dont use working_dir for temporary files at all

intact/intact.py

@@ -45,9 +45,9 @@ def __init__(self, name, start, end, deletion_tolerence):
         self.end = end
         self.deletion_tolerence = deletion_tolerence
 
-    def subtyped(working_dir, subtype, name, start, end, deletion_tolerence):
-        start_s = st.convert_from_hxb2_to_subtype(working_dir, start, subtype)
-        end_s = st.convert_from_hxb2_to_subtype(working_dir, end, subtype)
+    def subtyped(subtype, name, start, end, deletion_tolerence):
+        start_s = st.convert_from_hxb2_to_subtype(start, subtype)
+        end_s = st.convert_from_hxb2_to_subtype(end, subtype)
         return ExpectedORF(name, start_s, end_s, deletion_tolerence)
 
 class ReceivedORF:
@@ -618,15 +618,15 @@ def intact( working_dir,
     # convert ORF positions to appropriate subtype
     forward_orfs, reverse_orfs, small_orfs = [
     [
-        ExpectedORF.subtyped(working_dir, subtype, n, s, e, delta) \
+        ExpectedORF.subtyped(subtype, n, s, e, delta) \
         for (n, s, e, delta) in orfs
     ] \
     for orfs in [hxb2_forward_orfs, hxb2_reverse_orfs, hxb2_small_orfs]
     ]
 
     # convert PSI locus and RRE locus to appropriate subtype
-    psi_locus = [st.convert_from_hxb2_to_subtype(working_dir, x, subtype) for x in hxb2_psi_locus]
-    rre_locus = [st.convert_from_hxb2_to_subtype(working_dir, x, subtype) for x in hxb2_rre_locus]
+    psi_locus = [st.convert_from_hxb2_to_subtype(x, subtype) for x in hxb2_psi_locus]
+    rre_locus = [st.convert_from_hxb2_to_subtype(x, subtype) for x in hxb2_rre_locus]
 
     reference = st.subtype_sequence(subtype)
 
@@ -641,8 +641,8 @@ def intact( working_dir,
                                        )
 
 
-            alignment = wrappers.mafft(working_dir, [reference, sequence])  
-            reverse_alignment = wrappers.mafft(working_dir, [reference, reverse_sequence])
+            alignment = wrappers.mafft([reference, sequence])  
+            reverse_alignment = wrappers.mafft([reference, reverse_sequence])
 
             forward_score = alignment_score(alignment)
             reverse_score = alignment_score(reverse_alignment)
@@ -666,8 +666,8 @@ def intact( working_dir,
 
             hxb2_found_orfs = [ORF(
                                     o.orientation,
-                                    st.convert_from_subtype_to_hxb2(working_dir, o.start, o.orientation, subtype),
-                                    st.convert_from_subtype_to_hxb2(working_dir, o.end, o.orientation, subtype)
+                                    st.convert_from_subtype_to_hxb2(o.start, o.orientation, subtype),
+                                    st.convert_from_subtype_to_hxb2(o.end, o.orientation, subtype)
                               ) for o in sequence_orfs]
 
             if include_packaging_signal:
@@ -687,8 +687,8 @@ def intact( working_dir,
 
             if check_major_splice_donor_site:
                 mutated_splice_donor_site = has_mutated_major_splice_donor_site(alignment,
-                                                st.convert_from_hxb2_to_subtype(working_dir, hxb2_msd_site_locus, subtype),
-                                                st.convert_from_hxb2_to_subtype(working_dir, hxb2_msd_site_locus + 1, subtype),
+                                                st.convert_from_hxb2_to_subtype(hxb2_msd_site_locus, subtype),
+                                                st.convert_from_hxb2_to_subtype(hxb2_msd_site_locus + 1, subtype),
                                                 const.DEFAULT_MSD_SEQUENCE)
                 if mutated_splice_donor_site is not None:
                     sequence_errors.append(mutated_splice_donor_site)

util/subtypes.py

@@ -42,19 +42,18 @@ def subtype_sequence(subtype):
         name = alignment[0].name
         )
 
-def convert_from_hxb2_to_subtype(working_dir, position, subtype):
+def convert_from_hxb2_to_subtype(position, subtype):
     """
     Convert a position number in HXB2 to the equivalent in another subtype.
 
     Args:
-        working_dir: working folder in which to place temporary files
         position: hxb2 coordinate position to convert
         subtype: subtype position to convert to
     """
 
     sequences = [HXB2(), subtype_sequence(subtype)]
 
-    alignment = wrappers.mafft(working_dir, sequences)
+    alignment = wrappers.mafft(sequences)
 
     hxb2_pos = 0
     subtype_pos = 0
@@ -66,12 +65,11 @@ def convert_from_hxb2_to_subtype(working_dir, position, subtype):
         if alignment[1][i] != "-":
             subtype_pos += 1
 
-def convert_from_subtype_to_hxb2(working_dir, position, orientation, subtype):
+def convert_from_subtype_to_hxb2(position, orientation, subtype):
     """
     Convert a position number in HXB2 to the equivalent in another subtype.
 
     Args:
-        working_dir: working folder in which to place temporary files
         position: hxb2 coordinate position to convert
         subtype: subtype position to convert to
     """
@@ -81,7 +79,7 @@ def convert_from_subtype_to_hxb2(working_dir, position, orientation, subtype):
         sequences = [SeqRecord.SeqRecord(Seq.reverse_complement(s.seq),
                                          id = s.id, name = s.name) for s in sequences]
 
-    alignment = wrappers.mafft(working_dir, sequences)
+    alignment = wrappers.mafft(sequences)
 
     hxb2_pos = 0
     subtype_pos = 0

util/wrappers.py

@@ -5,7 +5,7 @@
 
 from Bio import SeqIO, AlignIO
 
-def mafft(working_dir, sequences):
+def mafft(sequences):
     '''
     Call mafft on a set of sequences and return the resulting alignment.