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from Martel import *
from Martel import Time
from Bio import Std
import ncbiblast
wublast_version = Re("2\.[^-]+-WashU")
# BLASTN 2.0a19MP-WashU [05-Feb-1998] [Build decunix3.2 01:53:29 05-Feb-1998]
# BLASTP 2.0a19MP-WashU [05-Feb-1998] [Build sol2.5-ultra 01:47:24 05-Feb-1998]
blastn_appheader = replace_groups(ncbiblast.blastn_appheader,
[("appversion", wublast_version)])
blastp_appheader = replace_groups(ncbiblast.blastp_appheader,
[("appversion", wublast_version)])
blastx_appheader = replace_groups(ncbiblast.blastx_appheader,
[("appversion", wublast_version)])
tblastn_appheader = replace_groups(ncbiblast.tblastn_appheader,
[("appversion", wublast_version)])
tblastx_appheader = replace_groups(ncbiblast.tblastx_appheader,
[("appversion", wublast_version)])
spaces_line = ncbiblast.spaces_line
Number = ncbiblast.Number
# Database: YeastORF-P
# 6183 sequences; 2,900,438 total letters.
# Database: Non-redundant GenBank CDS translations+PDB+SwissProt+SPupdate+PIR
# 307,320 sequences; 92,696,426 total letters.
# Database: mgpep
# 468 sequences; 170,400 total letters
# Database: plantPept
# 6418 sequences; 2,370,771 total letters.
# Database: Non-redundant GenBank CDS
# translations+PDB+SwissProt+SPupdate+PIR
# 301,269 sequences; 90,873,415 total letters
query_database = (Str("Database:") + Opt(Spaces()) +
Std.database_name(UntilEol()) + AnyEol() +
Spaces() +
Std.database_num_sequences(Number(),
{"bioformat:decode": "int.comma"}) +
Str(" sequences;") + Spaces() +
Std.database_num_letters(Number(),
{"bioformat:decode": "int.comma"}) +
Spaces() + Str("total letters.") + ToEol())
# notice the "." -----^^^
# Smallest
# Sum
# High Probability
# Sequences producing High-scoring Segment Pairs: Score P(N) N
#
# sp|P09429|HMG1_HUMAN HIGH MOBILITY GROUP PROTEIN HMG1 (HM... 1144 8.6e-117 1
# sp|P10103|HMG1_BOVIN HIGH MOBILITY GROUP PROTEIN HMG1 (HM... 1140 2.3e-116 1
to_table = (SkipLinesUntil(Str("Sequences producing High-scoring Segment")) +
ToEol() +
AnyEol())
table_entry = (AssertNot(AnyEol()) +
Std.search_table_description(Re(r".{60}")) + Spaces() +
Std.search_table_value(Float(), {"name": "score",
"bioformat:decode": "float"}) +
Spaces() +
Std.search_table_value(Float(), {"name": "P",
"bioformat:decode": "float"}) +
Spaces() +
Std.search_table_value(Digits(), {"name": "N",
"bioformat:decode": "float"}) +
AnyEol())
header = replace_groups(ncbiblast.header,
(("query_database", query_database),
("to_table", to_table),
("table_entry", table_entry)))
# >sp|P09429|HMG1_HUMAN HIGH MOBILITY GROUP PROTEIN HMG1 (HMG-1).
# Length = 214
#
# Score = 1144 (402.7 bits), Expect = 8.6e-117, P = 8.6e-117
# Identities = 214/214 (100%), Positives = 214/214 (100%)
#
# Query: 1 GKGDPKKPRGKMSSYAFFVQTCREEHKKKHPDASVNFSEFSKKCSERWKTMSAKEKGKFE 60
# GKGDPKKPRGKMSSYAFFVQTCREEHKKKHPDASVNFSEFSKKCSERWKTMSAKEKGKFE
# Sbjct: 1 GKGDPKKPRGKMSSYAFFVQTCREEHKKKHPDASVNFSEFSKKCSERWKTMSAKEKGKFE 60
hit_descr = ncbiblast.hit_descr
hit_length = ncbiblast.hit_length
# Score = 1144 (402.7 bits), Expect = 8.6e-117, P = 8.6e-117
# Score = 79 (27.8 bits), Expect = 0.0088, Sum P(2) = 0.0088
# Score = 65 (22.9 bits), Expect = 3.1, Sum P(3) = 0.96
blastp_score = (Re(r" *Score = *") +
Std.hsp_value(Digits(), {"name": "bits",
"bioformat:decode": "int",
}) +
# XXX Skipping the "402.7 bits" field, what's it called?
ToSep(sep = "=") +
Spaces() +
Std.hsp_value(Float(), {"name": "expect",
"bioformat:decode": "float",
}) +
# What should I do with the (2)?, or the (3)?
(Str(", P =") | Re(r", Sum P\(\d+\) =")) +
Spaces() +
Std.hsp_value(Float(), {"name": "P",
"bioformat:decode": "float",
}) +
ToEol()
)
# Identities = 214/214 (100%), Positives = 214/214 (100%)
identities = (Re(r" *Identities = ") +
Std.hsp_value(Digits(), {"name": "identical",
"bioformat:decode": "int",
}) +
Str("/") +
Std.hsp_value(Digits(), {"name": "length",
"bioformat:decode": "int",
}) +
ToSep(sep = ",") +
Str(" Positives =") +
Spaces() +
Std.hsp_value(Digits(), {"name": "positives",
"bioformat:decode": "int",
}) +
ToEol())
blastp_hsp_header = blastp_score + identities + spaces_line
######################### blastn_hit
# >U51677 Human non-histone chromatin protein HMG1 (HMG1) gene, complete cds.
# Length = 2575
#
# Plus Strand HSPs:
#
# Score = 12875 (1931.8 bits), Expect = 0.0, P = 0.0
# Identities = 2575/2575 (100%), Positives = 2575/2575 (100%), Strand = Plus / Plus
#
# Query: 1 ATGGGCAAAGGAGATCCTAAGAAGCCGAGAGGCAAAATGTCATCATATGCATTTTTTGTG 60
# ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
# Sbjct: 1 ATGGGCAAAGGAGATCCTAAGAAGCCGAGAGGCAAAATGTCATCATATGCATTTTTTGTG 60
# ....
# Don't need to parse this since it comes from the identities line
blastn_strand =Re(r" *(Plus|Minus) Strand HSPs:\R")
blastn_score = blastp_score
blastn_identities = (
Re(r" *Identities = ") +
Std.hsp_value(Digits(), {"name": "identical",
"bioformat:decode": "int",
}) +
Str("/") +
Std.hsp_value(Digits(), {"name": "length",
"bioformat:decode": "int",
}) +
ToSep(sep = ",") +
Str(" Positives =") +
Spaces() +
Std.hsp_value(Digits(), {"name": "positives",
"bioformat:decode": "int",
}) +
ToSep(sep = ",") + Str(" ") +
ncbiblast.strand
# that 'strand' already includes a newline
)
blastn_hsp_header = (Opt(blastn_strand + spaces_line) +
blastn_score + blastn_identities + spaces_line)
######################### blastx
# Smallest
# Sum
# Reading High Probability
# Sequences producing High-scoring Segment Pairs: Frame Score P(N) N
#
# sp|P09429|HMG1_HUMAN HIGH MOBILITY GROUP PROTEIN HMG1 ... +2 311 5.0e-108 4
# sp|P10103|HMG1_BOVIN HIGH MOBILITY GROUP PROTEIN HMG1 ... +2 311 1.3e-107 4
# sp|P07155|HMG1_MOUSE HIGH MOBILITY GROUP PROTEIN HMG1 ... +2 311 2.7e-107 4
blastx_table_entry = (
AssertNot(AnyEol()) +
Std.search_table_description(Re(r".{57}")) + Spaces() +
Std.search_table_value(Integer(), {"name": "frame",
"bioformat:decode": "int"}) +
Spaces() +
Std.search_table_value(Float(), {"name": "score",
"bioformat:decode": "float"}) +
Spaces() +
Std.search_table_value(Float(), {"name": "P",
"bioformat:decode": "float"}) +
Spaces() +
Std.search_table_value(Digits(), {"name": "N",
"bioformat:decode": "int"}) +
AnyEol())
blastx_to_database = (
Str(" Translating both strands of query sequence in all 6 reading frames") +
AnyEol() +
AnyEol())
blastx_identities = (
Re(r" *Identities = ") +
Std.hsp_value(Digits(), {"name": "identical",
"bioformat:decode": "int",
}) +
Str("/") +
Std.hsp_value(Digits(), {"name": "length",
"bioformat:decode": "int",
}) +
ToSep(sep = ",") +
Str(" Positives =") +
Spaces() +
Std.hsp_value(Digits(), {"name": "positives",
"bioformat:decode": "int",
}) +
ToSep(sep = "=") + Str(" ") +
Std.hsp_frame(Integer(), {"which": "query"}) +
AnyEol()
)
blastx_score = blastp_score
blastx_strand = blastn_strand
blastx_hsp_header = (Opt(blastx_strand + spaces_line) +
blastx_score + blastx_identities + spaces_line)
#############################
######################### tblastn
tblastn_strand =Re(r" *(Plus|Minus) Strand HSPs:\R")
tblastn_score = blastp_score
tblastn_identities = (
Re(r" *Identities = ") +
Std.hsp_value(Digits(), {"name": "identical",
"bioformat:decode": "int",
}) +
Str("/") +
Std.hsp_value(Digits(), {"name": "length",
"bioformat:decode": "int",
}) +
ToSep(sep = ",") +
Str(" Positives =") +
Spaces() +
Std.hsp_value(Digits(), {"name": "positives",
"bioformat:decode": "int",
}) +
ToSep(sep = ",") +
ncbiblast.frame
# that 'strand' already includes a newline
)
tblastn_hsp_header = (Opt(tblastn_strand + spaces_line) +
tblastn_score + tblastn_identities + spaces_line)
#############################
# May have to skip the WARNING section
ending_start = (Opt(Str("WARNING") + ToEol() +
Rep(AssertNot(Str(">")) +
AssertNot(Str("Parameters")) +
ToEol())) +
Str("Parameters:") + ToEol())
parameters = SkipLinesUntil(Str("Statistics:"))
_nv = ncbiblast._nv
int_stat = ncbiblast.int_stat
timestamp = Time.make_expression(
"%(Mon) %(Jan) %(day) %(hour):%(minute):%(second) %(YYYY)")
statistics = (
Str("Statistics:") + AnyEol() +
spaces_line +
# Database: /dbEST1/wublast/database/swissprot/sprot.fa
_nv(" Database: ",
Std.search_statistic(UntilEol(), {"name": "database"})) +
# Title: swissprot
_nv(" Title: ",
Std.search_statistic(UntilEol(), {"name": "database_title"})) +
# Release date: unknown
_nv(" Release date: ",
Std.search_statistic(UntilEol(), {"name": "release_date"})) +
# Posted date: 11:37 AM GMT Feb 21, 2000
_nv(" Posted date: ",
Std.search_statistic(UntilEol(), {"name": "posted_date"})) +
# Format: BLAST
_nv(" Format: ",
Std.search_statistic(UntilEol(), {"name": "format"})) +
# # of letters in database: 26,335,942
_nv(" # of letters in database: ",
int_stat("num_letters_in_database", comma = 1)) +
# # of sequences in database: 72,615
_nv(" # of sequences in database: ",
int_stat("num_sequences_in_database", comma = 1)) +
# # of database sequences satisfying E: 1119
_nv(" # of database sequences satisfying E: ",
int_stat("num_sequences_satisying_E")) +
# No. of states in DFA: 549 (54 KB)
_nv(" No. of states in DFA: ",
Std.search_statistic(UntilEol(), {"name": "num_dfa_states"})) +
# Total size of DFA: 117 KB (128 KB)
_nv(" Total size of DFA: ",
Std.search_statistic(UntilEol(), {"name": "total_dfa_size"})) +
# Time to generate neighborhood: 0.01u 0.00s 0.01t Elapsed: 00:00:00
_nv(" Time to generate neighborhood: ",
Std.search_statistic(UntilEol(),
{"name": "neighborhood_generation_time"})) +
# No. of threads or processors used: 2
Opt(
_nv(" No. of threads or processors used: ",
int_stat("num_threads"))) +
# Search cpu time: 38.04u 0.15s 38.19t Elapsed: 00:00:33
_nv(" Search cpu time: ",
Std.search_statistic(UntilEol(), {"name": "search_cpu_time"})) +
# Total cpu time: 38.96u 0.29s 39.25t Elapsed: 00:00:34
_nv(" Total cpu time: ",
Std.search_statistic(UntilEol(), {"name": "total_time"})) +
# Start: Mon Feb 21 14:33:13 2000 End: Mon Feb 21 14:33:47 2000
_nv(" Start: ",
Std.search_statistic(timestamp, {"name": "start_time"}) +
Spaces() + Str("End: ") +
Std.search_statistic(timestamp, {"name": "end_time"})) +
Opt(spaces_line +
#WARNINGS ISSUED: 2
_nv("WARNINGS ISSUED: ",
int_stat("num_warnings")))
)
ending = ending_start + parameters + statistics
blastp_ending = ending_start + parameters + statistics
blastn_ending = ending_start + parameters + statistics
blastx_ending = ending_start + parameters + statistics
format = replace_groups(ncbiblast.format,
(("to_table", to_table),
("table_entry", table_entry),
("ending", ending)))
blastp = replace_groups(format,
(("appheader", blastp_appheader),
("hsp_header", blastp_hsp_header)))
blastn = replace_groups(format,
(("appheader", blastn_appheader),
("hsp_header", blastn_hsp_header)))
blastx = replace_groups(format,
(("appheader", blastx_appheader),
("table_entry", blastx_table_entry),
("to_database", blastx_to_database),
("hsp_header", blastx_hsp_header)))
tblastn = replace_groups(format,
(("appheader", tblastn_appheader),
("table_entry", blastx_table_entry),
("hsp_header", tblastn_hsp_header)))
def main(outf):
from xml.sax import saxutils
parser = blastn.make_parser(debug_level = 0)
parser.setContentHandler(saxutils.XMLGenerator())
parser.parse(outf)
#parser.parse("wu-sh_blastp.out")
if __name__ == "__main__":
main()
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