diff --git a/__main__.py b/__main__.py
index 6b48dda4480ea7f507fd7a338112b62e3be3b302..b5d478939f3fa8803ded4d2592b38b6e3eafd127 100644
--- a/__main__.py
+++ b/__main__.py
@@ -324,7 +324,6 @@ if __name__ == "__main__":
sys.exit(0)
resistance_db = find_resistance_db(args)
- prediction_db = args.path +"/data/virulence"
if args.overwrite :
args, final_output_path = redefine_output_file(args)
@@ -335,7 +334,7 @@ if __name__ == "__main__":
except OSError :
print("Directory '%s' can not be created \n" %args.outdir)
sys.exit(0)
-
+
dict_results = {}
data_resistance = pd.DataFrame()
for genome in args.assemblies :
@@ -344,7 +343,7 @@ if __name__ == "__main__":
fasta = get_path +'/'+genome
dict_genome = get_species_results(fasta, args.path + '/data/species', str(args.threads))
-
+
if args.mlst :
cd_complex = is_cd_complex(dict_genome)
dict_genome.update(get_chromosome_mlst_results(MLST_db, fasta, cd_complex, args))
@@ -387,8 +386,8 @@ if __name__ == "__main__":
table_results = pd.DataFrame(dict_results)
table_results = table_results.T
- if len(data_resistance.index) != 0 :
- table_resistance = armfinder_to_table(data_resistance)
+ if len(data_resistance.index) != 0 :
+ table_resistance = armfinder_to_table(data_resistance, fasta)
for family in table_resistance.columns:
table_resistance[family] = table_resistance[family].apply(lambda x : ";".join(sorted(x.split(';'))))
diff --git a/module/utils.py b/module/utils.py
index 3749aaa0cc6c5620d70570f7f2e8552a147dd4b6..36de7834ffa7073d0a0b8b7a36e0d88f466a8056 100644
--- a/module/utils.py
+++ b/module/utils.py
@@ -91,29 +91,75 @@ def get_tox_results(infoTOX:tuple, contigs:str, args) -> dict:
#results.update(dict(zip(infoTOX[0], chr_st_detail)))
return results
+def is_contig_edge(data_resistance:pd.DataFrame, file:str) -> bool:
-def armfinder_to_table(data_resistance:pd.DataFrame) -> pd.DataFrame:
+ len_seq_ref = int(data_resistance['Reference sequence length'])*3
+ pos_start = int(data_resistance['Start'])
+ pos_stop = int(data_resistance['Stop'])
+ len_seq_found = pos_stop - (pos_start-1)
+
+ if len_seq_found < len_seq_ref :
+ missing_nucleotides = len_seq_ref - len_seq_found
+ over_start = (pos_start-missing_nucleotides) < 0
+ over_stop = (find_len_contig(file, data_resistance['Contig id']) - (pos_stop + missing_nucleotides)) < 0
+
+ if over_start or over_stop :
+ return True
+
+ return False
+
+
+def find_len_contig(file:str, contig :str):
+ """Finds and returns the length of a specific contig in a FASTA file.
+
+ :param file: Path to the FASTA file.
+ :param contig: Contig number.
+ :return: Length of the specified contig or None if not found.
+ """
+ with open(file, 'r') as fichier:
+ line = fichier.readline()
+ while line:
+ if line.startswith('>' + contig):
+ length = 0
+ line = fichier.readline()
+ while line and not line.startswith('>'):
+ length += len(line.strip())
+ line = fichier.readline()
+ return length
+ else:
+ line = fichier.readline()
+ return None
+
+
+def armfinder_to_table(data_resistance:pd.DataFrame, fasta:str) -> pd.DataFrame:
dico_Method = {'ALLELEX' : "",
'EXACTX' : "",
'POINTX' : "!",
'BLASTX' : "*",
'PARTIALX' : "?",
- 'PARTIAL_CONTIG_ENDX' : "?$",
+ 'PARTIAL_CONTIG_ENDX' : "?$", #The PARTIAL_CONTIG_ENDX method is only attributedd when the start or end position of the sequence being searched coincides exactly with the start or end of the contig.
'INTERNAL_STOP' : "#"}
data_resistance['Class'] = data_resistance['Class'].fillna ('NoClass')
Class = data_resistance['Class'].value_counts().keys()
Strains = data_resistance['Name'].value_counts().keys()
table = pd.DataFrame('',index=Strains, columns=Class)
- for res in data_resistance.index :
+
+ for res in data_resistance.index :
gene = data_resistance['Gene symbol'][res] + dico_Method[data_resistance['Method'][res]]
- if 'tox' in data_resistance['Gene symbol'][res] :
- if float(data_resistance['% Coverage of reference sequence'][res]) != 100.00 :
- if (data_resistance['Method'][res] == 'BLASTX') :
- gene = data_resistance['Gene symbol'][res] + "-NTTB?-"+str(round(100-float(data_resistance['% Coverage of reference sequence'][res])))+"%"
- else :
- gene = data_resistance['Gene symbol'][res] + "-NTTB" + dico_Method[data_resistance['Method'][res]]
+
+ if 'tox' in data_resistance['Gene symbol'][res] :
+ if float(data_resistance['% Coverage of reference sequence'][res]) != 100.00 :
+ if (data_resistance['Method'][res] == 'BLASTX') :
+ gene = data_resistance['Gene symbol'][res] + "-NTTB?-"+str(round(100-float(data_resistance['% Coverage of reference sequence'][res])))+"%"
+ else :
+ gene = data_resistance['Gene symbol'][res] + "-NTTB" + dico_Method[data_resistance['Method'][res]]
+
+ if is_contig_edge(data_resistance.iloc[res], fasta) : # Used to find certain cases of interruption due to a contig end that AMRfinder is unable to find.
+ gene = f"{data_resistance['Gene symbol'][res]}_end_of_contig"
+
if (data_resistance['Method'][res] == 'PARTIALX') or \
(data_resistance['Method'][res] == 'PARTIAL_CONTIG_ENDX') or \
+ ("end_of_contig" in gene) or \
(data_resistance['Method'][res] == 'INTERNAL_STOP') :
gene += "-"+str(round(100-float(data_resistance['% Coverage of reference sequence'][res])))+"%"