fixed paths

pfaster.py

@@ -4,20 +4,23 @@
 12 September 2022
 '''
 
+from pathlib import Path
+
 from predict import Mash, call_features, threshold, model_predict
 from tools import cmd_parser
 from tools import exporters as exp
 
 
 def screen_fasta(fasta, db = 'sketch_k70.pkl'):
-    screener = Mash.MashScreen('ref/sketch/{}'.format(db))
+    db_path = Path(__file__).parent / "ref/sketch" / db
+    screener = Mash.MashScreen(db_path)
     screener.screen(fasta)
     matches = screener.ref_counts
     return list(matches.values())
 
 def run_model(mash_results, model = 'model.rfm'):
-    model = 'model/{}'.format(model)
-    st = model_predict.RFClassify(mash_results, model).serotype
+    model_path = Path(__file__).parent / "model" / model
+    st = model_predict.RFClassify(mash_results, model_path).serotype
     return st # tuple - serotype, probability
 
 def call_serotype(fasta, outdir):
@@ -43,9 +46,8 @@ def call_serotype(fasta, outdir):
             prediction[3] = prediction[3] + feature_check.flag
         prediction[1] = pred_sero
         prediction[2] = prob
-    except:
-        prediction = [fasta, 'not typed', 'N/A', 'failed to predict serotype']
-        return prediction
+    except Exception as e:
+        raise RuntimeError("calling serotype") from e
     #probability thresholding
     high_confidence = threshold.ThresholdCall(prediction[1], prediction[2]).valid
     if not high_confidence:

predict/call_features.py

@@ -5,6 +5,7 @@
 '''
 
 import os
+from pathlib import Path
 import re
 import xml.etree.ElementTree as ET
 
@@ -22,7 +23,7 @@ def __init__(self, fasta, serogroup):
 
     # run blast search for causal gene
     def blast(self):
-        ref = 'ref/blast/causal_genes.fasta'
+        ref = Path(__file__).parent.parent / 'ref/blast/causal_genes.fasta'
         self.blst = self.fasta.split('.f')[0] + '_blast.xml'
         cmd = 'blastn -db {0} -query {1} -out {2} -outfmt 5'.format(ref, self.fasta, self.blst)
         os.system(cmd)

predict/threshold.py

@@ -5,13 +5,14 @@
 '''
 
 import csv
+from pathlib import Path
 
 class ThresholdCall:
 
     def __init__(self, serotype, prob):
         self.serotype = serotype
         self.prob = float(prob)
-        self.threshold_file = 'ref/threshold/prob_thresholds.csv'
+        self.threshold_file = Path(__file__).parent.parent / "ref/threshold/prob_thresholds.csv"
         self.thresholds = None
         self.valid = True
         self.run_check()