[Biopython-dev] Notification: incoming/35

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Message summary for PR#35
	From: tarjei at mit.edu
	Subject: NCBIStandalone.BlastParser bug
	Date: Tue, 19 Jun 2001 10:57:42 -0400
	0 replies 	0 followups
	Notes: format change, got fixed and released in biopython 1.0a2

-Jeff


====> ORIGINAL MESSAGE FOLLOWS <====

>From tarjei at mit.edu Tue Jun 19 10:57:42 2001
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Date: Tue, 19 Jun 2001 10:57:42 -0400
Message-Id: <200106191457.f5JEvg826272 at pw600a.bioperl.org>
From: tarjei at mit.edu
To: biopython-bugs at bioperl.org
Subject: NCBIStandalone.BlastParser bug

Full_Name: Tarjei Mikkelsen
Module: Bio.Blast.NCBIStandalone.BlastParser
Version: 1.00a
OS: Dec/Alpha OSF1
Submission from: incognito.mit.edu (18.246.0.239)


The standalone BLAST record parser (Bio.Blast.NCBISTandalone.BlastParser) fails
with a SyntaxError when the (path)name of the database spans more than one
line.

The following code stub/BLAST output will reproduce the bug: (Even though this
example is from BLAST 2.0.5 the same thing happens in newer versions)

<<<<<CUT: blast_parser_bug.py>>>>>
from Bio.Blast import NCBIStandalone

blast_out = open("blast_parser_bug.out", "r")
blast_parser = NCBIStandalone.BlastParser()
blast_record = blast_parser.parse(blast_out)
<<<<<CUT>>>>>

<<<<<CUT: blast_parser_bug.out>>>>>
BLASTP 2.0.5 [May-5-1998]


Reference: Altschul, Stephen F., Thomas L. Madden, Alejandro A. Schaffer, 
Jinghui Zhang, Zheng Zhang, Webb Miller, and David J. Lipman (1997), 
"Gapped BLAST and PSI-BLAST: a new generation of protein database search
programs",  Nucleic Acids Res. 25:3389-3402.

Query= eco:b1416
         (83 letters)

Database: /home/strontium/tarjei/pathway/src/Bio/Pathway/data/2.7.1.11
.fa
           39 sequences; 18,779 total letters

Searching......................................done

                                                                   Score     E
Sequences producing significant alignments:                        (bits) 
Value

spy:SPy1283                                                           20  0.64
lla:L0002                                                             20  0.84

>spy:SPy1283
           Length = 337
           
 Score = 20.4 bits (41), Expect = 0.64
 Identities = 10/26 (38%), Positives = 17/26 (64%), Gaps = 1/26 (3%)

Query: 21  GYTDEEIVSSDIIG-SHFGSVFDATQ 45
           G  +EE+V S I+G +  G++F  T+
Sbjct: 287 GIHNEELVESPILGTAEEGALFSLTE 312


>lla:L0002
           Length = 340
           
 Score = 20.0 bits (40), Expect = 0.84
 Identities = 10/25 (40%), Positives = 16/25 (64%), Gaps = 1/25 (4%)

Query: 21  GYTDEEIVSSDIIG-SHFGSVFDAT 44
           G  +EE+V S I+G +  G++F  T
Sbjct: 286 GIRNEELVESPILGTAEEGALFSLT 310


 Score = 18.8 bits (37), Expect = 1.9
 Identities = 9/29 (31%), Positives = 17/29 (58%), Gaps = 1/29 (3%)

Query: 28  VSSDIIGSHFGSVFD-ATQTEITAVGDLQ 55
           + +DI+G+ F   FD A  T + A+  ++
Sbjct: 126 IDNDIVGTDFTIGFDTAVSTVVDALDKIR 154


  Database: /home/strontium/tarjei/pathway/src/Bio/Pathway/data/2.7.1.
  11.fa
    Posted date:  Jun 18, 2001  1:19 PM
  Number of letters in database: 18,779
  Number of sequences in database:  39
  
Lambda     K      H
   0.313    0.129    0.352 

Gapped
Lambda     K      H
   0.270   0.0470    0.230 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 2788
Number of Sequences: 39
Number of extensions: 119
Number of successful extensions: 3
Number of sequences better than 10: 2
Number of HSP's better than 10.0 without gapping: 2
Number of HSP's successfully gapped in prelim test: 0
Number of HSP's that attempted gapping in prelim test: 0
Number of HSP's gapped (non-prelim): 3
length of query: 83
length of database: 18779
effective HSP length: 33
effective length of query: 50
effective length of database: 17492
effective search space:   874600
T: 11
A: 40
X1: 16 ( 7.2 bits)
X2: 38 (14.8 bits)
X3: 64 (24.9 bits)
S1: 34 (18.3 bits)
S2: 31 (16.5 bits)
<<<<<CUT>>>>>