Package Bio :: Package expressions :: Package blast :: Module wublast
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Module wublast

source code

Functions [hide private]
 
main(outf) source code
Variables [hide private]
  wublast_version = Re("2\.[^-]+-WashU")
  blastn_appheader = replace_groups(ncbiblast.blastn_appheader, ...
  blastp_appheader = replace_groups(ncbiblast.blastp_appheader, ...
  blastx_appheader = replace_groups(ncbiblast.blastx_appheader, ...
  tblastn_appheader = replace_groups(ncbiblast.tblastn_appheader...
  tblastx_appheader = replace_groups(ncbiblast.tblastx_appheader...
  spaces_line = Opt(Spaces())+ AnyEol()
  query_database = Str("Database:")+ Opt(Spaces())+ Std.database...
  to_table = SkipLinesUntil(Str("Sequences producing High-scorin...
  table_entry = AssertNot(AnyEol())+ Std.search_table_descriptio...
  header = replace_groups(ncbiblast.header, (("query_database", ...
  hit_descr = Str(">")+ Std.hit_description(UntilEol())+ AnyEol(...
  hit_length = Spaces()+ Str("Length = ")+ Std.hit_length(Digits...
  blastp_score = Re(r" *Score = *")+ Std.hsp_value(Digits(), {"n...
  identities = Re(r" *Identities = ")+ Std.hsp_value(Digits(), {...
  blastp_hsp_header = blastp_score+ identities+ spaces_line
  blastn_strand = Re(r" *(Plus|Minus) Strand HSPs:\R")
  blastn_score = Re(r" *Score = *")+ Std.hsp_value(Digits(), {"n...
  blastn_identities = Re(r" *Identities = ")+ Std.hsp_value(Digi...
  blastn_hsp_header = Opt(blastn_strand+ spaces_line)+ blastn_sc...
  blastx_table_entry = AssertNot(AnyEol())+ Std.search_table_des...
  blastx_to_database = Str(" Translating both strands of query ...
  blastx_identities = Re(r" *Identities = ")+ Std.hsp_value(Digi...
  blastx_score = Re(r" *Score = *")+ Std.hsp_value(Digits(), {"n...
  blastx_strand = Re(r" *(Plus|Minus) Strand HSPs:\R")
  blastx_hsp_header = Opt(blastx_strand+ spaces_line)+ blastx_sc...
  tblastn_strand = Re(r" *(Plus|Minus) Strand HSPs:\R")
  tblastn_score = Re(r" *Score = *")+ Std.hsp_value(Digits(), {"...
  tblastn_identities = Re(r" *Identities = ")+ Std.hsp_value(Dig...
  tblastn_hsp_header = Opt(tblastn_strand+ spaces_line)+ tblastn...
  ending_start = Opt(Str("WARNING")+ ToEol()+ Rep(AssertNot(Str(...
  parameters = SkipLinesUntil(Str("Statistics:"))
  timestamp = Time.make_expression("%(Mon) %(Jan) %(day) %(hour)...
  statistics = Str("Statistics:")+ AnyEol()+ spaces_line+ _nv(" ...
  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_tab...
  blastp = replace_groups(format, (("appheader", blastp_appheade...
  blastn = replace_groups(format, (("appheader", blastn_appheade...
  blastx = replace_groups(format, (("appheader", blastx_appheade...
  tblastn = replace_groups(format, (("appheader", tblastn_apphea...
  __warningregistry__ = {('Bio.expressions was deprecated, as it...
Variables Details [hide private]

blastn_appheader

Value:
replace_groups(ncbiblast.blastn_appheader, [("appversion", wublast_ver\
sion)])

blastp_appheader

Value:
replace_groups(ncbiblast.blastp_appheader, [("appversion", wublast_ver\
sion)])

blastx_appheader

Value:
replace_groups(ncbiblast.blastx_appheader, [("appversion", wublast_ver\
sion)])

tblastn_appheader

Value:
replace_groups(ncbiblast.tblastn_appheader, [("appversion", wublast_ve\
rsion)])

tblastx_appheader

Value:
replace_groups(ncbiblast.tblastx_appheader, [("appversion", wublast_ve\
rsion)])

query_database

Value:
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_letter\
s(Number(), {"bioformat:decode": "int.comma"})+ Spaces()+ Str("total l\
etters.")+ ToEol()

to_table

Value:
SkipLinesUntil(Str("Sequences producing High-scoring Segment"))+ ToEol\
()+ AnyEol()

table_entry

Value:
AssertNot(AnyEol())+ Std.search_table_description(Re(r".{60}"))+ Space\
s()+ Std.search_table_value(Float(), {"name": "score", "bioformat:deco\
de": "float"})+ Spaces()+ Std.search_table_value(Float(), {"name": "P"\
, "bioformat:decode": "float"})+ Spaces()+ Std.search_table_value(Digi\
ts(), {"name": "N", "bioformat:decode": "float"})+ AnyEol()

header

Value:
replace_groups(ncbiblast.header, (("query_database", query_database), \
("to_table", to_table), ("table_entry", table_entry)))

hit_descr

Value:
Str(">")+ Std.hit_description(UntilEol())+ AnyEol()+ Rep(AssertNot(hit\
_length)+ Std.hit_description(UntilEol())+ AnyEol())

hit_length

Value:
Spaces()+ Str("Length = ")+ Std.hit_length(Digits())+ AnyEol()+ Opt(Sp\
aces())+ AnyEol()

blastp_score

Value:
Re(r" *Score = *")+ Std.hsp_value(Digits(), {"name": "bits", "bioforma\
t:decode": "int",})+ ToSep(sep= "=")+ Spaces()+ Std.hsp_value(Float(),\
 {"name": "expect", "bioformat:decode": "float",})+(Str(", P =") | Re(\
r", Sum P\(\d+\) ="))+ Spaces()+ Std.hsp_value(Float(), {"name": "P", \
"bioformat:decode": "float",})+ ToEol()

identities

Value:
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(" Posi\
tives =")+ Spaces()+ Std.hsp_value(Digits(), {"name": "positives", "bi\
oformat:decode": "int",})+ ToEol()

blastn_score

Value:
Re(r" *Score = *")+ Std.hsp_value(Digits(), {"name": "bits", "bioforma\
t:decode": "int",})+ ToSep(sep= "=")+ Spaces()+ Std.hsp_value(Float(),\
 {"name": "expect", "bioformat:decode": "float",})+(Str(", P =") | Re(\
r", Sum P\(\d+\) ="))+ Spaces()+ Std.hsp_value(Float(), {"name": "P", \
"bioformat:decode": "float",})+ ToEol()

blastn_identities

Value:
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(" Posi\
tives =")+ Spaces()+ Std.hsp_value(Digits(), {"name": "positives", "bi\
oformat:decode": "int",})+ ToSep(sep= ",")+ Str(" ")+ ncbiblast.strand

blastn_hsp_header

Value:
Opt(blastn_strand+ spaces_line)+ blastn_score+ blastn_identities+ spac\
es_line

blastx_table_entry

Value:
AssertNot(AnyEol())+ Std.search_table_description(Re(r".{57}"))+ Space\
s()+ Std.search_table_value(Integer(), {"name": "frame", "bioformat:de\
code": "int"})+ Spaces()+ Std.search_table_value(Float(), {"name": "sc\
ore", "bioformat:decode": "float"})+ Spaces()+ Std.search_table_value(\
Float(), {"name": "P", "bioformat:decode": "float"})+ Spaces()+ Std.se\
arch_table_value(Digits(), {"name": "N", "bioformat:decode": "int"})+ \
AnyEol()

blastx_to_database

Value:
Str("  Translating both strands of query sequence in all 6 reading fra\
mes")+ AnyEol()+ AnyEol()

blastx_identities

Value:
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(" Posi\
tives =")+ Spaces()+ Std.hsp_value(Digits(), {"name": "positives", "bi\
oformat:decode": "int",})+ ToSep(sep= "=")+ Str(" ")+ Std.hsp_frame(In\
teger(), {"which": "query"})+ AnyEol()

blastx_score

Value:
Re(r" *Score = *")+ Std.hsp_value(Digits(), {"name": "bits", "bioforma\
t:decode": "int",})+ ToSep(sep= "=")+ Spaces()+ Std.hsp_value(Float(),\
 {"name": "expect", "bioformat:decode": "float",})+(Str(", P =") | Re(\
r", Sum P\(\d+\) ="))+ Spaces()+ Std.hsp_value(Float(), {"name": "P", \
"bioformat:decode": "float",})+ ToEol()

blastx_hsp_header

Value:
Opt(blastx_strand+ spaces_line)+ blastx_score+ blastx_identities+ spac\
es_line

tblastn_score

Value:
Re(r" *Score = *")+ Std.hsp_value(Digits(), {"name": "bits", "bioforma\
t:decode": "int",})+ ToSep(sep= "=")+ Spaces()+ Std.hsp_value(Float(),\
 {"name": "expect", "bioformat:decode": "float",})+(Str(", P =") | Re(\
r", Sum P\(\d+\) ="))+ Spaces()+ Std.hsp_value(Float(), {"name": "P", \
"bioformat:decode": "float",})+ ToEol()

tblastn_identities

Value:
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(" Posi\
tives =")+ Spaces()+ Std.hsp_value(Digits(), {"name": "positives", "bi\
oformat:decode": "int",})+ ToSep(sep= ",")+ ncbiblast.frame

tblastn_hsp_header

Value:
Opt(tblastn_strand+ spaces_line)+ tblastn_score+ tblastn_identities+ s\
paces_line

ending_start

Value:
Opt(Str("WARNING")+ ToEol()+ Rep(AssertNot(Str(">"))+ AssertNot(Str("P\
arameters"))+ ToEol()))+ Str("Parameters:")+ ToEol()

timestamp

Value:
Time.make_expression("%(Mon) %(Jan) %(day) %(hour):%(minute):%(second)\
 %(YYYY)")

statistics

Value:
Str("Statistics:")+ AnyEol()+ spaces_line+ _nv("  Database: ", Std.sea\
rch_statistic(UntilEol(), {"name": "database"}))+ _nv("    Title: ", S\
td.search_statistic(UntilEol(), {"name": "database_title"}))+ _nv("   \
 Release date: ", Std.search_statistic(UntilEol(), {"name": "release_d\
ate"}))+ _nv("    Posted date: ", Std.search_statistic(UntilEol(), {"n\
ame": "posted_date"}))+ _nv("    Format: ", Std.search_statistic(Until\
Eol(), {"name": "format"}))+ _nv("  # of letters in database:  ", int_\
stat("num_letters_in_database", comma= 1))+ _nv("  # of sequences in d\
...

format

Value:
replace_groups(ncbiblast.format, (("to_table", to_table), ("table_entr\
y", table_entry), ("ending", ending)))

blastp

Value:
replace_groups(format, (("appheader", blastp_appheader), ("hsp_header"\
, blastp_hsp_header)))

blastn

Value:
replace_groups(format, (("appheader", blastn_appheader), ("hsp_header"\
, blastn_hsp_header)))

blastx

Value:
replace_groups(format, (("appheader", blastx_appheader), ("table_entry\
", blastx_table_entry), ("to_database", blastx_to_database), ("hsp_hea\
der", blastx_hsp_header)))

tblastn

Value:
replace_groups(format, (("appheader", tblastn_appheader), ("table_entr\
y", blastx_table_entry), ("hsp_header", tblastn_hsp_header)))

__warningregistry__

Value:
{('Bio.expressions was deprecated, as it does not work with recent ver\
sions of mxTextTools. If you want to continue to use this module, plea\
se get in contact with the Biopython developers at biopython-dev@biopy\
thon.org to avoid permanent removal of this module from Biopython',
  <type 'exceptions.DeprecationWarning'>,
  2): 1}