using perl to print columnwise

Shell Programming and Scripting
1

Suppose we have two files
one file
FAAA_HUMAN.input1
2
5
7
11

and another file

FAAA_HUMAN.output
M*0.0540*0.0039*0.2212*0.0082*0.0020*0.0137*0.0028*0.0029*0.2198*0.0104*0.0889*0.0282*0.0049*0.0804*0.1743*0.0215*0.0531*0.0071*0.0007*0.0021*0.7270*2.5000*
S*0.0197*0.0043*0.0037*0.0032*0.0018*0.0039*0.0015*0.0027*0.0030*0.0039*0.0012*0.2281*0.0025*0.0022*0.0027*0.6511*0.0586*0.0040*0.0005*0.0016*0.3700*2.5000*
F*0.0029*0.0008*0.0021*0.0026*0.2621*0.0025*0.2339*0.0018*0.0023*0.0033*0.0010*0.0022*0.0017*0.0024*0.0024*0.0028*0.0023*0.0023*0.4673*0.0015*0.4240*2.5000*
I*0.0046*0.0012*0.2219*0.0020*0.0069*0.0024*0.0055*0.1693*0.0020*0.2029*0.0021*0.0014*0.0019*0.0014*0.0018*0.0025*0.0029*0.3649*0.0006*0.0018*0.5222*2.5000*
P*0.0515*0.0014*0.0849*0.0630*0.0027*0.2258*0.0282*0.0076*0.0126*0.0135*0.0016*0.0183*0.0637*0.0732*0.0176*0.2021*0.0568*0.0655*0.0011*0.0091*0.7958*2.5000*
V*0.3128*0.0031*0.0190*0.0029*0.2206*0.0070*0.0015*0.1142*0.0109*0.0096*0.0028*0.0022*0.0083*0.0021*0.0026*0.0205*0.0171*0.2189*0.0010*0.0231*0.6230*2.5000*
A*0.0941*0.0018*0.0247*0.0222*0.2207*0.0252*0.0084*0.0047*0.0062*0.0079*0.0020*0.2878*0.2066*0.0039*0.0051*0.0547*0.0136*0.0061*0.0012*0.0032*0.6645*2.5000*
E*0.0993*0.0014*0.0975*0.3559*0.0030*0.0988*0.0057*0.0042*0.0914*0.0130*0.0021*0.0120*0.0475*0.0277*0.0190*0.0762*0.0294*0.0119*0.0011*0.0027*0.7241*2.5000*
D*0.0790*0.0014*0.1773*0.0207*0.0025*0.0465*0.1021*0.0027*0.0151*0.0074*0.0015*0.1091*0.0950*0.0147*0.0077*0.0723*0.2283*0.0040*0.0010*0.0117*0.7629*2.5000*
S*0.0337*0.0919*0.0055*0.0059*0.0034*0.0201*0.0194*0.0050*0.0055*0.0078*0.0023*0.0101*0.0589*0.0039*0.2287*0.3931*0.0941*0.0069*0.0011*0.0029*0.6322*2.5000*
D*0.0074*0.0008*0.5185*0.0237*0.0015*0.0077*0.0809*0.0020*0.0038*0.0034*0.0009*0.0084*0.0960*0.0102*0.0029*0.2229*0.0041*0.0027*0.0005*0.0015*0.5000*2.5000*
F*0.0029*0.0007*0.0021*0.0026*0.7291*0.0025*0.0019*0.0018*0.0022*0.0033*0.0010*0.0022*0.0017*0.0023*0.2344*0.0028*0.0022*0.0022*0.0006*0.0014*0.2651*2.5000*
P*0.0090*0.0010*0.0049*0.0061*0.0025*0.0055*0.0019*0.0038*0.0054*0.2186*0.0015*0.0033*0.5570*0.0031*0.0043*0.1334*0.0306*0.0053*0.0008*0.0021*0.4543*2.5000*
I*0.0037*0.0010*0.0017*0.0021*0.0042*0.0024*0.0009*0.4114*0.0021*0.3121*0.0034*0.0015*0.0018*0.0016*0.0019*0.2273*0.0024*0.0117*0.0007*0.0063*0.4469*2.5000*
H*0.1051*0.0007*0.0031*0.2746*0.0014*0.0027*0.0798*0.0018*0.0120*0.0102*0.0010*0.0595*0.0019*0.4283*0.0027*0.0031*0.0025*0.0024*0.0006*0.0063*0.5353*2.5000*

So ,we want to have output
where from first file is having number and then use second file accordingly
it wil print

S*0.0197*0.0043*0.0037*0.0032*0.0018*0.0039*0.0015*0.0027*0.0030*0.0039*0.0012*0.2281*0.0025*0.0022*0.0027*0.6511*0.0586*0.0040*0.0005*0.0016*0.3700*2.5000*
P*0.0515*0.0014*0.0849*0.0630*0.0027*0.2258*0.0282*0.0076*0.0126*0.0135*0.0016*0.0183*0.0637*0.0732*0.0176*0.2021*0.0568*0.0655*0.0011*0.0091*0.7958*2.5000*
A*0.0941*0.0018*0.0247*0.0222*0.2207*0.0252*0.0084*0.0047*0.0062*0.0079*0.0020*0.2878*0.2066*0.0039*0.0051*0.0547*0.0136*0.0061*0.0012*0.0032*0.6645*2.5000*
D*0.0074*0.0008*0.5185*0.0237*0.0015*0.0077*0.0809*0.0020*0.0038*0.0034*0.0009*0.0084*0.0960*0.0102*0.0029*0.2229*0.0041*0.0027*0.0005*0.0015*0.5000*2.5000*


#!/usr/bin/perl -w

open(LIST,"FAAA_HUMAN.input1");
@list=<LIST>;
close(LIST);
open(NEW,"> OUTPUT_txt");


{
        #print "$file\n";
        #open(RONALDO,"/home/Raja/MORE_DISEASE_HUMAN_ALIGNMENT/WORK/OUTPUT_FILE/$file");
        open (RONALDO,"FAAA_HUMAN.output");
        @outputfile=<RONALDO>;
        close(RONALDO);
        foreach $x(@list)
        {
                foreach $y(@outputfile)
                  {
        system "cat $y|awk -v num=$x '{if(NR==num) print($0);}' ";

        }
}
}
close(DIR);
close(NEW);
exit;

what can be possible solution?

2

What's the algorithm here?
Guessing that it's number from file1 == line number file 2:

#!/usr/bin/perl -W
use strict;

my $fh;
my @numbers;
my $line;

open $fh, '<', '/path/to/file1' or die "Can't open: $!";
@numbers = <$fh>;
close $fh;
open $fh, '<', '/path/to/file2' or die "Can't open: $!";
while ( $line = <$fh> ) {
    print $line if ( grep { $. == $_ } @numbers );
}
close $fh;
3

the line numbers in file one do not seem match the output and the line numbers in the file have to be offset by negative one to match in the array, which will start at zero instead of one like the file. @numers should probably be chomped to remove the newlines before using it with the numeric operator ==.

4

below should be ok, how to make up the hash with first file leave to you:)

my %hash=(2=>1,5=>1,7=>1,11=>1);
while(<DATA>){
	print if (exists $hash{$.});
}
__DATA__
M*0.0540*0.0039*0.2212*0.0082*0.0020*0.0137*0.0028*0.0029*0.2198*0.0104*0.0889*0.0282*0.0049*0.0804* 0.1743*0.0215*0.0531*0.0071*0.0007*0.0021*0.7270*2.5000*
S*0.0197*0.0043*0.0037*0.0032*0.0018*0.0039*0.0015*0.0027*0.0030*0.0039*0.0012*0.2281*0.0025*0.0022* 0.0027*0.6511*0.0586*0.0040*0.0005*0.0016*0.3700*2.5000*
F*0.0029*0.0008*0.0021*0.0026*0.2621*0.0025*0.2339*0.0018*0.0023*0.0033*0.0010*0.0022*0.0017*0.0024* 0.0024*0.0028*0.0023*0.0023*0.4673*0.0015*0.4240*2.5000*
I*0.0046*0.0012*0.2219*0.0020*0.0069*0.0024*0.0055*0.1693*0.0020*0.2029*0.0021*0.0014*0.0019*0.0014* 0.0018*0.0025*0.0029*0.3649*0.0006*0.0018*0.5222*2.5000*
P*0.0515*0.0014*0.0849*0.0630*0.0027*0.2258*0.0282*0.0076*0.0126*0.0135*0.0016*0.0183*0.0637*0.0732* 0.0176*0.2021*0.0568*0.0655*0.0011*0.0091*0.7958*2.5000*
V*0.3128*0.0031*0.0190*0.0029*0.2206*0.0070*0.0015*0.1142*0.0109*0.0096*0.0028*0.0022*0.0083*0.0021* 0.0026*0.0205*0.0171*0.2189*0.0010*0.0231*0.6230*2.5000*
A*0.0941*0.0018*0.0247*0.0222*0.2207*0.0252*0.0084*0.0047*0.0062*0.0079*0.0020*0.2878*0.2066*0.0039* 0.0051*0.0547*0.0136*0.0061*0.0012*0.0032*0.6645*2.5000*
E*0.0993*0.0014*0.0975*0.3559*0.0030*0.0988*0.0057*0.0042*0.0914*0.0130*0.0021*0.0120*0.0475*0.0277* 0.0190*0.0762*0.0294*0.0119*0.0011*0.0027*0.7241*2.5000*
D*0.0790*0.0014*0.1773*0.0207*0.0025*0.0465*0.1021*0.0027*0.0151*0.0074*0.0015*0.1091*0.0950*0.0147* 0.0077*0.0723*0.2283*0.0040*0.0010*0.0117*0.7629*2.5000*
S*0.0337*0.0919*0.0055*0.0059*0.0034*0.0201*0.0194*0.0050*0.0055*0.0078*0.0023*0.0101*0.0589*0.0039* 0.2287*0.3931*0.0941*0.0069*0.0011*0.0029*0.6322*2.5000*
D*0.0074*0.0008*0.5185*0.0237*0.0015*0.0077*0.0809*0.0020*0.0038*0.0034*0.0009*0.0084*0.0960*0.0102* 0.0029*0.2229*0.0041*0.0027*0.0005*0.0015*0.5000*2.5000*
F*0.0029*0.0007*0.0021*0.0026*0.7291*0.0025*0.0019*0.0018*0.0022*0.0033*0.0010*0.0022*0.0017*0.0023* 0.2344*0.0028*0.0022*0.0022*0.0006*0.0014*0.2651*2.5000*
P*0.0090*0.0010*0.0049*0.0061*0.0025*0.0055*0.0019*0.0038*0.0054*0.2186*0.0015*0.0033*0.5570*0.0031* 0.0043*0.1334*0.0306*0.0053*0.0008*0.0021*0.4543*2.5000*
I*0.0037*0.0010*0.0017*0.0021*0.0042*0.0024*0.0009*0.4114*0.0021*0.3121*0.0034*0.0015*0.0018*0.0016* 0.0019*0.2273*0.0024*0.0117*0.0007*0.0063*0.4469*2.5000*
H*0.1051*0.0007*0.0031*0.2746*0.0014*0.0027*0.0798*0.0018*0.0120*0.0102*0.0010*0.0595*0.0019*0.4283* 0.0027*0.0031*0.0025*0.0024*0.0006*0.0063*0.5353*2.5000*
5

I assumed that the lines "FAAA_HUMAN.input1" and "FAAA_HUMAN.output" are filenames, not actual content.

You're right, they should be chomp()ed (for good style points), but I tried both (chomp()ing and the posted version), there's no difference.