[BioPython] PSI-BLAST parsing problem
Erdahl Teber
e.teber at mmb.usyd.edu.au
Mon Feb 14 03:52:06 EST 2005
Skipped content of type multipart/alternative-------------- next part --------------
BLASTP 2.0.11 [Jan-20-2000]
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= myTest
(5 letters)
Database: C:\formatdb\db
3,241,261 sequences; 16,206,305 total letters
Score E
Sequences producing significant alignments: (bits) Value
1VXG |19 18 380
1VXF |19 18 380
1VXE |19 18 380
1VXD |19 18 380
1UFJA |19 18 380
2MBW |19 18 380
1YOG |19 18 380
1YOI |19 18 380
1YOH |19 18 380
1VXH |19 18 380
1VXC |19 18 380
1UFPA |19 18 380
1TES |20 18 380
1OBM |19 18 380
1N9XA |19 18 380
1N9HA |19 18 380
1N9FA |19 18 380
1MWCA |19 18 380
1LUEA |19 18 380
1JPBA |19 18 380
1F65A |19 18 380
1DXDA |19 18 380
1DO7A |19 18 380
1CO8A |19 18 380
1CH9A |19 18 380
107M |19 18 380
105M |19 18 380
104M |19 18 380
1OFJ |19 18 380
1OFK |19 18 380
1MWDB |19 18 380
1MWDA |19 18 380
1M6MB |19 18 380
1M6MA |19 18 380
1JP8A |19 18 380
1J52A |19 18 380
1O16A |19 18 380
1NAZA |19 18 380
1N9IA |19 18 380
1JW8A |20 18 380
1LTW |19 18 380
1JP6A |19 18 380
1DXCA |19 18 380
1CO9A |19 18 380
1CIOA |19 18 380
1CH1A |19 18 380
103M |19 18 380
101M |19 18 380
1IOP |19 18 380
1HJT |19 18 380
1JDO |19 18 380
1H1XA |19 18 380
1F63A |19 18 380
1CP5A |19 18 380
112M |19 18 380
111M |19 18 380
110M |19 18 380
109M |19 18 380
108M |19 18 380
106M |19 18 380
1DO4A |19 18 380
1DO3A |19 18 380
1DO1A |19 18 380
1CPWA |19 18 380
1CP0A |19 18 380
1CIKA |19 18 380
1CH3A |19 18 380
1CH2A |19 18 380
1ABS |19 18 380
102M |19 18 380
>1VXG |19
Length = 5
Score = 18.4 bits (36), Expect = 380
Identities = 5/5 (100%), Positives = 5/5 (100%)
Query: 1 VEADV 5
VEADV
Sbjct: 1 VEADV 5
>1VXF |19
Length = 5
Score = 18.4 bits (36), Expect = 380
Identities = 5/5 (100%), Positives = 5/5 (100%)
Query: 1 VEADV 5
VEADV
Sbjct: 1 VEADV 5
>1VXE |19
Length = 5
Score = 18.4 bits (36), Expect = 380
Identities = 5/5 (100%), Positives = 5/5 (100%)
Query: 1 VEADV 5
VEADV
Sbjct: 1 VEADV 5
>1VXD |19
Length = 5
Score = 18.4 bits (36), Expect = 380
Identities = 5/5 (100%), Positives = 5/5 (100%)
Query: 1 VEADV 5
VEADV
Sbjct: 1 VEADV 5
>1UFJA |19
Length = 5
Score = 18.4 bits (36), Expect = 380
Identities = 5/5 (100%), Positives = 5/5 (100%)
Query: 1 VEADV 5
VEADV
Sbjct: 1 VEADV 5
>2MBW |19
Length = 5
Score = 18.4 bits (36), Expect = 380
Identities = 5/5 (100%), Positives = 5/5 (100%)
Query: 1 VEADV 5
VEADV
Sbjct: 1 VEADV 5
>1YOG |19
Length = 5
Score = 18.4 bits (36), Expect = 380
Identities = 5/5 (100%), Positives = 5/5 (100%)
Query: 1 VEADV 5
VEADV
Sbjct: 1 VEADV 5
>1YOI |19
Length = 5
Score = 18.4 bits (36), Expect = 380
Identities = 5/5 (100%), Positives = 5/5 (100%)
Query: 1 VEADV 5
VEADV
Sbjct: 1 VEADV 5
>1YOH |19
Length = 5
Score = 18.4 bits (36), Expect = 380
Identities = 5/5 (100%), Positives = 5/5 (100%)
Query: 1 VEADV 5
VEADV
Sbjct: 1 VEADV 5
>1VXH |19
Length = 5
Score = 18.4 bits (36), Expect = 380
Identities = 5/5 (100%), Positives = 5/5 (100%)
Query: 1 VEADV 5
VEADV
Sbjct: 1 VEADV 5
>1VXC |19
Length = 5
Score = 18.4 bits (36), Expect = 380
Identities = 5/5 (100%), Positives = 5/5 (100%)
Query: 1 VEADV 5
VEADV
Sbjct: 1 VEADV 5
>1UFPA |19
Length = 5
Score = 18.4 bits (36), Expect = 380
Identities = 5/5 (100%), Positives = 5/5 (100%)
Query: 1 VEADV 5
VEADV
Sbjct: 1 VEADV 5
>1TES |20
Length = 5
Score = 18.4 bits (36), Expect = 380
Identities = 5/5 (100%), Positives = 5/5 (100%)
Query: 1 VEADV 5
VEADV
Sbjct: 1 VEADV 5
>1OBM |19
Length = 5
Score = 18.4 bits (36), Expect = 380
Identities = 5/5 (100%), Positives = 5/5 (100%)
Query: 1 VEADV 5
VEADV
Sbjct: 1 VEADV 5
>1N9XA |19
Length = 5
Score = 18.4 bits (36), Expect = 380
Identities = 5/5 (100%), Positives = 5/5 (100%)
Query: 1 VEADV 5
VEADV
Sbjct: 1 VEADV 5
>1N9HA |19
Length = 5
Score = 18.4 bits (36), Expect = 380
Identities = 5/5 (100%), Positives = 5/5 (100%)
Query: 1 VEADV 5
VEADV
Sbjct: 1 VEADV 5
>1N9FA |19
Length = 5
Score = 18.4 bits (36), Expect = 380
Identities = 5/5 (100%), Positives = 5/5 (100%)
Query: 1 VEADV 5
VEADV
Sbjct: 1 VEADV 5
>1MWCA |19
Length = 5
Score = 18.4 bits (36), Expect = 380
Identities = 5/5 (100%), Positives = 5/5 (100%)
Query: 1 VEADV 5
VEADV
Sbjct: 1 VEADV 5
>1LUEA |19
Length = 5
Score = 18.4 bits (36), Expect = 380
Identities = 5/5 (100%), Positives = 5/5 (100%)
Query: 1 VEADV 5
VEADV
Sbjct: 1 VEADV 5
>1JPBA |19
Length = 5
Score = 18.4 bits (36), Expect = 380
Identities = 5/5 (100%), Positives = 5/5 (100%)
Query: 1 VEADV 5
VEADV
Sbjct: 1 VEADV 5
>1F65A |19
Length = 5
Score = 18.4 bits (36), Expect = 380
Identities = 5/5 (100%), Positives = 5/5 (100%)
Query: 1 VEADV 5
VEADV
Sbjct: 1 VEADV 5
>1DXDA |19
Length = 5
Score = 18.4 bits (36), Expect = 380
Identities = 5/5 (100%), Positives = 5/5 (100%)
Query: 1 VEADV 5
VEADV
Sbjct: 1 VEADV 5
>1DO7A |19
Length = 5
Score = 18.4 bits (36), Expect = 380
Identities = 5/5 (100%), Positives = 5/5 (100%)
Query: 1 VEADV 5
VEADV
Sbjct: 1 VEADV 5
>1CO8A |19
Length = 5
Score = 18.4 bits (36), Expect = 380
Identities = 5/5 (100%), Positives = 5/5 (100%)
Query: 1 VEADV 5
VEADV
Sbjct: 1 VEADV 5
>1CH9A |19
Length = 5
Score = 18.4 bits (36), Expect = 380
Identities = 5/5 (100%), Positives = 5/5 (100%)
Query: 1 VEADV 5
VEADV
Sbjct: 1 VEADV 5
>107M |19
Length = 5
Score = 18.4 bits (36), Expect = 380
Identities = 5/5 (100%), Positives = 5/5 (100%)
Query: 1 VEADV 5
VEADV
Sbjct: 1 VEADV 5
>105M |19
Length = 5
Score = 18.4 bits (36), Expect = 380
Identities = 5/5 (100%), Positives = 5/5 (100%)
Query: 1 VEADV 5
VEADV
Sbjct: 1 VEADV 5
>104M |19
Length = 5
Score = 18.4 bits (36), Expect = 380
Identities = 5/5 (100%), Positives = 5/5 (100%)
Query: 1 VEADV 5
VEADV
Sbjct: 1 VEADV 5
>1OFJ |19
Length = 5
Score = 18.4 bits (36), Expect = 380
Identities = 5/5 (100%), Positives = 5/5 (100%)
Query: 1 VEADV 5
VEADV
Sbjct: 1 VEADV 5
>1OFK |19
Length = 5
Score = 18.4 bits (36), Expect = 380
Identities = 5/5 (100%), Positives = 5/5 (100%)
Query: 1 VEADV 5
VEADV
Sbjct: 1 VEADV 5
>1MWDB |19
Length = 5
Score = 18.4 bits (36), Expect = 380
Identities = 5/5 (100%), Positives = 5/5 (100%)
Query: 1 VEADV 5
VEADV
Sbjct: 1 VEADV 5
>1MWDA |19
Length = 5
Score = 18.4 bits (36), Expect = 380
Identities = 5/5 (100%), Positives = 5/5 (100%)
Query: 1 VEADV 5
VEADV
Sbjct: 1 VEADV 5
>1M6MB |19
Length = 5
Score = 18.4 bits (36), Expect = 380
Identities = 5/5 (100%), Positives = 5/5 (100%)
Query: 1 VEADV 5
VEADV
Sbjct: 1 VEADV 5
>1M6MA |19
Length = 5
Score = 18.4 bits (36), Expect = 380
Identities = 5/5 (100%), Positives = 5/5 (100%)
Query: 1 VEADV 5
VEADV
Sbjct: 1 VEADV 5
>1JP8A |19
Length = 5
Score = 18.4 bits (36), Expect = 380
Identities = 5/5 (100%), Positives = 5/5 (100%)
Query: 1 VEADV 5
VEADV
Sbjct: 1 VEADV 5
>1J52A |19
Length = 5
Score = 18.4 bits (36), Expect = 380
Identities = 5/5 (100%), Positives = 5/5 (100%)
Query: 1 VEADV 5
VEADV
Sbjct: 1 VEADV 5
>1O16A |19
Length = 5
Score = 18.4 bits (36), Expect = 380
Identities = 5/5 (100%), Positives = 5/5 (100%)
Query: 1 VEADV 5
VEADV
Sbjct: 1 VEADV 5
>1NAZA |19
Length = 5
Score = 18.4 bits (36), Expect = 380
Identities = 5/5 (100%), Positives = 5/5 (100%)
Query: 1 VEADV 5
VEADV
Sbjct: 1 VEADV 5
>1N9IA |19
Length = 5
Score = 18.4 bits (36), Expect = 380
Identities = 5/5 (100%), Positives = 5/5 (100%)
Query: 1 VEADV 5
VEADV
Sbjct: 1 VEADV 5
>1JW8A |20
Length = 5
Score = 18.4 bits (36), Expect = 380
Identities = 5/5 (100%), Positives = 5/5 (100%)
Query: 1 VEADV 5
VEADV
Sbjct: 1 VEADV 5
>1LTW |19
Length = 5
Score = 18.4 bits (36), Expect = 380
Identities = 5/5 (100%), Positives = 5/5 (100%)
Query: 1 VEADV 5
VEADV
Sbjct: 1 VEADV 5
>1JP6A |19
Length = 5
Score = 18.4 bits (36), Expect = 380
Identities = 5/5 (100%), Positives = 5/5 (100%)
Query: 1 VEADV 5
VEADV
Sbjct: 1 VEADV 5
>1DXCA |19
Length = 5
Score = 18.4 bits (36), Expect = 380
Identities = 5/5 (100%), Positives = 5/5 (100%)
Query: 1 VEADV 5
VEADV
Sbjct: 1 VEADV 5
>1CO9A |19
Length = 5
Score = 18.4 bits (36), Expect = 380
Identities = 5/5 (100%), Positives = 5/5 (100%)
Query: 1 VEADV 5
VEADV
Sbjct: 1 VEADV 5
>1CIOA |19
Length = 5
Score = 18.4 bits (36), Expect = 380
Identities = 5/5 (100%), Positives = 5/5 (100%)
Query: 1 VEADV 5
VEADV
Sbjct: 1 VEADV 5
>1CH1A |19
Length = 5
Score = 18.4 bits (36), Expect = 380
Identities = 5/5 (100%), Positives = 5/5 (100%)
Query: 1 VEADV 5
VEADV
Sbjct: 1 VEADV 5
>103M |19
Length = 5
Score = 18.4 bits (36), Expect = 380
Identities = 5/5 (100%), Positives = 5/5 (100%)
Query: 1 VEADV 5
VEADV
Sbjct: 1 VEADV 5
>101M |19
Length = 5
Score = 18.4 bits (36), Expect = 380
Identities = 5/5 (100%), Positives = 5/5 (100%)
Query: 1 VEADV 5
VEADV
Sbjct: 1 VEADV 5
>1IOP |19
Length = 5
Score = 18.4 bits (36), Expect = 380
Identities = 5/5 (100%), Positives = 5/5 (100%)
Query: 1 VEADV 5
VEADV
Sbjct: 1 VEADV 5
>1HJT |19
Length = 5
Score = 18.4 bits (36), Expect = 380
Identities = 5/5 (100%), Positives = 5/5 (100%)
Query: 1 VEADV 5
VEADV
Sbjct: 1 VEADV 5
>1JDO |19
Length = 5
Score = 18.4 bits (36), Expect = 380
Identities = 5/5 (100%), Positives = 5/5 (100%)
Query: 1 VEADV 5
VEADV
Sbjct: 1 VEADV 5
>1H1XA |19
Length = 5
Score = 18.4 bits (36), Expect = 380
Identities = 5/5 (100%), Positives = 5/5 (100%)
Query: 1 VEADV 5
VEADV
Sbjct: 1 VEADV 5
>1F63A |19
Length = 5
Score = 18.4 bits (36), Expect = 380
Identities = 5/5 (100%), Positives = 5/5 (100%)
Query: 1 VEADV 5
VEADV
Sbjct: 1 VEADV 5
>1CP5A |19
Length = 5
Score = 18.4 bits (36), Expect = 380
Identities = 5/5 (100%), Positives = 5/5 (100%)
Query: 1 VEADV 5
VEADV
Sbjct: 1 VEADV 5
>112M |19
Length = 5
Score = 18.4 bits (36), Expect = 380
Identities = 5/5 (100%), Positives = 5/5 (100%)
Query: 1 VEADV 5
VEADV
Sbjct: 1 VEADV 5
>111M |19
Length = 5
Score = 18.4 bits (36), Expect = 380
Identities = 5/5 (100%), Positives = 5/5 (100%)
Query: 1 VEADV 5
VEADV
Sbjct: 1 VEADV 5
>110M |19
Length = 5
Score = 18.4 bits (36), Expect = 380
Identities = 5/5 (100%), Positives = 5/5 (100%)
Query: 1 VEADV 5
VEADV
Sbjct: 1 VEADV 5
>109M |19
Length = 5
Score = 18.4 bits (36), Expect = 380
Identities = 5/5 (100%), Positives = 5/5 (100%)
Query: 1 VEADV 5
VEADV
Sbjct: 1 VEADV 5
>108M |19
Length = 5
Score = 18.4 bits (36), Expect = 380
Identities = 5/5 (100%), Positives = 5/5 (100%)
Query: 1 VEADV 5
VEADV
Sbjct: 1 VEADV 5
>106M |19
Length = 5
Score = 18.4 bits (36), Expect = 380
Identities = 5/5 (100%), Positives = 5/5 (100%)
Query: 1 VEADV 5
VEADV
Sbjct: 1 VEADV 5
>1DO4A |19
Length = 5
Score = 18.4 bits (36), Expect = 380
Identities = 5/5 (100%), Positives = 5/5 (100%)
Query: 1 VEADV 5
VEADV
Sbjct: 1 VEADV 5
>1DO3A |19
Length = 5
Score = 18.4 bits (36), Expect = 380
Identities = 5/5 (100%), Positives = 5/5 (100%)
Query: 1 VEADV 5
VEADV
Sbjct: 1 VEADV 5
>1DO1A |19
Length = 5
Score = 18.4 bits (36), Expect = 380
Identities = 5/5 (100%), Positives = 5/5 (100%)
Query: 1 VEADV 5
VEADV
Sbjct: 1 VEADV 5
>1CPWA |19
Length = 5
Score = 18.4 bits (36), Expect = 380
Identities = 5/5 (100%), Positives = 5/5 (100%)
Query: 1 VEADV 5
VEADV
Sbjct: 1 VEADV 5
>1CP0A |19
Length = 5
Score = 18.4 bits (36), Expect = 380
Identities = 5/5 (100%), Positives = 5/5 (100%)
Query: 1 VEADV 5
VEADV
Sbjct: 1 VEADV 5
>1CIKA |19
Length = 5
Score = 18.4 bits (36), Expect = 380
Identities = 5/5 (100%), Positives = 5/5 (100%)
Query: 1 VEADV 5
VEADV
Sbjct: 1 VEADV 5
>1CH3A |19
Length = 5
Score = 18.4 bits (36), Expect = 380
Identities = 5/5 (100%), Positives = 5/5 (100%)
Query: 1 VEADV 5
VEADV
Sbjct: 1 VEADV 5
>1CH2A |19
Length = 5
Score = 18.4 bits (36), Expect = 380
Identities = 5/5 (100%), Positives = 5/5 (100%)
Query: 1 VEADV 5
VEADV
Sbjct: 1 VEADV 5
>1ABS |19
Length = 5
Score = 18.4 bits (36), Expect = 380
Identities = 5/5 (100%), Positives = 5/5 (100%)
Query: 1 VEADV 5
VEADV
Sbjct: 1 VEADV 5
>102M |19
Length = 5
Score = 18.4 bits (36), Expect = 380
Identities = 5/5 (100%), Positives = 5/5 (100%)
Query: 1 VEADV 5
VEADV
Sbjct: 1 VEADV 5
Database: C:\formatdb\db
Posted date: Feb 14, 2005 2:42 PM
Number of letters in database: 16,206,305
Number of sequences in database: 3,241,261
Lambda K H
0.325 0.286 1.44
Lambda K H
0.295 0.120 0.850
Matrix: PAM30
Gap Penalties: Existence: 9, Extension: 1
Number of Hits to DB: 247004
Number of Sequences: 3241261
Number of extensions: 444
Number of successful extensions: 70
Number of sequences better than 1000.0: 70
Number of HSP's better than 1000.0 without gapping: 70
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): 70
length of query: 5
length of database: 16,206,305
effective HSP length: 0
effective length of query: 8
effective length of database: 16,206,305
effective search space: 129650440
effective search space used: 129650440
T: 11
A: 40
X1: 15 ( 7.0 bits)
X2: 35 (14.9 bits)
X3: 58 (24.7 bits)
S1: 33 (17.3 bits)
S2: 33 (17.1 bits)
-------------- next part --------------
>>>
parsed step 1
Traceback (most recent call last):
File "C:/BiopythonPrograms/PSIBLAST.py", line 25, in -toplevel-
b_record = b_parser.parse(blast_data)
File "C:\Python24\Lib\site-packages\Bio\Blast\NCBIStandalone.py", line 581, in parse
self._scanner.feed(handle, self._consumer)
File "C:\Python24\Lib\site-packages\Bio\Blast\NCBIStandalone.py", line 96, in feed
self._scan_rounds(uhandle, consumer)
File "C:\Python24\Lib\site-packages\Bio\Blast\NCBIStandalone.py", line 155, in _scan_rounds
self._scan_alignments(uhandle, consumer)
File "C:\Python24\Lib\site-packages\Bio\Blast\NCBIStandalone.py", line 294, in _scan_alignments
self._scan_pairwise_alignments(uhandle, consumer)
File "C:\Python24\Lib\site-packages\Bio\Blast\NCBIStandalone.py", line 304, in _scan_pairwise_alignments
self._scan_one_pairwise_alignment(uhandle, consumer)
File "C:\Python24\Lib\site-packages\Bio\Blast\NCBIStandalone.py", line 309, in _scan_one_pairwise_alignment
self._scan_alignment_header(uhandle, consumer)
File "C:\Python24\Lib\site-packages\Bio\Blast\NCBIStandalone.py", line 339, in _scan_alignment_header
read_and_call(uhandle, consumer.noevent, blank=1)
File "C:\Python24\Lib\site-packages\Bio\ParserSupport.py", line 300, in read_and_call
raise SyntaxError, errmsg
SyntaxError: Expected blank line, but got:
>>>
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