Package Bio :: Package dbdefs :: Module genbank
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Module genbank

source code

Variables [hide private]
  proxy_error_expr = has_expr(Alt(Str("500"), Str("502"))+ Str("...
  diagnostic_error_expr = has_str("WWW Error 500 Diagnostic")
  error_expr = Str("ERROR")
  ncbi_failures = [(proxy_error_expr, "proxy error"), (diagnosti...
  nucleotide_genbank_eutils = EUtilsDB(name= "nucleotide-genbank...
  genome_genbank_eutils = EUtilsDB(name= "genome-genbank-eutils"...
  not_exist_expr = Str("ERROR")+ Re("[^d]*")+ Str("does not exis...
  protein_genbank_eutils = EUtilsDB(name= "protein-genbank-eutil...
  gb_nucleotide = DBGroup(name= "genbank-nucleotide", behavior= ...
  gb_protein = DBGroup(name= "genbank-protein", behavior= "serial")
  gb_genome = DBGroup(name= "genbank-genome", behavior= "serial")
Variables Details [hide private]

proxy_error_expr

Value:
has_expr(Alt(Str("500"), Str("502"))+ Str(" Proxy Error"))

ncbi_failures

Value:
[(proxy_error_expr, "proxy error"), (diagnostic_error_expr, "diagnosti\
c error"), (error_expr, "ERROR"), (html_expr, "I got HTML and shouldn'\
t have"), (Str("Please try again later"), "Please try again later"), (\
Str("The sequence has been intentionally withdrawn"), "Sequence withdr\
awn"), (blank_expr, "No data returned")]

nucleotide_genbank_eutils

Value:
EUtilsDB(name= "nucleotide-genbank-eutils", doc= "Retrieve nucleotide \
GenBank sequences from NCBI using EUtils", delay= 5.0, db= "nucleotide\
", rettype= "gb", failure_cases= ncbi_failures)

genome_genbank_eutils

Value:
EUtilsDB(name= "genome-genbank-eutils", doc= "Retrieve genome GenBank \
sequences from NCBI using EUtils", delay= 5.0, db= "genome", rettype= \
"gb", failure_cases= ncbi_failures)

not_exist_expr

Value:
Str("ERROR")+ Re("[^d]*")+ Str("does not exist for gi")

protein_genbank_eutils

Value:
EUtilsDB(name= "protein-genbank-eutils", doc= "Retrieve protein GenPep\
t sequences from NCBI using EUtils", delay= 5.0, db= "protein", rettyp\
e= "gp", failure_cases= ncbi_failures+ [(not_exist_expr, "GI does not \
exist")])

gb_nucleotide

Value:
DBGroup(name= "genbank-nucleotide", behavior= "serial")