[Bioperl-l] BinarySearch.pm

Fields, Christopher J cjfields at illinois.edu
Tue Nov 29 17:30:58 EST 2011


Can you send a test file that is failing?  I added a few tests using an example file with a ';' in the ID line, but everything is passing with our other EMBL example files.  I'm also looking into adding a method to return secondary IDs for a specific type ('ACC' for instance) so we can test the repeat issue for accessions.  Both changes pass tests as is, though, so I have committed them in the meantime.


On Nov 29, 2011, at 7:39 AM, Peter Rice wrote:

> In trying to use bioflat_index.pl index files in EMBOSS, I ran into some problems.
> 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);
> regards,
> Peter Rice
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