Fixes #293 and integrates pyrodigal v3 and pyrodigal-gv releases, add…

…s some tests

bin/input_commands.py

@@ -205,13 +205,33 @@ def validate_fasta(filename):
     else:
         with open(filename, "r") as handle:
             fasta = SeqIO.parse(handle, "fasta")
-            logger.info("Checking Input FASTA.")
+            logger.info(f"Checking input {filename}.")
             if any(fasta):
-                logger.info("FASTA checked.")
+                logger.info(f"Input {filename} is in FASTA format.")
             else:
                 logger.error("Error: Input file is not in the FASTA format.")
 
+    # check for duplicate headers
+    check_duplicate_headers(filename)
+    logger.info(f"All entries in {filename} has unique headers.")
 
+def check_duplicate_headers(fasta_file):
+    """
+    checks if there are duplicated in the FASTA header
+    in response to Tina's issue
+    https://github.com/gbouras13/pharokka/issues/293
+    """
+    header_set = set()
+
+    # Iterate through the FASTA file and check for duplicate headers
+    for record in SeqIO.parse(fasta_file, "fasta"):
+        header = record.description
+        if header in header_set:
+            logger.error(f"Duplicate header found: {header}") # errors if duplicate header found
+        else:
+            header_set.add(header)
+    # if it finished it will be fine
+
 def validate_gene_predictor(gene_predictor, genbank_flag):
     if gene_predictor == "phanotate":
         logger.info("Phanotate will be used for gene prediction.")
@@ -230,7 +250,7 @@ def validate_gene_predictor(gene_predictor, genbank_flag):
             )
     else:
         logger.error(
-            "Error: gene predictor was incorrectly specified. Please use 'phanotate', 'prodigal', 'prodigal-gv' or 'custom'."
+            "Error: gene predictor was incorrectly specified. Please use 'phanotate', 'prodigal' or 'prodigal-gv'."
         )
 
 

environment.yml

@@ -13,7 +13,7 @@ dependencies:
   - aragorn >=1.2.41
   - mash >=2.2
   - dnaapler >=0.3.0
-  - pyrodigal >=2.0.1
+  - pyrodigal >=3.0.0
   - pycirclize >=0.3.1
   - alive-progress >=3.0.1
   - requests >=2.25.1

setup.py

@@ -92,7 +92,7 @@ def package_files(directory):
         "alive-progress>=3.0.1",
         "requests>=2.25.1",
         "bcbio-gff >=0.7.0",
-        #"pyrodigal >=3.0.0",
-        #"pyrodigal_gv >= 0.1.0"
+        "pyrodigal >=3.0.0",
+        "pyrodigal_gv >= 0.1.0"
     ],
 )

tests/test_data/overall/Standard_examples/dupe_header.fasta

@@ -0,0 +1,34 @@
+>MW460250_1
+CCCCACCCCGCCATCCCCGATTCATGAGCTATGTTCTAAGTCGATACCATTTAATAAGATAGGGTCATCT
+TCTTTACCTACCATATAATCAGATAGTAAGTCTGCTTCAGCTTTTTGCCCTGGTCGTGATAGTTTAGATT
+TCTTAGTTTCAATACGCATAATGTGACCATTGTATTAAATAATTAGAATACTATTTTAAAAGATTCTATT
+CTGTTTGGATTAATATATACTTGAGGTGAAGTTATAGCACTTTCAGTATATACTTTTATAGAGGTTTCAT
+CCATTCCTCTTAACATATAATCTATATCTTGCCTATTGTAACTCTTTTCATCAGTAGATACTAAAAAGTA
+TTTAGCTCCACTTGACATTGTTATTTCAATATGTTTTGACATCTACAATCTCTCCTATGCAAATTTGTTA
+AAGACAAAGGATAATATAGCTCCTAGAACAAGTAAAAGAACCTTCTCAGTTGTATCCTTTTTCTCAGTAT
+CCTTAGTTTTTGTACTTTCAGCAAGTTCTGAAATCTTTTCATCAAGTCTTTCTAATTGGACGTAAATTGC
+TGATTGTTTTTCACTATTGACAGCTACATCTTTATCTATACTAACTATCATTTTTCTTAGTTCAGCTACC
+TCAACTTCTAAATCTTTGAAAGTTCCTCTATCTATATAATTACCTTCTTGTATCTTAGACTTAATAGTTT
+CTACTTGAGAAACAAGGTTGTTTATCTCCTTATCCAACTAGAATCACCTCTAAGGTCTAACCGTTTCAGA
+TTCAGAATGGATATCATAATTTTCTAAGAAATCATTGATAATCTCCATATAATTATCCGTAACGACTTTT
+CCGTAAGATGTTTTTGTATCAATTTCAAACCTAAGCTTACCAAAACTTTGGAGGTCTAATTCTTTTATTA
+CAATATTAGGGTCATCAGAAGGAAGGTAATAATAGTCGAAGTATATAATTGAGCCATTTATTAATACTCT
+GTCTATTCTATAGACGTGGAAATAGCGTCTGTCTCTTTTAAAATGGGCTAGTGCATCTTTAAACTCTAAC
+TTAAGGATATCCTTATATTTAATCAAAGTGGTAACCTCCTTACTATTAATTTTTAAATTTACTTATTTTG
+>MW460250_1
+CCCCACCCCGCCATCCCCGATTCATGAGCTATGTTCTAAGTCGATACCATTTAATAAGATAGGGTCATCT
+TCTTTACCTACCATATAATCAGATAGTAAGTCTGCTTCAGCTTTTTGCCCTGGTCGTGATAGTTTAGATT
+TCTTAGTTTCAATACGCATAATGTGACCATTGTATTAAATAATTAGAATACTATTTTAAAAGATTCTATT
+CTGTTTGGATTAATATATACTTGAGGTGAAGTTATAGCACTTTCAGTATATACTTTTATAGAGGTTTCAT
+CCATTCCTCTTAACATATAATCTATATCTTGCCTATTGTAACTCTTTTCATCAGTAGATACTAAAAAGTA
+TTTAGCTCCACTTGACATTGTTATTTCAATATGTTTTGACATCTACAATCTCTCCTATGCAAATTTGTTA
+AAGACAAAGGATAATATAGCTCCTAGAACAAGTAAAAGAACCTTCTCAGTTGTATCCTTTTTCTCAGTAT
+CCTTAGTTTTTGTACTTTCAGCAAGTTCTGAAATCTTTTCATCAAGTCTTTCTAATTGGACGTAAATTGC
+TGATTGTTTTTCACTATTGACAGCTACATCTTTATCTATACTAACTATCATTTTTCTTAGTTCAGCTACC
+TCAACTTCTAAATCTTTGAAAGTTCCTCTATCTATATAATTACCTTCTTGTATCTTAGACTTAATAGTTT
+CTACTTGAGAAACAAGGTTGTTTATCTCCTTATCCAACTAGAATCACCTCTAAGGTCTAACCGTTTCAGA
+TTCAGAATGGATATCATAATTTTCTAAGAAATCATTGATAATCTCCATATAATTATCCGTAACGACTTTT
+CCGTAAGATGTTTTTGTATCAATTTCAAACCTAAGCTTACCAAAACTTTGGAGGTCTAATTCTTTTATTA
+CAATATTAGGGTCATCAGAAGGAAGGTAATAATAGTCGAAGTATATAATTGAGCCATTTATTAATACTCT
+GTCTATTCTATAGACGTGGAAATAGCGTCTGTCTCTTTTAAAATGGGCTAGTGCATCTTTAAACTCTAAC
+TTAAGGATATCCTTATATTTAATCAAAGTGGTAACCTCCTTACTATTAATTTTTAAATTTACTTATTTTG

tests/test_overall.py

@@ -119,14 +119,18 @@ def test_meta(tmp_dir):
     cmd = f"pharokka.py -i {input_fasta} -d {database_dir} -o {tmp_dir} -t {threads} -f -m"
     exec_command(cmd)
 
+def test_meta(tmp_dir):
+    """test pharokka meta with prodigal-gv"""
+    input_fasta: Path = f"{meta_data}/combined_meta.fasta"
+    cmd = f"pharokka.py -i {input_fasta} -d {database_dir} -o {tmp_dir} -t {threads} -f -m -g prodigal-gv"
+    exec_command(cmd)
 
 def test_meta_dnaapler_all_bug(tmp_dir):
     """test pharokka meta dnaapler bug and split"""
     input_fasta: Path = f"{meta_data}/combined_meta.fasta"
     cmd = f"pharokka.py -i {input_fasta} -d {database_dir} -o {tmp_dir} -t {threads} -f -m -s --dnaapler --meta_hmm"
     exec_command(cmd)
 
-
 def test_overall_locus(tmp_dir):
     """test pharokka overall locus tag prefix"""
     input_fasta: Path = f"{standard_data}/SAOMS1.fasta"
@@ -189,6 +193,10 @@ def test_meta_no_cds_contig(tmp_dir):
     cmd = f"pharokka.py -i {input_fasta} -d {database_dir} -o {tmp_dir} -t {threads} -f -m"
     exec_command(cmd)
 
+######
+# pharokka CI was timing out (>6 hours)
+# These are covered by other rules anyway
+# so just run as is
 
 # def test_meta_hmm(tmp_dir):
 #     """test pharokka meta hmm"""
@@ -228,6 +236,13 @@ def test_overall_genbank_meta(tmp_dir):
 class testFails(unittest.TestCase):
     """Tests for fails"""
 
+    def test_dupe_header(self):
+        """tests that pharokka exits if a duplicate header is passed"""
+        with self.assertRaises(RuntimeError):
+            input_fasta: Path = f"{standard_data}/dupe_header.fasta"
+            cmd = f"pharokka.py -i {input_fasta} -d {database_dir} -o {temp_dir} -t 1 -f -m"
+            exec_command(cmd)
+
     def test_meta_with_single_contig(self):
         """tests that pharokka exits if single contig is passed to meta"""
         with self.assertRaises(RuntimeError):