fix lint

src/covsonar/cache.py

@@ -375,9 +375,9 @@ def process_fasta_entry(self, header, seq):
         if not refmol:
             sys.exit(
                 "input error: "
-                + record.id
+                + sample_id
                 + " refers to an unknown reference molecule ("
-                + self._molregex.search(record.description)
+                + refmol
                 + ")."
             )
         seq = sonarBasics.harmonize(seq)
@@ -412,10 +412,10 @@ def iter_fasta(self, *fnames):
                     pbar.update(len(line))
                     line = line.strip()
                     if line.startswith(">"):
+                        header = line[1:]
                         if seq:
                             yield self.process_fasta_entry(header, "".join(seq))
                             seq = []
-                        header = line[1:]
                     else:
                         seq.append(line)
                 if seq:
@@ -593,9 +593,9 @@ def import_cached_samples(self):  # noqa: C901
                 try:
                     # nucleotide level import
                     if not sample_data["seqhash"] is None:
-                        sampleid = dbm.insert_sample(
-                            sample_data["name"], sample_data["seqhash"]
-                        )
+                        # sampleid = dbm.insert_sample(
+                        #     sample_data["name"], sample_data["seqhash"]
+                        # )
                         algnid = dbm.insert_alignment(
                             sample_data["seqhash"], sample_data["refmolid"]
                         )

src/covsonar/dbm.py

@@ -576,15 +576,6 @@ def get_alignment_data(self, sample_name, reference_accession=None):
         sql = 'SELECT "element.sequence", "element.symbol", "element.id" FROM alignmentView WHERE "sample.name" = ? AND "reference.accession" = ? '
         return self.cursor.execute(sql, [sample_name, reference_accession])
 
-    def get_alignment_id(self, seqhash, element_id):
-        sql = (
-            'SELECT id FROM alignment WHERE "element_id" = ? AND "seqhash" = ? LIMIT 1;'
-        )
-        row = self.cursor.execute(sql, [element_id, seqhash]).fetchone()
-        if row:
-            return row["id"]
-        return None
-
     def get_variant_id(self, element_id, start, end, ref, alt):
         sql = "SELECT id FROM variant WHERE element_id = ? AND start = ? AND end = ? AND ref = ? AND alt = ?;"
         row = self.cursor.execute(sql, [element_id, start, end, ref, alt]).fetchone()

src/covsonar/sonar.py

@@ -183,7 +183,7 @@ def parse_args(args):
     )
 
     # view-prop parser
-    parser_viewprops = subparsers.add_parser(
+    subparsers.add_parser(
         "list-prop",
         parents=[general_parser],
         help="View sample properties added to the database.",
@@ -271,12 +271,12 @@ def parse_args(args):
     )
 
     # delete parser
-    parser_restore = subparsers.add_parser(
+    parser_delete = subparsers.add_parser(
         "delete",
         parents=[ref_parser, sample_parser, general_parser],
         help="delete one or more samples from the database.",
     )
-    parser_restore.add_argument(
+    parser_delete.add_argument(
         "--aligned",
         help="ise aligned form (deletions indicated by - and insertions by lower-case letters)",
         action="store_true",
@@ -295,27 +295,27 @@ def parse_args(args):
     )
 
     # info parser
-    parser_info = subparsers.add_parser(
+    subparsers.add_parser(
         "info", parents=[general_parser], help="show software and database info"
     )
 
     # optimize parser
-    parser_opt = subparsers.add_parser(
+    subparsers.add_parser(
         "optimize", parents=[general_parser], help="optimizes the database."
     )
 
     # dev parser
-    parser_dev = subparsers.add_parser("dev", parents=[general_parser])
+    subparsers.add_parser("dev", parents=[general_parser])
 
     # db-upgrade parser
-    parser_opt = subparsers.add_parser(
+    subparsers.add_parser(
         "db-upgrade",
         parents=[general_parser],
         help="upgrade a database to the latest version",
     )
 
     # update-lineage-info parser
-    parser_update_anno = subparsers.add_parser(
+    subparsers.add_parser(
         "update-lineage-info",
         parents=[general_parser],
         help="download latest lineage information",

src/covsonar/sonardb.py

@@ -750,7 +750,6 @@ def process_gff3(self, gff, fna):  # noqa: C901
         symbol_regex = re.compile("gene=([^;]+)(?:;|$)")
         locus_regex = re.compile("locus_tag=([^;]+)(?:;|$)")
         id_regex = re.compile("ID=([^;]+)(?:;|$)")
-        symbols = set()
 
         record = SeqIO.read(fna, "fasta")
         gseq = str(record.seq).upper()
@@ -1761,7 +1760,7 @@ def import_genome_from_fasta_files(
             if dbm is None:
                 dbm = stack.enter_context(sonarDBManager(self.db))
             for i in tqdm(
-                range(len(fnames)), desc=msg, disable_progressbar=disable_progress
+                range(len(fnames)), desc=msg, disable_progressbar=disable_progressbar
             ):
                 self.import_genome(**self.process_fasta(fnames[i]), dbm=dbm)
 
@@ -2658,7 +2657,7 @@ def restore_alignment(self, acc, dbm=None):
         with ExitStack() as stack:
             if dbm is None:
                 dbm = stack.enter_context(sonarDBManager(self.db, readonly=True))
-            row = dbm.get_dna_vars(acc)
+            rows = dbm.get_dna_vars(acc)
         if rows:
             refseq = list(self.refseq)
             qryseq = refseq[:]
@@ -2927,7 +2926,7 @@ def deslugify(string):
 
     @staticmethod
     def get_seqhash_from_fasta_name(fname):
-        return sonarCache.deslugify(os.path.basename(fname))[: -len(self._fasta_ext)]
+        return sonarCache.deslugify(os.path.basename(fname))
 
     def iter_fasta(self, fname):
         """