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I am presently running my complete dataset with your program. The program has been merrily churning away for about 48 hours. When it completes this task I'll let you know how things turned out.

update

Oops, I had to restart the run. When I set up the program I added specific code to hardwire the name of my data file into the program. When I did this I created a bug, which caused the program to idle. I had not removed the $_ = <>; line, so the program was waiting for me to enter data from the keyboard.

commented out the if (@argv != 1){...} and added the following:

my $file = "mydata.txt"; open FILE, $file or die "Can't open $file: $!\n"; my $out = "outdata.txt"; open OUT , '>', $out or die "Can't open $out: $!\n"; # all print and printf statements now print to # this file handle # Read in the strings chomp(my @file = <FILE>); # declare variables my @strings = (); my $place = 1; my $strName = ''; # necessary for resolution of # an undeclared global variable # warning for (@file){ if ($place){ $strName = $_; # seq ID $place = 0; }else{ push @strings, [$strName, $_]; # push seq ID, seq $place = 1; } }

In reply to Re^7: Fast common substring matching by bioMan
in thread Fast common substring matching by GrandFather

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