[Bioperl-l] bp_classify_hits_kingdom.pl

[Bernd Web]

Hi Jason,

I was reading through your script and running it.
I noticed, at least the new BLASTP+, is parsed incorrectly.
The %positves field is missing. All fields are:

# Fields: query id, subject ids, % identity, % positives, alignment
length, mismatches, gap opens, q. start, q. end, s. start, s. end,
evalue, bit score

So
my ($qname,$hname,$pid,$qaln,$mismatch,$gaps,
	    $qstart,$qend,$hstart,$hend,
	    $evalue,$bits,$score) = split(/\t/,$_);

should be:
my ($qname,$hname,$pid, $posid, $qaln,$mismatch,$gaps,
	    $qstart,$qend,$hstart,$hend,
	    $evalue,$bit_score) = split(/\t/,$_);

$evalue was set to $hend, instead of the E-value. And $bit_score as one field.


Cheers,
Bernd

On Wed, Jun 22, 2011 at 10:07 PM, Jason Stajich <jason.stajich at gmail.com> wrote:
> Bernd - oops - thanks very much for noticing this - I was too fast in copy & paste. I see another typo in there now that the midday light is shining on the code that I'll fix.
>
> Should be able to check in this in a second.
>
> Jason
>
> On Jun 22, 2011, at 11:07 AM, Bernd Web wrote:
>
>> Hi Jason,
>>
>> I did GI to TAX mapping in Perl alone. Nice to know this script
>> exists. Thanks for this.
>> Just one question, I noticed on
>> https://github.com/bioperl/bioperl-live/blob/master/scripts/taxa/classify_hits_kingdom.PLS:
>>
>> line 96: my $dbh = tie(%gi2node, 'DB_File', 'gi2class');
>> and
>> line 100: my $dbh2 = my $dbh =
>> DBI->connect("dbi:SQLite:dbname=$giidxfile","","");
>>
>> So  the second $dbh masks earlier declaration.
>>
>>
>> Cheers,
>> Bernd