Scan BLAST output from blastall or blastpgp.
Tested with blastall and blastpgp v2.0.10, v2.0.11
Methods:
feed Feed data into the scanner.
Methods
|
|
|
|
_scan_alignment_header
|
_scan_alignment_header (
self,
uhandle,
consumer,
)
Exceptions
|
|
SyntaxError, "I missed the Length in an alignment header"
|
|
|
_scan_alignments
|
_scan_alignments (
self,
uhandle,
consumer,
)
|
|
_scan_database_report
|
_scan_database_report (
self,
uhandle,
consumer,
)
Database: sdqib40-1.35.seg.fa
Posted date: Nov 1, 1999 4:25 PM
Number of letters in database: 223,339
Number of sequences in database: 1323 Lambda K H
Gapped
Lambda K H
|
|
_scan_descriptions
|
_scan_descriptions (
self,
uhandle,
consumer,
)
Searching..................................................done
Results from round 2 Sc
Sequences producing significant alignments: (b
Sequences used in model and found again:
d1tde2 3.4.1.4.4 (119-244) Thioredoxin reductase [Escherichia ...
d1tcob 1.31.1.5.16 Calcineurin regulatory subunit (B-chain) [B...
d1symb_ 1.31.1.2.2 Calcyclin (S100) [RAT (RATTUS NORVEGICUS)]
Sequences not found previously or not previously below threshold:
d1osa__ 1.31.1.5.11 Calmodulin [Paramecium tetraurelia]
d1aoza3 2.5.1.3.3 (339-552) Ascorbate oxidase [zucchini (Cucurb...
Exceptions
|
|
SyntaxError, "Unexpected end of blast report. " + "Looks suspiciously like a PSI-BLAST crash."
|
|
|
_scan_header
|
_scan_header (
self,
uhandle,
consumer,
)
Reference: Altschul, Stephen F., Thomas L. Madden, Alejandro A. Schaf
Jinghui Zhang, Zheng Zhang, Webb Miller, and David J. Lipman (1997),
"Gapped BLAST and PSI-BLAST: a new generation of protein database sea
programs", Nucleic Acids Res. 25:3389-3402.
Query= test
(140 letters)
Database: sdqib40-1.35.seg.fa
1323 sequences; 223,339 total letters
|
|
_scan_hsp
|
_scan_hsp (
self,
uhandle,
consumer,
)
|
|
_scan_hsp_alignment
|
_scan_hsp_alignment (
self,
uhandle,
consumer,
)
Query: 11 GRGVSACA-------TCDGFFYRNQKVAVIGGGNTAVEEALYLSNIASEVHLIHRRDGF
GRGVS+ TC Y + + V GGG+ + EE L + I R+
Sbjct: 12 GRGVSSVVRRCIHKPTCKE--YAVKIIDVTGGGSFSAEEVQELREATLKEVDILRKVSG Query: 64 AEKILIKR 71
I +K
Sbjct: 70 PNIIQLKD 77
|
|
_scan_hsp_header
|
_scan_hsp_header (
self,
uhandle,
consumer,
)
Score = 22.7 bits (47), Expect = 2.5
Identities = 10/36 (27%), Positives = 18/36 (49%)
Strand = Plus / Plus
Frame = +3
|
|
_scan_masterslave_alignment
|
_scan_masterslave_alignment (
self,
uhandle,
consumer,
)
|
|
_scan_one_pairwise_alignment
|
_scan_one_pairwise_alignment (
self,
uhandle,
consumer,
)
|
|
_scan_pairwise_alignments
|
_scan_pairwise_alignments (
self,
uhandle,
consumer,
)
|
|
_scan_parameters
|
_scan_parameters (
self,
uhandle,
consumer,
)
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 50604
Number of Sequences: 1323
Number of extensions: 1526
Number of successful extensions: 6
Number of sequences better than 10.0: 5
Number of HSP's better than 10.0 without gapping: 5
Number of HSP's successfully gapped in prelim test: 0
Number of HSP's that attempted gapping in prelim test: 1
Number of HSP's gapped (non-prelim): 5
length of query: 140
length of database: 223,339
effective HSP length: 39
effective length of query: 101
effective length of database: 171,742
effective search space: 17345942
effective search space used: 17345942
T: 11
A: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.8 bits)
X3: 64 (24.9 bits)
S1: 41 (21.9 bits)
S2: 42 (20.8 bits)
|
|
_scan_rounds
|
_scan_rounds (
self,
uhandle,
consumer,
)
Scan a bunch of rounds.
Each round begins with either a "Searching......" line
or a Score E line followed by descriptions and alignments.
The email server doesn't give the "Searching....." line.
|
|
feed
|
feed (
self,
handle,
consumer,
)
feed(handle, consumer) Feed in a BLAST report for scanning. handle is a file-like
object that contains the BLAST report. consumer is a Consumer
object that will receive events as the report is scanned.
|
|