format and fix

Author: ThijsMaas

Diff for: iss/app.py

@@ -34,7 +34,9 @@ def generate_reads(args):
     logger.debug("Using verbose logger")
     logger.info("Starting iss generate")
 
-    error_model = load_error_model(args.mode, args.seed, args.model, args.fragment_length, args.fragment_length_sd, args.store_mutations)
+    error_model = load_error_model(
+        args.mode, args.seed, args.model, args.fragment_length, args.fragment_length_sd, args.store_mutations
+    )
 
     genome_list, genome_file = load_genomes(
         args.genomes, args.draft, args.ncbi, args.n_genomes_ncbi, args.output, args.n_genomes
@@ -54,6 +56,9 @@ def generate_reads(args):
         error_model,
     )
 
+    if args.store_mutations:
+        logger.info(f"Storing inserted sequence errors in {args.output}.vcf")
+
     logger.info("Using %s cpus for read generation" % args.cpus)
 
     if readcount_dic is not None:
@@ -123,8 +128,8 @@ def generate_reads(args):
         if args.store_mutations:
             util.concatenate(
                 temp_mut,
-                args.output + '.vcf',
-                "##fileformat=VCFv4.1\n" + "\t".join(["#CHROM", "POS", "ID", "REF", "ALT", "QUAL", "FILTER", "INFO"])
+                args.output + ".vcf",
+                "##fileformat=VCFv4.1\n" + "\t".join(["#CHROM", "POS", "ID", "REF", "ALT", "QUAL", "FILTER", "INFO"]),
             )
         full_tmp_list = temp_R1 + temp_R2
         full_tmp_list.append(genome_file)
@@ -135,7 +140,7 @@ def generate_reads(args):
             util.compress(args.output + "_R1.fastq")
             util.compress(args.output + "_R2.fastq")
             if args.store_mutations:
-                util.compress(args.output + '.vcf')
+                util.compress(args.output + ".vcf")
         logger.info("Read generation complete")
 
 
@@ -392,11 +397,11 @@ def main():
         help="Fragment length standard deviation for metagenomics sequencing (default: %(default)s).",
     )
     parser_gen.add_argument(
-        '--store_mutations',
-        '-M',
-        action='store_true',
+        "--store_mutations",
+        "-M",
+        action="store_true",
         default=False,
-        help='Generates an additional VCF file with the mutations introduced in the reads',
+        help="Generates an additional VCF file with the mutations introduced in the reads",
     )
     parser_gen._optionals.title = "arguments"
     parser_gen.set_defaults(func=generate_reads)

Diff for: iss/error_models/__init__.py

@@ -96,14 +96,16 @@ def mut_sequence(self, record, orientation):
                     np.random.choice(nucl_choices[position][nucl.upper()][0], p=nucl_choices[position][nucl.upper()][1])
                 )
                 if self.store_mutations and mutated_nuc != record.annotations["original"][position]:
-                    record.annotations["mutations"].append({
+                    record.annotations["mutations"].append(
+                        {
                             "id": record.id,
                             "position": position,
                             "ref": mutable_seq[position],
                             "alt": mutated_nuc,
                             "quality": qual,
                             "type": "snp",
-                            })
+                        }
+                    )
                 mutable_seq[position] = mutated_nuc
             position += 1
         record.seq = Seq(mutable_seq)

Diff for: iss/generator.py

@@ -72,7 +72,6 @@ def reads_generator(n_pairs, record, error_model, cpu_number, gc_bias, sequence_
     i = 0
     while i < n_pairs:
         try:
-            # forward, reverse = simulate_read(record, error_model, i, cpu_number, sequence_type)
             forward, reverse, mutations = simulate_read(record, error_model, i, cpu_number, sequence_type)
 
         except AssertionError:
@@ -190,7 +189,7 @@ def simulate_read(record, error_model, i, cpu_number, sequence_type):
     reverse = error_model.introduce_error_scores(reverse, "reverse")
     reverse.seq = error_model.mut_sequence(reverse, "reverse")
 
-    return (forward, reverse) # mutations
+    return (forward, reverse, forward.annotations["mutations"] + reverse.annotations["mutations"])
 
 
 def to_fastq(generator, output):
@@ -602,13 +601,14 @@ def write_mutations(mutations, mutations_handle):
             "\t".join(
                 [
                     str(vcf_dict["id"]),
-                    str(vcf_dict["position"] + 1), # vcf files have 1-based index
+                    str(vcf_dict["position"] + 1),  # vcf files have 1-based index
                     ".",
                     vcf_dict["ref"],
                     str(vcf_dict["alt"]),
                     str(vcf_dict["quality"]),
                     "",
-                    ""
+                    "",
                 ]
-            ) + "\n"
-        )
+            )
+            + "\n"
+        )

Diff for: iss/test/test_generator.py

@@ -13,18 +13,17 @@
 from iss.error_models import basic, kde
 from iss.util import cleanup
 
-# due to inconsistent seeding between python 2 and 3, some of the following
-# tests are disabled with python2
-
-
-def teardown_cleanup():
-    cleanup(["data/.test.iss.tmp.my_genome.0_R1.fastq", "data/.test.iss.tmp.my_genome.0_R2.fastq"])
-
 
 @pytest.fixture
 def setup_and_teardown():
     yield
-    cleanup(["data/.test.iss.tmp.my_genome.0_R1.fastq", "data/.test.iss.tmp.my_genome.0_R2.fastq"])
+    cleanup(
+        [
+            "data/.test.iss.tmp.my_genome.0_R1.fastq",
+            "data/.test.iss.tmp.my_genome.0_R2.fastq",
+            "data/.test.iss.tmp.my_genome.tsv",
+        ]
+    )
 
 
 def test_cleanup_fail():
@@ -43,15 +42,21 @@ def test_simulate_and_save(setup_and_teardown):
     ref_genome = SeqRecord(Seq(str("AAAAACCCCC" * 100)), id="my_genome", description="test genome")
     forward_handle = open("data/.test.iss.tmp.my_genome.0_R1.fastq", "w")
     reverse_handle = open("data/.test.iss.tmp.my_genome.0_R2.fastq", "w")
-    generator.simulate_reads(ref_genome, err_mod, 1000, 0, forward_handle, reverse_handle, "metagenomics", gc_bias=True)
+    mutations_handle = open("data/.test.iss.tmp.my_genome.tsv", "w")
+    generator.simulate_reads(
+        ref_genome, err_mod, 1000, 0, forward_handle, reverse_handle, mutations_handle, "metagenomics", gc_bias=True
+    )
 
 
 def test_simulate_and_save_short(setup_and_teardown):
     err_mod = basic.BasicErrorModel()
     ref_genome = SeqRecord(Seq(str("AACCC" * 100)), id="my_genome", description="test genome")
     forward_handle = open("data/.test.iss.tmp.my_genome.0_R1.fastq", "w")
     reverse_handle = open("data/.test.iss.tmp.my_genome.0_R2.fastq", "w")
-    generator.simulate_reads(ref_genome, err_mod, 1000, 0, forward_handle, reverse_handle, "metagenomics", gc_bias=True)
+    mutations_handle = open("data/.test.iss.tmp.my_genome.tsv", "w")
+    generator.simulate_reads(
+        ref_genome, err_mod, 1000, 0, forward_handle, reverse_handle, mutations_handle, "metagenomics", gc_bias=True
+    )
 
 
 def test_small_input():
@@ -88,7 +93,6 @@ def test_kde_short(with_seed):
 
 def test_amp(with_seed):
     err_mod = kde.KDErrorModel(os.path.join(os.path.dirname(__file__), "../profiles/MiSeq"), 1000, 10)
-    print(err_mod.read_length)
     ref_genome = SeqRecord(
         Seq(
             (

Diff for: iss/util.py

@@ -210,7 +210,7 @@ def reservoir(records, record_list, n=None):
             yield record
 
 
-def concatenate(file_list, output, header = None):
+def concatenate(file_list, output, header=None):
     """Concatenate files together
 
     Args: