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# Copyright 2002 by Jeffrey Chang. All rights reserved.
# This code is part of the Biopython distribution and governed by its
# license. Please see the LICENSE file that should have been included
# as part of this package.
from Bio.config.DBRegistry import CGIDB, DBGroup, EUtilsDB
from _support import *
from Martel import *
proxy_error_expr = has_expr(Alt(Str("500"), Str("502")) + Str(" Proxy Error"))
diagnostic_error_expr = has_str("WWW Error 500 Diagnostic")
error_expr = Str("ERROR")
ncbi_failures=[
(proxy_error_expr, "proxy error"),
(diagnostic_error_expr, "diagnostic 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(Str("The sequence has been intentionally withdrawn"),
"Sequence withdrawn"),
(blank_expr, "No data returned")
]
nucleotide_genbank_eutils = 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
)
# If the id is not in the database, I get a message like:
# ERROR : GenPept does not exist for gi = 433174
not_exist_expr = Str("ERROR") + Re("[^d]*") + Str("does not exist for gi")
protein_genbank_eutils = EUtilsDB(
name = "protein-genbank-eutils",
doc = "Retrieve protein GenPept sequences from NCBI using EUtils",
delay = 5.0,
db = "protein",
rettype = "gp",
failure_cases = ncbi_failures+[(not_exist_expr, "GI does not exist")]
)
gb_nucleotide = DBGroup(
name = "genbank-nucleotide",
behavior = "serial"
)
gb_nucleotide.add(nucleotide_genbank_eutils)
gb_protein = DBGroup(
name = "genbank-protein",
behavior = "serial")
gb_protein.add(protein_genbank_eutils)
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