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python-biopython  1.60
Public Member Functions
test_TogoWS.TogoFields Class Reference

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Public Member Functions

def test_invalid_database
def test_databases
def test_pubmed
def test_ncbi_protein
def test_ddbj
def test_embl
def test_uniprot
def test_pdb

Detailed Description

Definition at line 26 of file test_TogoWS.py.


Member Function Documentation

Check supported databases

Definition at line 32 of file test_TogoWS.py.

00032 
00033     def test_databases(self):
00034         """Check supported databases"""
00035         dbs = set(TogoWS._get_entry_dbs())
00036         self.assert_(dbs.issuperset(['nuccore', 'nucest', 'nucgss',
00037                                      'nucleotide', 'protein', 'gene',
00038                                      'omim', 'homologene', 'snp',
00039                                      'mesh', 'pubmed', 'embl',
00040                                      'uniprot', 'uniparc', 'uniref100',
00041                                      'uniref90', 'uniref50', 'ddbj',
00042                                      'dad', 'pdb', 'compound', 'drug',
00043                                      'enzyme', 'genes', 'glycan',
00044                                      'orthology', 'reaction', 'module',
00045                                      'pathway']), dbs)

Check supported fields for ddbj database

Definition at line 65 of file test_TogoWS.py.

00065 
00066     def test_ddbj(self):
00067         """Check supported fields for ddbj database"""
00068         fields = set(TogoWS._get_entry_fields("ddbj"))
00069         self.assert_(fields.issuperset(['entry_id', 'length', 'strand',
00070                                         'moltype', 'linearity', 'division',
00071                                         'date', 'definition', 'accession',
00072                                         'accessions', 'version', 'versions',
00073                                         'acc_version', 'gi', 'keywords',
00074                                         'organism', 'common_name',
00075                                         'taxonomy', 'comment', 'seq']),
00076                                         fields)

Check supported fields for embl database

Definition at line 77 of file test_TogoWS.py.

00077 
00078     def test_embl(self):
00079         """Check supported fields for embl database"""
00080         fields = set(TogoWS._get_entry_fields("embl"))
00081         self.assert_(fields.issuperset(["definition", "entry_id", "seq"]),
00082                      fields)

Check asking for fields of invalid database fails

Definition at line 27 of file test_TogoWS.py.

00027 
00028     def test_invalid_database(self):
00029         """Check asking for fields of invalid database fails"""
00030         self.assertRaises(IOError, TogoWS._get_fields,
00031                           "http://togows.dbcls.jp/entry/invalid?fields")

Check supported fields for NCBI protein database

Definition at line 53 of file test_TogoWS.py.

00053 
00054     def test_ncbi_protein(self):
00055         """Check supported fields for NCBI protein database"""
00056         fields = set(TogoWS._get_entry_fields("ncbi-protein"))
00057         self.assert_(fields.issuperset(['entry_id', 'length', 'strand',
00058                                         'moltype', 'linearity', 'division',
00059                                         'date', 'definition', 'accession',
00060                                         'accessions', 'version', 'versions',
00061                                         'acc_version', 'gi', 'keywords',
00062                                         'organism', 'common_name',
00063                                         'taxonomy', 'comment', 'seq']),
00064                                         fields)

Check supported fields for pdb database

Definition at line 89 of file test_TogoWS.py.

00089 
00090     def test_pdb(self):
00091         """Check supported fields for pdb database"""
00092         fields = set(TogoWS._get_entry_fields("pdb"))
00093         self.assert_(fields.issuperset(["accession", "chains", "keywords",
00094                                         "models"]), fields)
00095 

Check supported fields for pubmed database

Definition at line 46 of file test_TogoWS.py.

00046 
00047     def test_pubmed(self):
00048         """Check supported fields for pubmed database"""
00049         fields = set(TogoWS._get_entry_fields("pubmed"))
00050         self.assert_(fields.issuperset(['abstract', 'au', 'authors',
00051                                         'doi', 'mesh', 'so', 'ti',
00052                                         'title']), fields)

Check supported fields for uniprot database

Definition at line 83 of file test_TogoWS.py.

00083 
00084     def test_uniprot(self):
00085         """Check supported fields for uniprot database"""
00086         fields = set(TogoWS._get_entry_fields("uniprot"))
00087         self.assert_(fields.issuperset(["definition", "entry_id", "seq"]),
00088                      fields)


The documentation for this class was generated from the following file: