[Bioperl-l] BinarySearch.pm

Peter Rice pmr at ebi.ac.uk
Tue Nov 29 08:39:52 EST 2011

In trying to use bioflat_index.pl index files in EMBOSS, I ran into some 

Both appear to be in the Bio/Flat/BinarySearch.pm source file.

EMBL ID lines are failing to drop the ';' from the ID. Updating the 
regular expression to make sure the ';' is not picked up seems to work:

   if ($format =~ /embl/i) {
     return ('ID',
	    "^ID   (\\S+[^; ])",
	    "^ID   (\\S+[^; ])",
	     ACC     => q/^AC   (\S+);/,
	     VERSION => q/^SV\s+(\S+)/

The ACC secondary index has every record duplicated.
This line is duplicated in the write_secondary_indices source code. Is 
that intentional?

  		    print $fh sprintf("%-${length}s",$record);


Peter Rice

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