[Biopython-dev] Notification: incoming/35

[Jeffrey Chang]

Good catch!  Yes, the parser is assuming 1 line for the database.  I've gone
through and fixed this in the NCBIStandalone.py file.  Please install this
over your previous one and let me know if it works.  I'm not sure if there
are more outstanding issues with the formatting of BLAST 2.0.5.  If there
are, please send me the offending output to me directly as an attachment --
the jitterbug remailer reformats text so I can't tell exactly what the
original output looks like.

Thanks,
Jeff




> From: biopython-bugs at bioperl.org
> Date: Tue, 19 Jun 2001 10:57:43 -0400
> To: biopython-dev at biopython.org
> Subject: [Biopython-dev] Notification: incoming/35
> 
> JitterBug notification
> 
> new message incoming/35
> 
> 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
> 
> ====> ORIGINAL MESSAGE FOLLOWS <====
> 
>> From tarjei at mit.edu Tue Jun 19 10:57:42 2001
> Received: from localhost (localhost [127.0.0.1])
> by pw600a.bioperl.org (8.11.2/8.11.2) with ESMTP id f5JEvg826272
> for <biopython-bugs at pw600a.bioperl.org>; Tue, 19 Jun 2001 10:57:42 -0400
> 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>>>>>
> 
> 
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