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Add a more comprehensive regression test, especially to test comment …
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…elements.
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@cbrueffer @peterjc
cbrueffer authored and peterjc committed Dec 21, 2012
1 parent 3f74d6c commit 0769bc7
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169 changes: 169 additions & 0 deletions Tests/test_Uniprot.py
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Expand Up @@ -73,6 +73,175 @@ def test_uni001(self):
self.assertEqual(seq_record.annotations['sequence_version'], 1)
self.assertEqual(seq_record.annotations['proteinExistence'], ['Predicted'])

def test_uni003(self):
"Parsing Uniprot file uni003"
filename = 'uni003'
# test the record parser

datafile = os.path.join('SwissProt', filename)

test_handle = open(datafile)
seq_record = SeqIO.read(test_handle, "uniprot-xml")
test_handle.close()

self.assertTrue(isinstance(seq_record, SeqRecord))

# test general record entries
self.assertEqual(seq_record.id, "O44185")
self.assertEqual(seq_record.name, "FLP13_CAEEL")
self.assertEqual(seq_record.description,
"FMRFamide-like neuropeptides 13")
self.assertEqual(repr(seq_record.seq),
"Seq('MMTSLLTISMFVVAIQAFDSSEIRMLDEQYDTKNPFFQFLENSKRSDRPTRAMD...GRK', ProteinAlphabet())")

self.assertEqual(len(seq_record.annotations['references']), 7)
self.assertEqual(seq_record.annotations['references'][5].authors,
'Kim K., Li C.')
self.assertEqual(seq_record.annotations['references'][5].title,
'Expression and regulation of an FMRFamide-related '
'neuropeptide gene family in Caenorhabditis elegans.')
self.assertEqual(seq_record.annotations['references'][5].journal,
'J. Comp. Neurol. 475:540-550(2004)')
self.assertEqual(seq_record.annotations['references'][5].comment,
'journal article | 2004 | Scope: TISSUE SPECIFICITY, '
'DEVELOPMENTAL STAGE | ')

self.assertEqual(seq_record.annotations["accessions"], ['O44185'])
self.assertEqual(seq_record.annotations["created"], "2004-05-10")
self.assertEqual(seq_record.annotations["dataset"], "Swiss-Prot")
self.assertEqual(seq_record.annotations["gene_name_ORF"], ['F33D4.3'])
self.assertEqual(seq_record.annotations["gene_name_primary"], "flp-13")
self.assertEqual(seq_record.annotations["keywords"],
['Amidation', 'Cleavage on pair of basic residues',
'Complete proteome', 'Direct protein sequencing',
'Neuropeptide', 'Reference proteome', 'Repeat',
'Secreted', 'Signal'])
self.assertEqual(seq_record.annotations["modified"], "2012-11-28")
self.assertEqual(seq_record.annotations["organism"],
"Caenorhabditis elegans")
self.assertEqual(seq_record.annotations["proteinExistence"],
['evidence at protein level'])
self.assertEqual(seq_record.annotations["recommendedName_fullName"],
['FMRFamide-like neuropeptides 13'])
self.assertEqual(seq_record.annotations["sequence_length"], 160)
self.assertEqual(seq_record.annotations["sequence_checksum"],
"BE4C24E9B85FCD11")
self.assertEqual(seq_record.annotations["sequence_mass"], 17736)
self.assertEqual(seq_record.annotations["sequence_modified"], "1998-06-01")
self.assertEqual(seq_record.annotations["sequence_precursor"], "true")
self.assertEqual(seq_record.annotations["sequence_version"], 1)
self.assertEqual(seq_record.annotations["taxonomy"],
['Eukaryota', 'Metazoa', 'Ecdysozoa', 'Nematoda',
'Chromadorea', 'Rhabditida', 'Rhabditoidea', 'Rhabditidae',
'Peloderinae', 'Caenorhabditis'])
self.assertEqual(seq_record.annotations["type"],
['ECO:0000006', 'ECO:0000001'])
self.assertEqual(seq_record.annotations["version"], 74)

# test comment entries
self.assertEqual(seq_record.annotations["comment_allergen"],
['Causes an allergic reaction in human.'])
self.assertEqual(seq_record.annotations["comment_alternativeproducts_isoform"],
['Q8W1X2-1', 'Q8W1X2-2'])
self.assertEqual(seq_record.annotations["comment_biotechnology"],
['Green fluorescent protein has been engineered to produce a '
'vast number of variously colored mutants, fusion proteins, '
'and biosensors. Fluorescent proteins and its mutated allelic '
'forms, blue, cyan and yellow have become a useful and '
'ubiquitous tool for making chimeric proteins, where they '
'function as a fluorescent protein tag. Typically they '
'tolerate N- and C-terminal fusion to a broad variety of '
'proteins. They have been expressed in most known cell types '
'and are used as a noninvasive fluorescent marker in living '
'cells and organisms. They enable a wide range of applications '
'where they have functioned as a cell lineage tracer, reporter '
'of gene expression, or as a measure of protein-protein '
'interactions.', 'Can also be used as a molecular thermometer, '
'allowing accurate temperature measurements in fluids. The '
'measurement process relies on the detection of the blinking '
'of GFP using fluorescence correlation spectroscopy.'])
self.assertEqual(seq_record.annotations["comment_catalyticactivity"],
['ATP + acetyl-CoA + HCO(3)(-) = ADP + phosphate + malonyl-CoA.',
'ATP + biotin-[carboxyl-carrier-protein] + CO(2) = ADP + '
'phosphate + carboxy-biotin-[carboxyl-carrier-protein].'])
self.assertEqual(seq_record.annotations["comment_caution"],
['Could be the product of a pseudogene. The existence of a '
'transcript at this locus is supported by only one sequence '
'submission (PubMed:2174397).'])
self.assertEqual(seq_record.annotations["comment_cofactor"],
['Biotin (By similarity).', 'Binds 2 manganese ions per '
'subunit (By similarity).'])
self.assertEqual(seq_record.annotations["comment_developmentalstage"],
['Expressed from the comma stage of embryogenesis, during all '
'larval stages, and in low levels in adults.'])
self.assertEqual(seq_record.annotations["comment_disease"],
['Defects in MC2R are the cause of glucocorticoid deficiency '
'type 1 (GCCD1) [MIM:202200]; also known as familial '
'glucocorticoid deficiency type 1 (FGD1). GCCD1 is an '
'autosomal recessive disorder due to congenital '
'insensitivity or resistance to adrenocorticotropin (ACTH). '
'It is characterized by progressive primary adrenal '
'insufficiency, without mineralocorticoid deficiency.'])
self.assertEqual(seq_record.annotations["comment_disruptionphenotype"],
['Mice display impaired B-cell development which does not '
'progress pass the progenitor stage.'])
self.assertEqual(seq_record.annotations["comment_domain"],
['Two regions, an N-terminal (aa 96-107) and a C-terminal '
'(aa 274-311) are required for binding FGF2.'])
self.assertEqual(seq_record.annotations["comment_enzymeregulation"],
['By phosphorylation. The catalytic activity is inhibited by '
'soraphen A, a polyketide isolated from the myxobacterium '
'Sorangium cellulosum and a potent inhibitor of fungal growth.'])
self.assertEqual(seq_record.annotations["comment_function"],
['FMRFamides and FMRFamide-like peptides are neuropeptides. '
'AADGAPLIRF-amide and APEASPFIRF-amide inhibit muscle tension '
'in somatic muscle. APEASPFIRF-amide is a potent inhibitor of '
'the activity of dissected pharyngeal myogenic muscle system.'])
self.assertEqual(seq_record.annotations["comment_induction"],
['Repressed in presence of fatty acids. Repressed 3-fold by '
'lipid precursors, inositol and choline, and also controlled '
'by regulatory factors INO2, INO4 and OPI1.'])
self.assertEqual(seq_record.annotations["comment_interaction_intactId"],
['EBI-356720', 'EBI-746969', 'EBI-720116'])
self.assertEqual(seq_record.annotations["comment_massspectrometry"],
['88..98:1032|MALDI', '100..110:1133.7|MALDI'])
self.assertEqual(seq_record.annotations["comment_miscellaneous"],
['Present with 20200 molecules/cell in log phase SD medium.'])
self.assertEqual(seq_record.annotations["comment_onlineinformation"],
['NIEHS-SNPs@http://egp.gs.washington.edu/data/api5/'])
self.assertEqual(seq_record.annotations["comment_pathway"],
['Lipid metabolism; malonyl-CoA biosynthesis; malonyl-CoA '
'from acetyl-CoA: step 1/1.'])
self.assertEqual(seq_record.annotations["comment_RNAediting"],
['Partially edited. RNA editing generates receptor isoforms '
'that differ in their ability to interact with the '
'phospholipase C signaling cascade in a transfected cell '
'line, suggesting that this RNA processing event may '
'contribute to the modulation of serotonergic '
'neurotransmission in the central nervous system.'])
self.assertEqual(seq_record.annotations["comment_PTM"],
['Acetylation at Lys-251 impairs antiapoptotic function.'])
self.assertEqual(seq_record.annotations["comment_pharmaceutical"],
['Could be used as a possible therapeutic agent for treating '
'rheumatoid arthritis.'])
self.assertEqual(seq_record.annotations["comment_polymorphism"],
['Position 23 is polymorphic; the frequencies in unrelated '
'Caucasians are 0.87 for Cys and 0.13 for Ser.'])
self.assertEqual(seq_record.annotations["comment_similarity"],
['Belongs to the FARP (FMRFamide related peptide) family.'])
self.assertEqual(seq_record.annotations["comment_subcellularlocation_location"],
['Secreted'])
self.assertEqual(seq_record.annotations["comment_subunit"],
['Homodimer.'])
self.assertEqual(seq_record.annotations["comment_tissuespecificity"],
['Each flp gene is expressed in a distinct set of neurons. '
'Flp-13 is expressed in the ASE sensory neurons, the DD motor '
'neurons, the 15, M3 and M5 cholinergic pharyngeal '
'motoneurons, and the ASG, ASK and BAG neurons.'])
self.assertEqual(seq_record.annotations["comment_toxicdose"],
['LD(50) is 50 ug/kg in mouse by intracerebroventricular '
'injection and 600 ng/g in Blatella germanica.'])

def compare_txt_xml(self, old, new):
self.assertEqual(old.id, new.id)
self.assertEqual(old.name, new.name)
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