Added a couple of extra tests and exception handling for the uniprot …

…functions if a bad uniprot ID is passed or the internet is down

.gitignore

@@ -6,6 +6,7 @@ __pycache__/
 # C extensions
 *.so
 .DS_Store
+*~
 
 # Distribution / packaging
 .Python

metapredict/backend/domain_definition.py

@@ -1,6 +1,7 @@
 import numpy as np
 import scipy
 from scipy.signal import savgol_filter
+from metapredict.metapredict_exceptions import DomainError
 """
 Functions for extracting out discrete disordered domains based on the linear disorder score
 calculated by metapredict.
@@ -9,8 +10,6 @@
 
 
 
-class DomainException(Exception):
-    pass
 
 
 ## ------------------------------------------------------------------------
@@ -114,7 +113,7 @@ def binerize_function(idr_score):
 
     # add to help debugging
     if len(B) != len(values):
-        raise DomainException('Error with binerize function. This is a bug. Please raise an issue on GitHub')
+        raise DomainError('Error with binerize function. This is a bug. Please raise an issue on GitHub')
 
 
     ## Part 1 - remove gaps

metapredict/meta.py

@@ -25,6 +25,7 @@
 # stuff for uniprot from backend
 import metapredict.backend.uniprot_predictions
 from metapredict.backend.uniprot_predictions import fetch_sequence
+from metapredict.metapredict_exceptions import MetapredictError
 
 def predict_disorder_domains(sequence, 
                              disorder_threshold=0.42, 
@@ -490,6 +491,12 @@ def predict_disorder_uniprot(uniprot_id, normalized=True):
 
     # fetch sequence from Uniprot
     sequence = fetch_sequence(uniprot_id)
+
+    # raise error if the webcall fails
+    if sequence is None:
+        raise MetapredictError('Error: unable to fetch UniProt with accession %s'%(uniprot_id))
+
+
     # return predicted values of disorder for sequence
     return meta_predict(sequence, normalized)
 
@@ -520,6 +527,11 @@ def graph_disorder_uniprot(uniprot_id, line_intervals=[], name = " ", DPI=150, s
     """
     #make all residues upper case 
     sequence = fetch_sequence(uniprot_id)
+
+    # raise error if the webcall fails
+    if sequence is None:
+        raise MetapredictError('Error: unable to fetch UniProt with accession %s'%(uniprot_id))
+
     #graph sequence
     graph(sequence = sequence, name = name, cutoffLines=line_intervals, DPI=DPI, save_fig=save, output_file=output)
 
@@ -598,6 +610,10 @@ def predict_disorder_domains_uniprot(uniprot_id,
     """
     sequence = fetch_sequence(uniprot_id)
 
+    # raise error if the webcall fails
+    if sequence is None:
+        raise MetapredictError('Error: unable to fetch UniProt with accession %s'%(uniprot_id))
+
     disorder = predict_disorder(sequence, normalized=normalized)
 
     return_tuple = domain_definition.get_domains(sequence, 

metapredict/metapredict_exceptions.py

@@ -0,0 +1,8 @@
+
+
+class DomainError(Exception):
+    pass
+
+
+class MetapredictError(Exception):
+    pass

metapredict/tests/test_uniprot_functionality.py

@@ -0,0 +1,95 @@
+"""
+Unit and regression test for the metapredict package.
+
+This is extremely underdone at this point... Sorry about that :'(
+"""
+
+# Import package, test suite, and other packages as needed
+from metapredict import meta
+from metapredict.metapredict_exceptions import MetapredictError
+import pytest
+import sys
+import os
+import numpy as np
+
+
+current_filepath = os.getcwd()
+fasta_filepath = "{}/testing.fasta".format(current_filepath)
+
+P53_UID = 'P04637'
+
+def test_metapredict_imported():
+    """Sample test, will always pass so long as import statement worked"""
+    assert "metapredict" in sys.modules
+
+
+# ....................................................................................
+#
+def test_predict_disorder_uniprot():
+
+    # checks that this fails when an invalid uniprot accession is passed
+    with pytest.raises(MetapredictError):
+        meta.predict_disorder_uniprot('aaaa')
+
+
+    # checks that when we pull p53 we get 393 residues of sweet,
+    # sweet disorder prediction
+    assert len(meta.predict_disorder_uniprot(P53_UID)) == 393
+
+    # check summed disorder is right
+    assert np.sum(meta.predict_disorder_uniprot(P53_UID)) == 172.965
+
+
+    # check summed disorder is right when we don't normalize (these are not magic values,
+    # just the expected 'truth' for the 1.0 release
+    assert np.sum(meta.predict_disorder_uniprot(P53_UID,normalized=False)) == 173.524
+
+
+# ....................................................................................
+#
+def test_graph_disorder_uniprot_():
+
+    # checks that this fails when an invalid uniprot accession is passed
+    with pytest.raises(MetapredictError):
+        meta.graph_disorder_uniprot('aaaa')
+
+
+    # probably should have some tests here...?
+
+
+# ....................................................................................
+#
+def test_predict_disorder_domains_uniprot_():
+
+    # checks that this fails when an invalid uniprot accession is passed
+    with pytest.raises(MetapredictError):
+        meta.predict_disorder_domains_uniprot('aaaa')
+
+
+    # checks that when we pull p53 we get 393 residues of sweet,
+    # sweet disorder prediction
+
+    dis_domains = meta.predict_disorder_domains_uniprot(P53_UID) 
+    assert len(dis_domains[0]) == 393
+    assert len(dis_domains[1]) == 393
+    assert np.sum(dis_domains[0]) == 172.965
+    assert np.sum(dis_domains[1]) == 173.04537763974946
+
+    # did we find 2 IDRs
+    assert len(dis_domains[2]) == 2
+
+    # IDR1
+    assert dis_domains[2][0][2] == 'MEEPQSDPSVEPPLSQETFSDLWKLLPENNVLSPLPSQAMDDLMLSPDDIEQWFTEDPGPDEAPRMPEAAPPVAPAPAAPTPAAPAPAPSWPLSSSVPSQKT'
+    assert dis_domains[2][0][0] == 0
+    assert dis_domains[2][0][1] == 102
+
+    # IDR2
+    assert dis_domains[2][1][2] == 'PGRDRRTEEENLRKKGEPHHELPPGSTKRALPNNTSSSPQPKKKPLDGEYFTLQIRGRERFEMFRELNEALELKDAQAGKEPGGSRAHSSHLKSKKGQSTSRHKKLMFKTEGPDSD'
+    assert dis_domains[2][1][0] == 277
+    assert dis_domains[2][1][1] == 393
+
+    # FD1
+    assert dis_domains[3][0][2] == 'YQGSYGFRLGFLHSGTAKSVTCTYSPALNKMFCQLAKTCPVQLWVDSTPPPGTRVRAMAIYKQSQHMTEVVRRCPHHERCSDSDGLAPPQHLIRVEGNLRVEYLDDRNTFRHSVVVPYEPPEVGSDCTTIHYNYMCNSSCMGGMNRRPILTIITLEDSSGNLLGRNSFEVRVCAC'
+    assert dis_domains[3][0][0] == 102
+    assert dis_domains[3][0][1] == 277
+