kleborate 3.2.2__tar.gz → 3.2.3__tar.gz

{kleborate-3.2.2 → kleborate-3.2.3}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: kleborate
-Version: 3.2.2
+Version: 3.2.3
 Summary: Kleborate: a tool for typing and screening pathogen genome assemblies
 Author-email: Mary Maranga <gathonimaranga@gmail.com>, Ryan Wick <rrwick@gmail.com>, Kathryn Holt <kat.holt@lshtm.ac.uk>
 License:                     GNU GENERAL PUBLIC LICENSE

{kleborate-3.2.2 → kleborate-3.2.3}/kleborate/__main__.py

@@ -603,18 +603,12 @@ def output_results_klebsiella_pneumo_complex_hAMRonization(full_headers, stdout_
     # Rename strain to Input_file_name
     input_file_name = results['strain']
 
-    res_headers = [
-        'AGly_acquired', 'Col_acquired', 'Fcyn_acquired', 'Flq_acquired', 'Gly_acquired',
-        'MLS_acquired', 'Phe_acquired', 'Rif_acquired', 'Sul_acquired', 'Tet_acquired',
-        'Tgc_acquired', 'Tmt_acquired', 'Bla_acquired', 'Bla_inhR_acquired',
-        'Bla_ESBL_acquired', 'Bla_ESBL_inhR_acquired', 'Bla_Carb_acquired', 'Bla_chr', 'truncated_resistance_hits',
-        'spurious_resistance_hits'
-    ]
-
     mutation_variant_headers = [
         'SHV_mutations', 'Omp_mutations', 'Col_mutations', 'Flq_mutations'
     ]
 
+    acquired_res_headers = [h for h in res_headers if h not in mutation_variant_headers]
+
     prefix = 'klebsiella_pneumo_complex__amr__'
 
     def clean(val):
@@ -636,13 +630,14 @@ def output_results_klebsiella_pneumo_complex_hAMRonization(full_headers, stdout_
 
     rows = []
 
-    software_name = results.get('Software_name', ['Kleborate'])[0]
-    software_version = results.get('Software_version', ['3.1.3'])[0]
-    db_name = results.get('Reference_database_name', ['CARD'])[0]
-    db_version = results.get('Reference_database_version', ['3.2.9'])[0]
+    software_name = results['klebsiella_pneumo_complex__amr__Software_name']
+    software_version = results['klebsiella_pneumo_complex__amr__Software_version']
+    db_name = results['klebsiella_pneumo_complex__amr__Reference_database_name']
+    db_version = results['klebsiella_pneumo_complex__amr__Reference_database_version']
+
 
     # ----- ACQUIRED GENES -----
-    for header in res_headers:
+    for header in acquired_res_headers:
         key = prefix + header
         variants = parsed.get(key, [])
         for variant in variants:
@@ -756,7 +751,7 @@ def output_results_klebsiella_pneumo_complex_hAMRonization(full_headers, stdout_
         if f.tell() == 0:
             f.write('\t'.join(headers) + '\n')
         for row in rows:
-            f.write('\t'.join([str(row.get(h, '-')) for h in headers]) + '\n')
+            f.write('\t'.join([str(row.get(h, '-')).strip("[]").replace("'", "") for h in headers]) + '\n')
 
 
 def output_results(full_headers, stdout_headers, outfile, results, trim_headers=False):
@@ -766,7 +761,8 @@ def output_results(full_headers, stdout_headers, outfile, results, trim_headers=
     """
     # Print results to the terminal using stdout_headers
     print('\t'.join([
-        str(results.get(x, "-")).strip("[]'\"") if not isinstance(results.get(x, "-"), list) 
+        str(results.get(x, "-")).strip("'\"") if not isinstance(results.get(x, "-"), list)
+        # str(results.get(x, "-")).strip("[]'\"") if not isinstance(results.get(x, "-"), list) 
         else ";".join(map(str, results.get(x, "-")))
         for x in stdout_headers
     ]))
@@ -781,7 +777,8 @@ def output_results(full_headers, stdout_headers, outfile, results, trim_headers=
         if o.tell() == 0:  # Write headers if file is empty
             o.write('\t'.join(headers_to_write) + '\n')
         o.write('\t'.join([
-            str(results.get(x, "-")).strip("[]'\"") if not isinstance(results.get(x, "-"), list) 
+            str(results.get(x, "-")).strip("'\"") if not isinstance(results.get(x, "-"), list)
+            # str(results.get(x, "-")).strip("[]'\"") if not isinstance(results.get(x, "-"), list) 
             else ";".join(map(str, results.get(x, "-")))
             for x in full_headers
         ]) + '\n')

{kleborate-3.2.2 → kleborate-3.2.3}/kleborate/modules/klebsiella_pneumo_complex__amr/klebsiella_pneumo_complex__amr.py

@@ -20,6 +20,7 @@ from pathlib import Path
 import csv
 import re
 
+from kleborate.__main__ import get_version
 from ...shared.resMinimap import read_class_file, get_res_headers, resminimap_assembly
 
 
@@ -181,7 +182,8 @@ def get_results(assembly, minimap2_index, args, previous_results):
     )
 
     # --- report in aac(6`)-Ib-cr* allele in both AGly_acquired and Flq_acquired---
-    aac6_pattern = re.compile(r"aac\(6[’']\)-Ib-cr", re.IGNORECASE)
+    aac6_pattern = re.compile(r"aac\(6[’']\)-Ib-cr[\w\.]*", re.IGNORECASE)
+    # aac6_pattern = re.compile(r"aac\(6[’']\)-Ib-cr", re.IGNORECASE)
     agly_hits = res_hits.get('AGly_acquired', [])
     flq_hits = res_hits['Flq_acquired']
 
@@ -197,7 +199,7 @@ def get_results(assembly, minimap2_index, args, previous_results):
 
     # --- software and database metadata ---
     res_hits['Software_name'] = 'Kleborate'
-    res_hits['Software_version'] = '3.1.3'
+    res_hits['Software_version'] = get_version()
     res_hits['Reference_database_name'] = 'CARD'
     res_hits['Reference_database_version'] = '3.2.9'
 

{kleborate-3.2.2 → kleborate-3.2.3}/kleborate/shared/alignment.py

@@ -350,5 +350,32 @@ def get_last_base_aa_before_gap(alignment):
             break
         ref_pos += 1
 
+
+    # Handle frameshift where the alignment starts with gaps in the query.
+    if last_base_pos is None: return (1, next((res for res in aligned_seq2 if res != '-'), None))
+
     return last_base_pos, last_base
+    
+
+# def get_last_base_aa_before_gap(alignment):
+#     aligned_seq1, aligned_seq2 = alignment[0], alignment[1]
+#     bases_per_ref_pos = {}
+#     ref_pos = 1
+#     last_base_pos = None
+#     last_base = None
+
+#     for i, ref_b in enumerate(aligned_seq1):
+#         if ref_b == '-' or ref_b == '.':
+#             continue
+#         assembly_b = aligned_seq2[i]
+#         bases_per_ref_pos[ref_pos] = assembly_b
+#         if assembly_b != '-':
+#             last_base_pos = ref_pos
+#             last_base = assembly_b
+#         else:
+#             # First occurrence of a gap at this position
+#             break
+#         ref_pos += 1
+
+#     return last_base_pos, last_base
 

{kleborate-3.2.2 → kleborate-3.2.3}/kleborate.egg-info/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: kleborate
-Version: 3.2.2
+Version: 3.2.3
 Summary: Kleborate: a tool for typing and screening pathogen genome assemblies
 Author-email: Mary Maranga <gathonimaranga@gmail.com>, Ryan Wick <rrwick@gmail.com>, Kathryn Holt <kat.holt@lshtm.ac.uk>
 License:                     GNU GENERAL PUBLIC LICENSE

{kleborate-3.2.2 → kleborate-3.2.3}/pyproject.toml

@@ -4,7 +4,7 @@ build-backend = "setuptools.build_meta"
 
 [project]
 name = "kleborate"
-version = "3.2.2"
+version = "3.2.3"
 description = "Kleborate: a tool for typing and screening pathogen genome assemblies"
 readme = "README.md"
 requires-python = ">=3.9"