Updated tests for Python 3

biocommons · Apr 7, 2021 · 35b2ed0 · 35b2ed0
1 parent 0143a40
commit 35b2ed0
Show file tree

Hide file tree

Showing 6 changed files with 8 additions and 8 deletions.
diff --git a/tests/test_uta_models.py b/tests/test_uta_models.py
@@ -1,4 +1,3 @@
-import ConfigParser
 import os
 import unittest
 
@@ -98,7 +97,7 @@ def setUpClass(cls):
         )
         cls.session.add(chr8_sa_n)
 
-        for ac, tx_info in transcripts.iteritems():
+        for ac, tx_info in transcripts.items():
             t_seq_n = usam.Seq(
                 seq=tx_info['seq']
             )

diff --git a/tests/test_uta_parsers_geneinfo.py b/tests/test_uta_parsers_geneinfo.py
@@ -15,7 +15,7 @@ class Test_parsers_geneinfoparser(unittest.TestCase):
 
     def test1(self):
         fn = os.path.join(data_dir, 'gene_info_100human.gz')
-        gip = uta.parsers.geneinfo.GeneInfoParser(gzip.open(fn))
+        gip = uta.parsers.geneinfo.GeneInfoParser(gzip.open(fn, "rt"))
         gi = gip.next()
         self.assertEqual(gi, {
             'Full_name_from_nomenclature_authority': 'alpha-1-B glycoprotein',

diff --git a/tests/test_uta_parsers_seqgene.py b/tests/test_uta_parsers_seqgene.py
@@ -15,7 +15,7 @@ class Test_parsers_seqgene(unittest.TestCase):
 
     def test1(self):
         fn = os.path.join(data_dir, 'seq_gene_100.md.gz')
-        parser = uta.parsers.seqgene.SeqGeneParser(gzip.open(fn))
+        parser = uta.parsers.seqgene.SeqGeneParser(gzip.open(fn, "rt"))
         rec = parser.next()
         self.assertEqual(rec, {
             'chr_orient': '+',

diff --git a/uta/models.py b/uta/models.py
@@ -57,7 +57,7 @@ class Seq(Base):
 
     def _seq_hash(context):
         seq = context.current_parameters["seq"]
-        return None if seq is None else hashlib.md5(seq.upper()).hexdigest()
+        return None if seq is None else hashlib.md5(seq.upper().encode("ascii")).hexdigest()
 
     def _seq_len(context):
         seq = context.current_parameters["seq"]

diff --git a/uta/parsers/geneinfo.py b/uta/parsers/geneinfo.py
@@ -10,7 +10,7 @@ class GeneInfoParser(object):
 
     def __init__(self, fh):
         self._fh = fh
-        header = self._fh.next().rstrip()
+        header = next(self._fh).rstrip()
         if header != "#Format: tax_id GeneID Symbol LocusTag Synonyms dbXrefs chromosome map_location description type_of_gene Symbol_from_nomenclature_authority Full_name_from_nomenclature_authority Nomenclature_status Other_designations Modification_date (tab is used as a separator, pound sign - start of a comment)":
             raise UTAError("""gene info doesn't contain expected header; got:\n{header}""".format(
                 header=header))
@@ -23,7 +23,8 @@ def __iter__(self):
         return self
 
     def next(self):
-        return self._csvreader.next()
+        return next(self._csvreader)
+
 
 # <LICENSE>
 # Copyright 2014 UTA Contributors (https://bitbucket.org/biocommons/uta)

diff --git a/uta/parsers/seqgene.py b/uta/parsers/seqgene.py
@@ -11,7 +11,7 @@ class SeqGeneParser(object):
     def __init__(self, fh, filter=None):
         self._fh = fh
         self._filter = filter if filter else lambda r: True
-        header = self._fh.next().rstrip()
+        header = next(self._fh).rstrip()
         if header != "#tax_id	chromosome	chr_start	chr_stop	chr_orient	contig	ctg_start	ctg_stop	ctg_orient	feature_name	feature_id	feature_type	group_label	transcript	evidence_code":
             raise UTAError("""file doesn't contain expected header; got:\n{header}""".format(
                 header=header))