Substituted SPAdes for IVA

Author: CBeelen

micall/core/denovo.py

@@ -20,7 +20,7 @@
 
 from micall.core.project_config import ProjectConfig
 
-IVA = "iva"
+SPAdes = "Spades/bin/spades.py"
 DEFAULT_DATABASE = os.path.join(os.path.dirname(__file__),
                                 '..',
                                 'blast_db',
@@ -201,34 +201,33 @@ def denovo(fastq1_path: str,
          '--interleave',
          '-o', joined_path],
         check=True)
-    iva_out_path = os.path.join(tmp_dir, 'iva_out')
-    contigs_fasta_path = os.path.join(iva_out_path, 'contigs.fasta')
-#    iva_args = [IVA, '--fr', joined_path, '-t', '2']
-    with open(os.path.join(tmp_dir, 'iva.log'), 'w') as log_file:
-        iva_args = [IVA, '-vv', '--fr', joined_path, '-t', '2']
-        if merged_contigs_csv is not None:
-            seeds_fasta_path = os.path.join(tmp_dir, 'seeds.fasta')
-            with open(seeds_fasta_path, 'w') as seeds_fasta:
-                SeqIO.write((SeqRecord(Seq(row['contig']), f'seed-{i}', '', '')
-                            for i, row in enumerate(DictReader(merged_contigs_csv))),
-                            seeds_fasta,
-                            'fasta')
-                seeds_size = seeds_fasta.tell()
-            if seeds_size > 0:
-                iva_args.extend(['--contigs', seeds_fasta_path, '--make_new_seeds'])
-        iva_args.append(iva_out_path)
-        try:
-            run(iva_args,
-                check=True,
-                stdout=log_file,
-                stderr=STDOUT)
-        except CalledProcessError as ex:
-            output = ex.output and ex.output.decode('UTF8')
-            if output != 'Failed to make first seed. Cannot continue\n':
-                logger.warning('iva failed to assemble.', exc_info=True)
-                logger.warning(output)
-            with open(contigs_fasta_path, 'a'):
-                pass
+    spades_out_path = os.path.join(tmp_dir, 'spades_out')
+    contigs_fasta_path = os.path.join(spades_out_path, 'contigs.fasta')
+    spades_args = [SPAdes, '--12', joined_path, '--phred-offset', '33']
+    # Setting Phred offset manually is only required for microtests
+    if merged_contigs_csv is not None:
+        seeds_fasta_path = os.path.join(tmp_dir, 'seeds.fasta')
+        with open(seeds_fasta_path, 'w') as seeds_fasta:
+            SeqIO.write((SeqRecord(Seq(row['contig']), f'seed-{i}', '', '')
+                         for i, row in enumerate(DictReader(merged_contigs_csv))),
+                        seeds_fasta,
+                        'fasta')
+            seeds_size = seeds_fasta.tell()
+        if seeds_size > 0:
+            spades_args.extend(['--trusted-contigs', seeds_fasta_path])
+    spades_args.extend(['-o', spades_out_path])
+    try:
+        run(spades_args,
+            check=True,
+            stdout=PIPE,
+            stderr=STDOUT)
+    except CalledProcessError as ex:
+        output = ex.output and ex.output.decode('UTF8')
+        if output != 'Failed to make first seed. Cannot continue\n':
+            logger.warning('SPAdes failed to assemble.', exc_info=True)
+            logger.warning(output)
+        with open(contigs_fasta_path, 'a'):
+            pass
 
     os.chdir(start_dir)
     duration = datetime.now() - start_time