Merge pull request #192 from HadrienG/dev

1.5.1
HadrienG · Oct 10, 2020 · 52ad1fb · 52ad1fb
2 parents 7c353e1 + c3d5815
commit 52ad1fb
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Showing 7 changed files with 141 additions and 160 deletions.
diff --git a/Pipfile b/Pipfile
@@ -7,7 +7,7 @@ name = "pypi"
 future = "*"
 numpy = "*"
 scipy = "*"
-biopython = "*"
+biopython = "==1.78"
 joblib = "*"
 pysam = "==0.15.4"
 requests = "*"

diff --git a/Pipfile.lock b/Pipfile.lock
diff --git a/iss/generator.py b/iss/generator.py
@@ -6,7 +6,6 @@
 from Bio import SeqIO
 from Bio.Seq import Seq
 from Bio.SeqUtils import GC
-from Bio.Alphabet import IUPAC
 from Bio.SeqRecord import SeqRecord
 from shutil import copyfileobj
 
@@ -131,9 +130,7 @@ def simulate_read(record, ErrorModel, i, cpu_number):
     bounds = (forward_start, forward_end)
     # create a perfect read
     forward = SeqRecord(
-        Seq(str(sequence[forward_start:forward_end]),
-            IUPAC.unambiguous_dna
-            ),
+        Seq(str(sequence[forward_start:forward_end])),
         id='%s_%s_%s/1' % (header, i, cpu_number),
         description=''
     )
@@ -156,9 +153,7 @@ def simulate_read(record, ErrorModel, i, cpu_number):
     bounds = (reverse_start, reverse_end)
     # create a perfect read
     reverse = SeqRecord(
-        Seq(rev_comp(str(sequence[reverse_start:reverse_end])),
-            IUPAC.unambiguous_dna
-            ),
+        Seq(rev_comp(str(sequence[reverse_start:reverse_end]))),
         id='%s_%s_%s/2' % (header, i, cpu_number),
         description=''
     )

diff --git a/iss/test/test_download.py b/iss/test/test_download.py
@@ -2,7 +2,6 @@
 # -*- coding: utf-8 -*-
 
 from Bio.Seq import Seq
-from Bio.Alphabet import IUPAC
 from Bio.SeqRecord import SeqRecord
 
 from iss import download

diff --git a/iss/test/test_error_model.py b/iss/test/test_error_model.py
@@ -4,7 +4,6 @@
 from iss.error_models import ErrorModel, basic, kde, perfect
 
 from Bio.Seq import Seq
-from Bio.Alphabet import IUPAC
 from Bio.SeqRecord import SeqRecord
 from nose.tools import raises
 
@@ -40,9 +39,7 @@ def test_introduce_errors():
     err_mod = basic.BasicErrorModel()
 
     read = SeqRecord(
-        Seq(str('AATGC' * 25),
-            IUPAC.unambiguous_dna
-            ),
+        Seq(str('AATGC' * 25)),
         id='read_1',
         description='test read'
     )
@@ -58,9 +55,7 @@ def test_mut_sequence():
     err_mod = basic.BasicErrorModel()
 
     read = SeqRecord(
-        Seq(str('AAAAA' * 25),
-            IUPAC.unambiguous_dna
-            ),
+        Seq(str('AAAAA' * 25)),
         id='read_1',
         description='test read'
     )
@@ -78,16 +73,12 @@ def test_introduce_indels():
     err_mod.del_for[0]['A'] = 1.0
     bounds = (5, 130)
     read = SeqRecord(
-        Seq(str('ATATA' * 25),
-            IUPAC.unambiguous_dna
-            ),
+        Seq(str('ATATA' * 25)),
         id='read_1',
         description='test read'
     )
     ref_genome = SeqRecord(
-        Seq(str('ATATA' * 100),
-            IUPAC.unambiguous_dna
-            ),
+        Seq(str('ATATA' * 100)),
         id='ref_genome',
         description='test reference'
     )

diff --git a/iss/test/test_generator.py b/iss/test/test_generator.py
@@ -8,7 +8,6 @@
 from iss.error_models import ErrorModel, basic, kde
 
 from Bio.Seq import Seq
-from Bio.Alphabet import IUPAC
 from Bio.SeqRecord import SeqRecord
 from nose.tools import with_setup, raises
 
@@ -39,9 +38,7 @@ def test_cleanup_fail():
 def test_simulate_and_save():
     err_mod = basic.BasicErrorModel()
     ref_genome = SeqRecord(
-        Seq(str('AAAAACCCCC' * 100),
-            IUPAC.unambiguous_dna
-            ),
+        Seq(str('AAAAACCCCC' * 100)),
         id='my_genome',
         description='test genome'
     )
@@ -52,9 +49,7 @@ def test_simulate_and_save():
 def test_simulate_and_save_short():
     err_mod = basic.BasicErrorModel()
     ref_genome = SeqRecord(
-        Seq(str('AACCC' * 100),
-            IUPAC.unambiguous_dna
-            ),
+        Seq(str('AACCC' * 100)),
         id='my_genome',
         description='test genome'
     )
@@ -65,9 +60,7 @@ def test_simulate_and_save_short():
 def test_small_input():
     err_mod = kde.KDErrorModel('data/ecoli.npz')
     ref_genome = SeqRecord(
-        Seq(str('AAAAACCCCC'),
-            IUPAC.unambiguous_dna
-            ),
+        Seq(str('AAAAACCCCC')),
         id='my_genome',
         description='test genome'
     )
@@ -80,9 +73,7 @@ def test_basic():
         np.random.seed(42)
         err_mod = basic.BasicErrorModel()
         ref_genome = SeqRecord(
-            Seq(str('AAAAACCCCC' * 100),
-                IUPAC.unambiguous_dna
-                ),
+            Seq(str('AAAAACCCCC' * 100)),
             id='my_genome',
             description='test genome'
         )
@@ -97,9 +88,7 @@ def test_kde():
         np.random.seed(42)
         err_mod = kde.KDErrorModel('data/ecoli.npz')
         ref_genome = SeqRecord(
-            Seq(str('CGTTTCAACC' * 400),
-                IUPAC.unambiguous_dna
-                ),
+            Seq(str('CGTTTCAACC' * 400)),
             id='my_genome',
             description='test genome'
         )
@@ -114,9 +103,7 @@ def test_kde_short():
         np.random.seed(42)
         err_mod = kde.KDErrorModel('data/ecoli.npz')
         ref_genome = SeqRecord(
-            Seq(str('AAACC' * 100),
-                IUPAC.unambiguous_dna
-                ),
+            Seq(str('AAACC' * 100)),
             id='my_genome',
             description='test genome'
         )

diff --git a/iss/version.py b/iss/version.py
@@ -1 +1 @@
-__version__ = '1.5.0'
+__version__ = '1.5.1'