row) containing MC9 into another output text file. I am a drug design student with biotechnology background. so don't have much knowledge on programming. Please help me. I have a code with me but is not working as the way I wanted.

#!/usr/bin/perl -w

use strict;
use IO::File;

use constant FILE => 'search.txt'; 
use constant FIND => 'string to find'; 

IO::File->input_record_separator(FIND);

my $fh = IO::File->new(FILE, O_RDONLY)
  or die 'Could not open file ', FILE, ": $!";

$fh->getline;  


print IO::File->input_record_separator 
  while $fh->getline; 

$fh->close;
[download]

it is printing MC9 again and again, not the whole row

Comment on reading and working with grow.out files Select or Download Code

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Re: reading and working with grow.out files by Riales (Hermit) on Apr 23, 2012 at 23:51 UTC
Is that the code you're actually running? I'm thinking your `FIND` constant is actually defined as 'MC9' so when you execute the following line, you just print the `input_record_separator` (which you earlier defined as `FIND`) once for each line your script reads in. `print IO::File->input_record_separator while $fh->getline;` [download] I'm not familiar with IO::File but that's my best guess as to what you're seeing. Something like this should work for your purposes: `use strict; use warnings; my $filename = 'search.txt'; my $find = 'MC9'; open(FILE, '<', $filename) or die "Cannot open file: $!"; while (my $line = <FILE>) { print $line if $line =~ /$find/; } close(FILE);` [download]	[reply] [d/l] [select]
Re^2: reading and working with grow.out files by rmgzsm9 (Novice) on Apr 24, 2012 at 01:33 UTC
It worked. Thank you so much. Can you help me little bit further? I ll be grateful. This program was for 1 text file and 1 ligand code. I want to make it general. I have a text file having names of all protein text files along with their ligand codes. I want this program to pick first text file name and its respective ligand code and then run this (coded by you) program for that. Then it moves to second text file name and ligand code and repeat it again. Please help.	[reply]
Re^3: reading and working with grow.out files by mrguy123 (Hermit) on Apr 24, 2012 at 06:55 UTC
Hi, take a look at this code: use strict; use warnings; use Carp qw(croak); { my $input_file = "input_file.txt"; my @lines = slurp($input_file); for my $line (@lines){ my ($filename, $ligand) = split(/\t/, $line); open(FILE, '<', $filename) or die "Cannot open file: $!"; while (my $line = <FILE>) { print $line if $line =~ /$ligand/; } close(FILE); } } ##Slurps a file into a list sub slurp { my ($file) = @_; my (@data, @data_chomped); open IN, "<", $file or croak "can't open $file\n"; @data = <IN>; for my $line (@data){ chomp($line); push (@data_chomped, $line); } close IN; return (@data_chomped); } [download] It assumes that the list of text files and ligand codes are in a tab delimited file called input_file.txt. It will look like this `file1.txt MC9 file2.txt ASH` [download] You can also delimit it by ',' or any other delimiter, but you will have to update the split function The program will match each ligand code to the given file and print out the lines where there is a match Good luck with your research Mr Guy	[reply] [d/l] [select]
Re^4: reading and working with grow.out files by rmgzsm9 (Novice) on Apr 24, 2012 at 07:22 UTC
Re^4: reading and working with grow.out files by rmgzsm9 (Novice) on Apr 24, 2012 at 07:39 UTC
Re^5: reading and working with grow.out files by mrguy123 (Hermit) on Apr 24, 2012 at 08:15 UTC
Some notes below your chosen depth have not been shown here
Re^4: reading and working with grow.out files by rmgzsm9 (Novice) on Apr 29, 2012 at 13:12 UTC
Re^4: reading and working with grow.out files by rmgzsm9 (Novice) on Apr 29, 2012 at 14:00 UTC
Re^5: reading and working with grow.out files by marto (Cardinal) on Apr 29, 2012 at 14:10 UTC
Some notes below your chosen depth have not been shown here
Re^2: reading and working with grow.out files by rmgzsm9 (Novice) on Apr 24, 2012 at 01:19 UTC
Thanks I ll try it now	[reply]
Re: reading and working with grow.out files by toolic (Bishop) on Apr 23, 2012 at 23:52 UTC
If that's all you need to do, I don't think you can do much better than grep `grep MC9 in.txt > out.txt` [download] See also: Writeup Formatting Tips. Use code tags instead of pre tags.	[reply] [d/l]
Re^2: reading and working with grow.out files by rmgzsm9 (Novice) on Apr 24, 2012 at 01:20 UTC
will that work with windows?	[reply]
Re^3: reading and working with grow.out files by toolic (Bishop) on Apr 24, 2012 at 01:39 UTC
Did you try it? If it's installed, it should work.	[reply]
Re^4: reading and working with grow.out files by rmgzsm9 (Novice) on Apr 24, 2012 at 01:49 UTC
Re^5: reading and working with grow.out files by Anonymous Monk on Apr 24, 2012 at 06:14 UTC