Merge pull request #33 from PennChopMicrobiomeProgram/32-address-code…

…-quality-issues-in-codacy-report

32 address code quality issues in codacy report

tests/unit/test_algorithm.py

@@ -9,7 +9,6 @@
     soft_species_probability,
     hard_species_probability,
     threshold_assignment_probability,
-    iter_threshold,
 )
 
 from unassigner.alignment import AlignedPair

tests/unit/test_aligned.py

@@ -53,17 +53,17 @@ def test_region_subject_to_query_no_endgaps(self):
         r = AlignedRegion.from_subject(a, 0, 3)
         self.assertEqual(r.in_alignment(), (0, 3))
         rq = AlignedRegion.from_query(a, 0, 3)
-        self.assertEqual(r.in_alignment(), (0, 3))
+        self.assertEqual(rq.in_alignment(), (0, 3))
 
         r = AlignedRegion.from_subject(a, 1, 5)
         self.assertEqual(r.in_alignment(), (1, 5))
         rq = AlignedRegion.from_query(a, 1, 5)
-        self.assertEqual(r.in_alignment(), (1, 5))
+        self.assertEqual(rq.in_alignment(), (1, 5))
 
         r = AlignedRegion.from_subject(a)
         self.assertEqual(r.in_alignment(), (0, 6))
         rq = AlignedRegion.from_query(a)
-        self.assertEqual(r.in_alignment(), (0, 6))
+        self.assertEqual(rq.in_alignment(), (0, 6))
 
     def test_region_subject_to_query_with_endgaps(self):
         a = AlignedPair(("a", "--ABC-EF---"), ("b", "HIJKLMNOPQR"))

tests/unit/test_mismatch_db.py

@@ -1,4 +1,3 @@
-import collections
 import os
 import io
 import tempfile
@@ -8,7 +7,6 @@
     MismatchLocationApp,
     main,
     group_by_n,
-    MutableMismatchDb,
 )
 
 DATA_DIR = os.path.join(os.path.dirname(os.path.realpath(__file__)), "data")

tests/unit/test_parse.py

@@ -1,6 +1,7 @@
 import tempfile
 import unittest
 
+
 from unassigner.parse import parse_fasta, parse_results, load_fasta, write_fasta
 
 

tests/unit/test_trim.py

@@ -153,7 +153,7 @@ def test_alignment_match_subj_left(self):
         )
         m = AlignmentMatcher(self.test_dir)
         alignment_matches = list(m.find_in_seqs(s))
-        match_id, matchobj = alignment_matches[0]
+        _, matchobj = alignment_matches[0]
         self.assertEqual(matchobj.start, 0)
         self.assertEqual(matchobj.end, 3)
 
@@ -167,7 +167,7 @@ def test_alignment_match_middle(self):
         )
         m = AlignmentMatcher(self.test_dir)
         alignment_matches = list(m.find_in_seqs(s))
-        match_id, matchobj = alignment_matches[0]
+        _, matchobj = alignment_matches[0]
         self.assertEqual((matchobj.start, matchobj.end), (7, 12))
 
     def test_alignment_match_middle_gaps(self):
@@ -180,7 +180,7 @@ def test_alignment_match_middle_gaps(self):
         )
         m = AlignmentMatcher(self.test_dir)
         alignment_matches = list(m.find_in_seqs(s))
-        match_id, matchobj = alignment_matches[0]
+        _, matchobj = alignment_matches[0]
         self.assertEqual((matchobj.start, matchobj.end), (7, 11))
 
     def test_trim_right(self):

unassigner/algorithm.py

@@ -78,7 +78,7 @@ def load_database(cls, f):
             line = line.rstrip()
             toks = line.split("\t")
             typestrain_id = toks[0]
-            ref_seq_id = toks[1]
+            # ref_seq_id = toks[1]
             mismatch_positions = [int(x) for x in toks[2:]]
             cls.db[typestrain_id].append(mismatch_positions)
 

unassigner/align.py

@@ -4,7 +4,7 @@
 import tempfile
 from Bio import pairwise2
 
-from unassigner.parse import write_fasta, load_fasta, parse_fasta
+from unassigner.parse import write_fasta, parse_fasta
 from unassigner.alignment import AlignedPair
 
 BLAST_FMT = (

unassigner/alignment.py

@@ -1,5 +1,4 @@
 import itertools
-import operator
 
 
 class AlignedPair(object):

unassigner/mismatch_db.py

@@ -6,7 +6,6 @@
 import collections
 import itertools
 import operator
-import sys
 import tempfile
 
 from unassigner.parse import parse_fasta, write_fasta

unassigner/parse.py

@@ -1,10 +1,9 @@
 import logging
-import re
 from io import StringIO
 
 
 def parse_species_names(f):
-    for desc, seq in parse_fasta(f):
+    for desc, _ in parse_fasta(f):
         vals = desc.split("\t", maxsplit=1)
         accession = vals[0]
         if len(vals) == 2:
@@ -62,7 +61,7 @@ def parse_desc(desc):
         # This is the old way of parsing the description, 01_2022
         # accession = re.findall(r"\[accession=(.*?)\]", desc)[0]
         # species_name = re.findall(r"\[organism=(.*?)\]", desc)[0]
-    except IndexError as e:
+    except IndexError:
         logging.error(f"Couldn't find accession and/or organism identifier in {desc}")
         logging.error(f"Skipping this sequence...")
         return None, None

unassigner/prepare_strain_data.py

@@ -77,7 +77,7 @@ def main(argv=None):
         clean(db_dir)
         sys.exit(0)
 
-    ltp_metadata_fp = use_or_download(args.ltp_metadata_fp, LTP_METADATA_URL, db_dir)
+    use_or_download(args.ltp_metadata_fp, LTP_METADATA_URL, db_dir)
     ltp_seqs_fp = use_or_download(args.ltp_seqs_fp, LTP_SEQS_URL, db_dir)
     process_ltp_seqs(ltp_seqs_fp, db_dir)
 

unassigner/trim.py

@@ -140,7 +140,7 @@ def find_match(self, seq):
                     else:
                         msg = "Complete, {0} mismatches".format(n_mismatches)
                     end_idx = start_idx + len(query)
-                    obs_primer = seq[start_idx:end_idx]
+                    # obs_primer = seq[start_idx:end_idx]
                     return PrimerMatch(start_idx, end_idx, 0, msg)
 
 

unassigner/unassignment_probability.py

@@ -5,7 +5,7 @@ def species_probability(self, species_alignment, refseq_alignments):
     start = species_alignment.start_pos
     end = species_alignment.end_pos
     for r in refseq_alignments:
-        refseq_id = r.subject_id
+        # refseq_id = r.subject_id
         a, b = r.count_matches(start, end)
         c, d = r.count_matches()
         yield query_id, species_id, a, b, r.subject_id, c, d