1
2
3
4
5
6 from Bio.config.DBRegistry import CGIDB, DBGroup
7 from _support import *
8
9 embl_xembl_cgi = CGIDB(
10 name="embl-xembl-cgi",
11 doc="Query XEMBL for EMBL sequence data in XML format.",
12 cgi="http://www.ebi.ac.uk/cgi-bin/xembl/XEMBL.pl",
13 url="http://www.ebi.ac.uk/xembl/",
14 delay=5.0,
15 params=[("format", "Bsml")],
16 key="id",
17 failure_cases=[(has_str("NOT EXIST"), "id does not exist")],
18 )
19
20 embl_dbfetch_cgi = CGIDB(
21 name="embl-dbfetch-cgi",
22 cgi="http://www.ebi.ac.uk/cgi-bin/dbfetch",
23 url="http://www.ebi.ac.uk/cgi-bin/dbfetch",
24 doc="dbfetch provides EMBL, Genbank, and SWALL sequences",
25 delay=5.0,
26 params=[("db", "embl"),
27 ("style", "raw"),
28 ("format", "embl"),
29 ],
30 key="id",
31 failure_cases=[(has_str("not found in database"), "id does not exist")]
32 )
33
34 embl_ebi_cgi = CGIDB(
35 name="embl-ebi-cgi",
36 cgi="http://www.ebi.ac.uk/cgi-bin/emblfetch",
37 url="http://www.ebi.ac.uk/cgi-bin/emblfetch",
38 doc="Retrieve many kinds of sequences from EBI",
39 delay=5.0,
40 params=[("db", "EMBL"),
41 ("format", "default"),
42 ("style", "raw")
43 ],
44 key="id",
45 failure_cases=[(blank_expr, "No results returned")]
46 )
47
48 embl = DBGroup(
49 name="embl",
50 behavior="serial",
51
52 )
53 embl.add(embl_dbfetch_cgi)
54 embl.add(embl_ebi_cgi)
55
56 embl_xml = DBGroup(
57 name = "embl-xml",
58 behavior = "serial")
59
60 embl_fast = DBGroup(
61 name="embl-fast",
62 behavior="concurrent",
63 )
64 embl_fast.add(embl_dbfetch_cgi)
65 embl_fast.add(embl_ebi_cgi)
66