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Merge pull request #241 from zclaas/master
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Add antibiotics to text output
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@raphenya
raphenya authored Aug 23, 2023
2 parents 0c1b588 + a2e7e15 commit 52eeb43
Showing 1 changed file with 39 additions and 34 deletions.
73 changes: 39 additions & 34 deletions app/ConvertRGIJsonToTSV.py
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Original file line number Diff line number Diff line change
Expand Up @@ -62,32 +62,33 @@ def run(self):
with open(os.path.join(f_path, "{}.txt".format(os.path.splitext(f_name)[0])), "w") as af:
writer = csv.writer(af, delimiter='\t', dialect='excel')
writer.writerow(["ORF_ID",
"Contig",
"Start",
"Stop",
"Orientation",
"Cut_Off",
"Pass_Bitscore",
"Best_Hit_Bitscore",
"Best_Hit_ARO",
"Best_Identities",
"ARO",
"Model_type",
"SNPs_in_Best_Hit_ARO",
"Contig",
"Start",
"Stop",
"Orientation",
"Cut_Off",
"Pass_Bitscore",
"Best_Hit_Bitscore",
"Best_Hit_ARO",
"Best_Identities",
"ARO",
"Model_type",
"SNPs_in_Best_Hit_ARO",
"Other_SNPs",
"Drug Class",
"Resistance Mechanism",
"AMR Gene Family",
"Predicted_DNA",
"Predicted_Protein",
"CARD_Protein_Sequence",
"Percentage Length of Reference Sequence",
"ID",
"Model_ID",
"Drug Class",
"Resistance Mechanism",
"AMR Gene Family",
"Predicted_DNA",
"Predicted_Protein",
"CARD_Protein_Sequence",
"Percentage Length of Reference Sequence",
"ID",
"Model_ID",
"Nudged",
"Note",
"Hit_Start",
"Hit_End"])
"Hit_End",
"Antibiotic"])

if os.path.isfile(self.filepath):
with open(self.filepath) as rgi_file:
Expand Down Expand Up @@ -238,16 +239,16 @@ def run(self):
rgi_data[hsp][ordered[0]]["bit_score"],
rgi_data[hsp][ordered[0]]["ARO_name"],
rgi_data[hsp][ordered[0]]["perc_identity"],
rgi_data[hsp][ordered[0]]["ARO_accession"],
rgi_data[hsp][ordered[0]]["ARO_accession"],
rgi_data[hsp][ordered[0]]["model_type"],
best_snps,
other_snps,
"; ".join(rgi_data[hsp][ordered[0]]["ARO_category"][x]["category_aro_name"] for x in rgi_data[hsp][ordered[0]]["ARO_category"] \
if rgi_data[hsp][ordered[0]]["ARO_category"][x]["category_aro_class_name"] == 'Drug Class'),
"; ".join(rgi_data[hsp][ordered[0]]["ARO_category"][x]["category_aro_name"] for x in rgi_data[hsp][ordered[0]]["ARO_category"] \
if rgi_data[hsp][ordered[0]]["ARO_category"][x]["category_aro_class_name"] == 'Resistance Mechanism'),
"; ".join(rgi_data[hsp][ordered[0]]["ARO_category"][x]["category_aro_name"] for x in rgi_data[hsp][ordered[0]]["ARO_category"] \
if rgi_data[hsp][ordered[0]]["ARO_category"][x]["category_aro_class_name"] == 'AMR Gene Family'),
"; ".join(rgi_data[hsp][ordered[0]]["ARO_category"][x]["category_aro_name"] for x in rgi_data[hsp][ordered[0]]["ARO_category"] \
if rgi_data[hsp][ordered[0]]["ARO_category"][x]["category_aro_class_name"] == 'Resistance Mechanism'),
"; ".join(rgi_data[hsp][ordered[0]]["ARO_category"][x]["category_aro_name"] for x in rgi_data[hsp][ordered[0]]["ARO_category"] \
if rgi_data[hsp][ordered[0]]["ARO_category"][x]["category_aro_class_name"] == 'AMR Gene Family'),
orf_dna,
orf_prot,
rgi_data[hsp][ordered[0]]["sequence_from_broadstreet"],
Expand All @@ -258,7 +259,9 @@ def run(self):
nudged,
note,
rgi_data[hsp][ordered[0]]["hit_start"],
rgi_data[hsp][ordered[0]]["hit_end"]
rgi_data[hsp][ordered[0]]["hit_end"],
"; ".join(rgi_data[hsp][ordered[0]]["ARO_category"][x]["category_aro_name"] for x in rgi_data[hsp][ordered[0]]["ARO_category"] \
if rgi_data[hsp][ordered[0]]["ARO_category"][x]["category_aro_class_name"] == 'Antibiotic')
]
for key, value in match_dict.items():
writer.writerow(value)
Expand Down Expand Up @@ -302,16 +305,16 @@ def run(self):
rgi_data[hsp][ordered[0]]["bit_score"],
rgi_data[hsp][ordered[0]]["ARO_name"],
rgi_data[hsp][ordered[0]]["perc_identity"],
rgi_data[hsp][ordered[0]]["ARO_accession"],
rgi_data[hsp][ordered[0]]["ARO_accession"],
rgi_data[hsp][ordered[0]]["model_type"],
best_snps,
other_snps,
"; ".join(rgi_data[hsp][ordered[0]]["ARO_category"][x]["category_aro_name"] for x in rgi_data[hsp][ordered[0]]["ARO_category"] \
if rgi_data[hsp][ordered[0]]["ARO_category"][x]["category_aro_class_name"] == 'Drug Class'),
"; ".join(rgi_data[hsp][ordered[0]]["ARO_category"][x]["category_aro_name"] for x in rgi_data[hsp][ordered[0]]["ARO_category"] \
if rgi_data[hsp][ordered[0]]["ARO_category"][x]["category_aro_class_name"] == 'Resistance Mechanism'),
"; ".join(rgi_data[hsp][ordered[0]]["ARO_category"][x]["category_aro_name"] for x in rgi_data[hsp][ordered[0]]["ARO_category"] \
if rgi_data[hsp][ordered[0]]["ARO_category"][x]["category_aro_class_name"] == 'AMR Gene Family'),
"; ".join(rgi_data[hsp][ordered[0]]["ARO_category"][x]["category_aro_name"] for x in rgi_data[hsp][ordered[0]]["ARO_category"] \
if rgi_data[hsp][ordered[0]]["ARO_category"][x]["category_aro_class_name"] == 'Resistance Mechanism'),
"; ".join(rgi_data[hsp][ordered[0]]["ARO_category"][x]["category_aro_name"] for x in rgi_data[hsp][ordered[0]]["ARO_category"] \
if rgi_data[hsp][ordered[0]]["ARO_category"][x]["category_aro_class_name"] == 'AMR Gene Family'),
"",
rgi_data[hsp][ordered[0]]["orf_prot_sequence"],
rgi_data[hsp][ordered[0]]["sequence_from_broadstreet"],
Expand All @@ -321,7 +324,9 @@ def run(self):
nudged,
note,
rgi_data[hsp][ordered[0]]["hit_start"],
rgi_data[hsp][ordered[0]]["hit_end"]
rgi_data[hsp][ordered[0]]["hit_end"],
"; ".join(rgi_data[hsp][ordered[0]]["ARO_category"][x]["category_aro_name"] for x in rgi_data[hsp][ordered[0]]["ARO_category"] \
if rgi_data[hsp][ordered[0]]["ARO_category"][x]["category_aro_class_name"] == 'Antibiotic'),
]

for key, value in match_dict.items():
Expand Down

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