[Bioperl-l] bp_classify_hits_kingdom.pl

[Jason Stajich]

Bernd - 

Thanks for seeing it -- however I it was written for the original blast m8 format, so if a different formatted input is provided then it requires now the option of supporting either format I would say - and/or manipulation of the input. so some more code.

I'm not going to work on this but if you want to report it as a bug that can be tracked and someone can then volunteer to work on it and submit a batch via git.

thanks.

On Jun 30, 2011, at 5:19 AM, Bernd Web wrote:

> 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