[BioPython] Changes in NCBI BLAST output format

[Martina]

Hello,

shouldn't the suggestion by Alexander in the _Scanner class:
"
     change:
         attempt_read_and_call(uhandle, consumer.noevent, start='<p>')
     to:
         attempt_read_and_call(uhandle, consumer.noevent)
"
be changed to something like:
        read_and_call_while(uhandle, consumer.noevent, blank=1)?

At least, that is what is working in my case.
This is because of the 2 different types of return files: one with the 
queries first, the other with the database info first. If it is database 
first, then there is an additional blank line which gave me problems.

Martina



meames at itsa.ucsf.edu wrote:
> Yes, I have also observed a similar problem - 
> 
> The new BLAST output has an extra empty line between the "RID:" line
> and the "<b>Database:" line, which chokes the parser. A temporary (albeit 
> bad programming) solution would be to eliminate the line in the saved
> BLAST output file before passing it on the parser.
> 
> Matt 
> 
> On 5 Sep 2005 11:10:39 +0200 "Martina" wrote:
> 
> 
>>Hello Michiel,
>>
>>I got your fix for NCBIWWW.py from the CVS, but now I get a diffrent 
>>error message:   SyntaxError: Line does not contain 'Database':
>>.
.
.