Package Bio :: Package dbdefs :: Module fasta
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Module fasta

source code

Database definitions for retrieval of FASTA formatted sequences.

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...
  fasta_sequence_eutils = EUtilsDB(name= "fasta-sequence-eutils"...
  fasta = DBGroup(name= "fasta", behavior= "serial")
  blank_expr = _M.AssertNot(_M.Re("."))
  html_expr = _M.Rep(_M.Any(_string.whitespace))+ _M.NoCase(_M.S...
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Str("The sequence has been intentionally withdrawn"), "Sequence withdr\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")]

fasta_sequence_eutils

Value:
EUtilsDB(name= "fasta-sequence-eutils", doc= "Retrieve Fasta formatted\
 sequence data from NCBI using EUtils", delay= 5.0, db= "sequences", r\
ettype= "fasta", failure_cases= ncbi_failures)

html_expr

Value:
_M.Rep(_M.Any(_string.whitespace))+ _M.NoCase(_M.Str("<html>"))