Hi all, I using the code below that uses the Getopt::Std to process the
arguments from the command line (init subroutine). However, for some
reason I do not get the arguments from the switches. If anyone sees
what is the mistake I will be happy to hear about it.
#!/usr/sbin/perl -w
use Getopt::Std;
&init;
open(F, "$FILE") || die "I could not open $FILE\n";
while(<F>){
if (! /ATOM/) {
print $_;
}
else{
if ( substr($_, $21,1) =~ $A ){
substr ($_, $21, 1, $B);
print $_;
}
else{
print $_;
}
}
}
close(F);
sub usage {
my $program = `basename $0`;
chop($program);
print STDERR "
$program [-p pdb ] [-a <chain_to_rename> ] [-b <new_chain_name>] [
-h ]
Rename chain id from pdb
-p : pdb file
-a : chain to rename
-b : new chain name
";
}
sub init {
getopts('pab');
if ($opt_p) {
$FILE = $opt_p;
print "$FILE\n";
} else {
&usage;
exit;
}
if ($opt_a) {
$A = $opt_a;
chomp($A);
}
else {
&usage;
exit;
}
if ($opt_b) {
$B = $opt_b;
chomp($B);
}
else {
&usage;
exit;
}
}
--
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PEDRO A. RECHE , pHD TL: 617 632 3824
Bioinformatics Research Scientist FX: 617 632 4569
Dana-Farber Cancer Institute, EM: [EMAIL PROTECTED]
Molecular Immunology Foundation, EM: [EMAIL PROTECTED]
Harvard Medical School, W3: http://www.mifoundation.org
44 Binney Street, D1510A,
Boston, MA 02115
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