[Bioperl-l] Re: problem in /usr/lib/perl5/site_perl/5.8.6/Bio/SearchIO/blast.pm

[Jason Stajich]

NCBI reserves the right to make the HTML or Text unparseable from the  
CGI, I guess they've now done that.

See these posts:
http://bioperl.org/pipermail/bioperl-l/2005-September/019760.html
http://bioperl.org/pipermail/bioperl-l/2005-September/019724.html

-jason
On Jan 13, 2006, at 7:54 AM, Guido Dieterich wrote:

> Hi, Jason
>
>
> RemoteBlast.pm
> I printed out the NCBI report that was requested!
>
> Guido
>
>
> Am Freitag, den 13.01.2006, 07:44 -0500 schrieb Jason Stajich:
>
>> This is from RemoteBlast or from blast run on the command line?
>>
>> On Jan 13, 2006, at 5:47 AM, Guido Dieterich wrote:
>>
>>> Hi Jason, hi all,
>>>
>>> it seems  so that ncbi changed again its blast output format:
>>> as example:
>>> they added a/more Feature line(s)
>>>>>>>
>>> Features in this part of subject sequence:
>>>    oxidoreductase, pyridine nucleotide-disulfide family
>>>>>>>
>>>
>>>
>>> Bio/SearchIO/blast.pm
>>>
>>> will cause a problem. Error message is:
>>>
>>> ------------- EXCEPTION: Bio::Root::Exception -------------
>>> MSG: no data for midline  Features flanking this part of subject
>>> sequence:
>>> STACK: Error::throw
>>> STACK:
>>> Bio::Root::Root::throw /usr/lib/perl5/site_perl/5.8.6/Bio/Root/
>>> Root.pm:328
>>> STACK:
>>> Bio::SearchIO::blast::next_result /usr/lib/perl5/site_perl/5.8.6/
>>> Bio/SearchIO/blast.pm:1166
>>> STACK: main::remoteBLAST /home/gdi/Perl-skripte/longestORF.pl:95
>>> STACK: /home/gdi/Perl-skripte/longestORF.pl:34
>>> -----------------------------------------------------------
>>>
>>>
>>>
>>> longer example of the blast ncbi report:
>>>
>>>> gb|AE016830.1| Enterococcus faecalis V583, complete genome
>>>           Length=3218031
>>>
>>>  Features in this part of subject sequence:
>>>    oxidoreductase, pyridine nucleotide-disulfide family
>>>
>>>  Score = 79.8 bits (40),  Expect = 3e-11
>>>  Identities = 82/96 (85%), Gaps = 0/96 (0%)
>>>  Strand=Plus/Plus
>>>
>>> Query  1129
>>> ATGAAACATATGGTTAACTTGTACTACTTCTTCGGTATCCGTAGTGGTTACTACATGTGG  1188
>>>                 ||||||||||| ||||||||| | |||||||| | ||| |||
>>> ||||||||||||||
>>> Sbjct  3136253
>>> ATGAAACATATCGTTAACTTGAAATACTTCTTTGATATTCGTTCTGGTTACTACATGTTC   
>>> 3136312
>>>
>>> Query  1189     CAATATATTATGCATGAATTCTTCCACATTAAAGAT  1224
>>>                 ||||| |||||||| ||| ||||||| |||||||||
>>> Sbjct  3136313  CAATACATTATGCACGAAATCTTCCATATTAAAGAT  3136348
>>>
>>>
>>>  Features in this part of subject sequence:oxidoreductase, pyridine
>>> nucleotide-disulfide family
>>>
>>>  Score = 77.8 bits (39),  Expect = 1e-10
>>>  Identities = 90/107 (84%), Gaps = 0/107 (0%)
>>>  Strand=Plus/Plus
>>>
>>> Query  469
>>> AAAGCGATGTTAACATTCGTTGTTTGTGGATCTGGATTTACTGGTATCGAAATGGTTGGG  528
>>>                 ||||| ||||||||||||||||| ||||| ||||| ||||||||
>>> |||||||||||
>>> ||
>>> Sbjct  3135587
>>> AAAGCAATGTTAACATTCGTTGTCTGTGGTTCTGGTTTTACTGGGATCGAAATGGTCGGC   
>>> 3135646
>>>
>>> Query  529      GAACTTTTAGAATGGAAAGATCGTCTTGCTAAAGATAACAAAATTGA  575
>>>                 ||| |  | || |||||||||||| | || ||||||  |||||||||
>>> Sbjct  3135647  GAATTAATCGACTGGAAAGATCGTTTAGCGAAAGATGCCAAAATTGA
>>> 3135693
>>>
>>>
>>
>> --
>> Jason Stajich
>> jason at bioperl.org
>> http://jason.open-bio.org/
>>

--
Jason Stajich
jason at bioperl.org
http://jason.open-bio.org/