# File:	searchAllsub2.pl
# Title: 	Given string and a substring (pattern)
#			Capture all the positions of the substring in string
#           use system function: pos($seq) - gives next position 
# C:\myPerl>perl searchAllsub.pl
#   There are 3 positions where 'at' is found in mathematica Result: 1 6 
### 		Find positions for a in mathematicat    ***
$seq = 'mathematica';		
$regex = 'at';    	#search substring 'at' in mathematica
@Places = searchAll($seq,$regex);	#call subroutine
$Places = @Places;					# find length array result
print "\nThere are ", $Places, " positions where $regex is found in $seq: ", @Places;
exit;

### Subroutine, takes 2 args: sequence and a substring and return list of positions ###
sub searchAll {
	my @Positions = ();			   # initialize array where you put positions
	my ($s,$r) = @_;               # array of arguments from main program: sequence and character
	while ( $s =~ m/$r/g ) 	{      # search globally (g) pattern $r is $s 
	    # you have to subtract length of pattern to find its start position
		push (@Positions,pos($s)-length($r));		# add to list of positions
	}
	return @Positions;
}