Hai ! I am doing a research on Bioinformatics and a part of the code in perl have to be converted to shell scripting. I am new to shell programming. Pls. kindly help me to convert this code to shell script though it is somewhat lengthy.
PLS KINDLY HELP ME. THANKS IN ADVANCE.
Code:
my @FreeEnergy = `grep -e \'dG\' t1.ct`;
my @dG;
foreach my $fE (@FreeEnergy) {
my @vals = split(' ',$fE);
push(@dG,$vals[3]);
}
my $recSep = $/;
$/ = 'Structure';
open STR, '<', 't1.out' or die "cannot open file \n";
my @structures = <STR>;
close STR;
$/ = $recSep;
my @hairpins = `grep -e \'Structure\' -e \'Hairpin loop:\' -e \'Multi\-loop\' t1.det`;
my ($h,$m) = (0,0);
my (@H,%HairPins,%Multi,@M);
for (my $i=0;$i <@hairpins;$i++) {
my $line = $hairpins[$i];
chomp $line;
if ($line =~ /Structure/) {
if (@H) {
$h++;
my @NH = @H;
my @NM = @M;
$HairPins{$h} = \@NH;
$Multi{$h} = \@NM;
@H = ();
@M = ();
}
} elsif($line =~ /Hairpin/) {
my ($s1,$s2) = ($line =~ /Closing pair is \D\(\s+(\d+)\)-D\(\s+(\d+)\)/);
my $hLoop = "$s1-$s2";
push(@H,$hLoop);
if($i == scalar @hairpins-1) {
$h++;
my @NH = @H;
$HairPins{$h} = \@NH;
my @NM = @M;
$Multi{$h} = \@NM;
@M = ();
@H = ();
}
}
else {
my ($s1,$s2) = ($line =~ /closing pair is \D\(\s+(\d+)\)-\D\(\s+(\d+)\)/);
my $mLoop = "$s1-$s2";
push(@M,$mLoop);
}
}
Last edited by Scott; 10-20-2010 at 02:35 PM..
Reason: Please use code tags, and less formatting of fonts, sizes and colours
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LEARN ABOUT MINIX
suspend
suspend(1) User Commands suspend(1)NAME
suspend - shell built-in function to halt the current shell
SYNOPSIS
sh
suspend
csh
suspend
ksh
suspend
DESCRIPTION
sh
Stops the execution of the current shell (but not if it is the login shell).
csh
Stop the shell in its tracks, much as if it had been sent a stop signal with ^Z. This is most often used to stop shells started by su.
ksh
Stops the execution of the current shell (but not if it is the login shell).
ATTRIBUTES
See attributes(5) for descriptions of the following attributes:
+-----------------------------+-----------------------------+
| ATTRIBUTE TYPE | ATTRIBUTE VALUE |
+-----------------------------+-----------------------------+
|Availability |SUNWcsu |
+-----------------------------+-----------------------------+
SEE ALSO csh(1), kill(1), ksh(1), sh(1), su(1M), attributes(5)SunOS 5.10 15 Apr 1994 suspend(1)