Change sequence attribute of DnaSpeciesType to sequence_path attribute

KarrLab · Dec 11, 2018 · 63470b0 · 63470b0
1 parent 8a97e59
commit 63470b0
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Showing 10 changed files with 160 additions and 240 deletions.
diff --git a/requirements.txt b/requirements.txt
@@ -3,5 +3,6 @@ cement >= 3.0.0
 enum34
 git+https://github.com/KarrLab/obj_model.git#egg=obj_model-0.0.5
 openbabel
+pyfaidx
 setuptools
 git+https://github.com/KarrLab/wc_utils.git#egg=wc_utils-0.0.1a5
diff --git a/tests/fixtures/core.xlsx b/tests/fixtures/core.xlsx
diff --git a/tests/fixtures/eukaryote_core.xlsx b/tests/fixtures/eukaryote_core.xlsx
diff --git a/tests/fixtures/seq.fna.fai b/tests/fixtures/seq.fna.fai
@@ -0,0 +1 @@
+chromosome	21000	12	70	71
diff --git a/tests/requirements.txt b/tests/requirements.txt
@@ -1,3 +1 @@
 mendeleev
-
-pyfaidx
diff --git a/tests/test_core.py b/tests/test_core.py
@@ -18,6 +18,9 @@
 import Bio.SeqUtils
 import mendeleev
 import numpy
+import os
+import shutil
+import tempfile
 import unittest
 
 
@@ -166,7 +169,12 @@ def get_seq(self): return Bio.Seq.Seq(
 
 class DnaSpeciesTypeTestCase(unittest.TestCase):
     def test(self):
-        dna = core.DnaSpeciesType(id='dna1', name='dna1', seq=Bio.Seq.Seq('ACGTACGT', alphabet=Bio.Alphabet.DNAAlphabet()),
+        self.tmp_dirname = tempfile.mkdtemp()
+        filepath = os.path.join(self.tmp_dirname, 'test_seq.fasta')
+        with open(filepath, 'w') as f:
+            f.write('>dna1\nACGTACGT\n')
+
+        dna = core.DnaSpeciesType(id='dna1', name='dna1', sequence_path=filepath,
                                   circular=False, double_stranded=False, ploidy=2)
 
         self.assertEqual(dna.id, 'dna1')
@@ -262,11 +270,19 @@ def test(self):
 
         self.assertAlmostEqual(dna.get_mol_wt(), exp_mol_wt, places=0)
 
+        shutil.rmtree(self.tmp_dirname)  
+
 
 class PolymerLocusTestCase(unittest.TestCase):
     def test_constructor(self):
         cell1 = core.Cell()
-        dna1 = core.DnaSpeciesType(id='dna1', seq=Bio.Seq.Seq('ACGTACGTACGTACG', alphabet=Bio.Alphabet.DNAAlphabet()),
+
+        self.tmp_dirname = tempfile.mkdtemp()
+        filepath = os.path.join(self.tmp_dirname, 'test_seq.fasta')
+        with open(filepath, 'w') as f:
+            f.write('>dna1\nACGTACGTACGTACG\n')
+
+        dna1 = core.DnaSpeciesType(id='dna1', sequence_path=filepath,
                                    circular=False, double_stranded=False)
 
         locus1 = core.PolymerLocus(id='locus1', cell=cell1, name='locus1', polymer=dna1,
@@ -291,6 +307,8 @@ def test_constructor(self):
         self.assertEqual(locus1.get_seq(), rev_comp_seq)
         self.assertEqual(locus1.get_len(), 15)
 
+        shutil.rmtree(self.tmp_dirname)  
+
 
 class MetaboliteSpeciesTypeTestCase(unittest.TestCase):
     def test_constructor(self):