cleanup after solo_ltr and trf; correct solo_ltr numbering

nested/core/solo_ltrs.py

@@ -41,6 +41,7 @@ class SoloLtrs(object):
     
     def create_ltr_multifasta(self, tes, seq):
         offset = len(self.ltr_lengths.keys())
+        num = 1
         with open("{}_ltrs.fa".format(self.seqId), 'a+') as file:
             for i in range(len(self.ltr_lengths.keys()), len(self.ltr_lengths.keys()) + len(tes)):
                 if (intervals.length(tes[i - offset].ltr_left_location) < 100
@@ -48,9 +49,10 @@ class SoloLtrs(object):
                     or math.isnan(tes[i - offset].tsr_right[0])):
                     continue
                 
-                file.write(">ltr_" + str(i) + "\n") 
+                file.write(">ltr_" + str(num) + "\n") 
                 file.write(str(seq[tes[i - offset].ltr_left_location[0]:tes[i - offset].ltr_left_location[1] + 1]) + "\n")
                 self.ltr_lengths["ltr_" + str(i)] = len(str(seq[tes[i - offset].ltr_left_location[0]:tes[i - offset].ltr_left_location[1] + 1]))
+                num += 1
     
     def run_blastn(self):
         args = dict(config['blastx']['args'])
@@ -114,6 +116,7 @@ class SoloLtrs(object):
         result.difference(intersections.keys())
         result.add(real_best)
 
+    # refactor this
     def cleanup(self):
         if os.path.isfile("{}.nhr".format(self.ltrs_fasta_path)):
             os.remove("{}.nhr".format(self.ltrs_fasta_path))
@@ -121,4 +124,13 @@ class SoloLtrs(object):
             os.remove("{}.nin".format(self.ltrs_fasta_path))
         if os.path.isfile("{}.nsq".format(self.ltrs_fasta_path)):
             os.remove("{}.nsq".format(self.ltrs_fasta_path))
+        if os.path.isfile("{}.ndb".format(self.ltrs_fasta_path)):
+            os.remove("{}.ndb".format(self.ltrs_fasta_path))
+        if os.path.isfile("{}.not".format(self.ltrs_fasta_path)):
+            os.remove("{}.not".format(self.ltrs_fasta_path))
+        if os.path.isfile("{}.ntf".format(self.ltrs_fasta_path)):
+            os.remove("{}.ntf".format(self.ltrs_fasta_path))
+        if os.path.isfile("{}.nto".format(self.ltrs_fasta_path)):
+            os.remove("{}.nto".format(self.ltrs_fasta_path))
+        
             

nested/core/tandem_repeat.py

@@ -74,6 +74,9 @@ def get_candidates(seqid):
             split = entry.split(' ')
             candidates.append(TandemRepeat([int(split[0]), int(split[1])], int(split[2]), float(split[3]),
                     int(split[5]), int(split[6]), int(split[7]), float(split[12]), split[-1]))
+
+    cleanup()
+    
     return candidates
 
 def filter_candidates(candidates):
@@ -101,5 +104,11 @@ def filter_candidates(candidates):
             repeats.append(candidate)
     return repeats
 
+def cleanup():
+    if os.path.isfile("{}.fa.2.5.7.80.10.50.2000.dat".format(seqid)):
+        os.remove("{}.fa.2.5.7.80.10.50.2000.dat".format(seqid))
+    if os.path.isfile("{}.fa.2.5.7.80.10.50.2000.mask".format(seqid)):
+        os.remove("{}.fa.2.5.7.80.10.50.2000.mask".format(seqid))
+