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Full Discussion: an error in perl program
Operating Systems Linux an error in perl program Post 302369223 by binnybio on Saturday 7th of November 2009 12:29:16 AM
Old 11-07-2009
an error in perl program
Hi

I am having a file with 243 lines..
The file format s given below

eg
P25787 hsa03050 1 P20618 hsa03050 1
P25786 hsa03050 1 P49721 hsa03050 1
P54132 hsa03440 1 Q13472 hsa03470 1
Q05513 hsa04530 hsa04910 hsa04930 3 Q04759 hsa04530 hsa04910 hsa04930 3
O43463 hsa00310 1 Q92769 hsa04330 hsa04110 hsa05200 hsa05220 hsa05016 5

Here i have to seperate this file in to two.. ie if the 8 letter alphanumerical word s same in both the ids den it should be printed in one file

eg.

P25787 hsa03050 1 P20618 hsa03050 1
P25786 hsa03050 1 P49721 hsa03050 1
Q05513 hsa04530 hsa04910 hsa04930 3 Q04759 hsa04530 hsa04910 hsa04930 3

The highlighted words shud be same


And the other one if the 8 letter alphanumerical word s different den it shud be printed in a file

eg

P54132 hsa03440 1 Q13472 hsa03470 1
O43463 hsa00310 1 Q92769 hsa04330 hsa04110 hsa05200 hsa05220 hsa05016 5

I wrote a perl code for this but its no working properly
the below given s the code

Code:
open(f1IN,"infile1.txt"); 
@id = <f1IN>; 
close(f1IN); 
 
open(f2IN,"infile2.txt"); 
@content = <f2IN>; 
close(f2IN); 
 
open(f3OUT,">same.txt"); 
open(f4OUT,">occurence1.txt");
open(f5OUT,">notsame.txt"); 
foreach my $id (@id) 
{ 
    chomp($id); 
    my $count = 0; 
    foreach my $line (@content)  
    { 
        chomp($line); 
        $line =~ s/(\t|\s{2,})/ /g; 
        while ( $line =~ /hsa$id/gi ) 
        { 
            $count ++; 
        } 
        @line = split(/ /,$line); 
        @count = grep /$id/,@line; 
        if ( scalar(@count) == 2 )  
        { 
            print f3OUT "$line\n";
}
        else
            {
                print f5OUT "$line\n";
            } 
         
    }     
    print f4OUT "$id --> $count\n" 
} 
close(f3OUT); 
close(f4OUT);
close(f5OUT);

The total number of lines in the input file s 243 so once i get two different files and the total of that 2 files shud come 243 but m getting sone 48,000 lines

pls reply me asap
Last edited by pludi; 11-07-2009 at 09:03 AM.. Reason: code tags, please...
 

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LEARN ABOUT OSX

set_color

set_color(1)							       fish							      set_color(1)

NAME

       set_color - set_color - set the terminal color

set_color - set the terminal color
   Synopsis
       set_color [-v --version] [-h --help] [-b --background COLOR] [COLOR]

   Description
       Change the foreground and/or background color of the terminal. COLOR is one of black, red, green, brown, yellow, blue, magenta, purple,
       cyan, white and normal.

       o -b, --background Set the background color

       o -c, --print-colors Prints a list of all valid color names

       o -h, --help Display help message and exit

       o -o, --bold Set bold or extra bright mode

       o -u, --underline Set underlined mode

       o -v, --version Display version and exit

       Calling set_color normal will set the terminal color to whatever is the default color of the terminal.

       Some terminals use the --bold escape sequence to switch to a brighter color set. On such terminals, set_color white will result in a grey
       font color, while set_color --bold white will result in a white font color.

       Not all terminal emulators support all these features. This is not a bug in set_color but a missing feature in the terminal emulator.

       set_color uses the terminfo database to look up how to change terminal colors on whatever terminal is in use. Some systems have old and
       incomplete terminfo databases, and may lack color information for terminals that support it. Download and install the latest version of
       ncurses and recompile fish against it in order to fix this issue.

Version 1.23.1							  Sun Jan 8 2012						      set_color(1)
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