[BioPython] Blast 2.2 or better
Jeffrey Chang
jeffrey_chang at stanfordalumni.org
Mon Nov 17 16:34:45 EST 2003
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
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