[BioPython] Blast 2.2 or better

[Jeffrey Chang]

On Nov 17, 2003, at 11:39 AM, Osborne, John wrote:

> Hi Jeff,
>
[...]

> I've included the blast output and the error file,

On the blast output file you sent, the parser seems to be working 
correctly, except that the file ends prematurely!  It is raising an 
"Unexpected end of stream" error because the file ends abruptly in the 
middle of a hit:
Query: 19  AIVDNEII-IAGGYNFNNPSLNKVYKINIENKIHVELPPMIMN---RCRFSLAVIDNTIY 
74
            A+V+  I+ + GGY FN+   N V   ++ ++  + L   + N   R   SLA+  + IY
Sbjct: 346 AVVNGNIMWVVGGYMFNHSDYNMVLAYDLASREWLPLNRSVNNVVVRYGHSLALYKDKIY 
405

Query: 75  AIGGQ 79
              GG+
Sbjct: 406 MYGGK 410

The rest of the file with the database and statistics is missing, which 
confuses the parser.  Did BLAST crash in the middle of the search?


> I have tried
> debugging this myself but I have run into some odd behaviour.  I tried
> adding a print statement (print "boo") to NCBIStandalone.py and as
> output I got 'print "boo"' ie) it included the word print and quotes?!
> I just started with python last week and found this odd to say the
> least.

I've been using python for 5 years, and I find it odd.  ;)  Where did 
you add it?  I don't understand how that can happen.


>   I also am also confused by read_and_call functions?  Is this
> biopython or python?  I tried grepping for "def read_and_call" in the
> biopython directory but can't find it, how would I go about finding 
> this
> (and similar) function?

This is being imported from ParserSupport with the line:
from Bio.ParserSupport import *

grepping in biopython/Bio for "def read_and_call" should have 
identified the function as being defined in ParserSupport.

Jeff