ref: update temp_dir

pachterlab · Oct 20, 2023 · d3ded6c · d3ded6c
1 parent dd970ca
commit d3ded6c
Showing 1 changed file with 19 additions and 10 deletions.
diff --git a/kb_python/ref.py b/kb_python/ref.py
@@ -242,6 +242,7 @@ def kallisto_index(
     aa: bool = False,
     distinguish: bool = False,
     max_ec_size: int = None,
+    temp_dir: str = 'tmp',
 ) -> Dict[str, str]:
     """Runs `kallisto index`.
 
@@ -279,6 +280,8 @@ def kallisto_index(
         command += ['-e', max_ec_size]
     if dlist_overhang > 1:
         command += ['--d-list-overhang', dlist_overhang]
+    if temp_dir != 'tmp':
+        command += ['-T', temp_dir]
     command += [fasta_path]
     run_executable(command)
     return {'index': index_path}
@@ -357,7 +360,7 @@ def split_and_index(
 
     built = []
     for fasta_part_path, index_part_path in zip(fastas, indices):
-        result = kallisto_index(fasta_part_path, index_part_path, k=k)
+        result = kallisto_index(fasta_part_path, index_part_path, k=k, temp_dir=temp_dir)
         built.append(result['index'])
 
     return {'indices': built}
@@ -651,6 +654,7 @@ def ref(
             aa=aa,
             make_unique=make_unique,
             max_ec_size=max_ec_size,
+            temp_dir=temp_dir,
         )
         results.update(index_result)
     else:
@@ -713,7 +717,7 @@ def ref_kite(
         index_result = split_and_index(
             kite_path, index_path, n=n, k=k or optimal_k, temp_dir=temp_dir
         ) if n > 1 else kallisto_index(
-            kite_path, index_path, k=k or optimal_k, threads=threads
+            kite_path, index_path, k=k or optimal_k, threads=threads, temp_dir=temp_dir
         )
         results.update(index_result)
     else:
@@ -781,7 +785,8 @@ def ref_custom(
             dlist_overhang=dlist_overhang,
             aa=aa,
             make_unique=make_unique,
-            distinguish=distinguish
+            distinguish=distinguish,
+            temp_dir=temp_dir
         )
         logger.info('Finished creating custom index')
         results.update(index_result)
@@ -988,7 +993,8 @@ def ref_nac(
                 dlist=dlist,
                 dlist_overhang=dlist_overhang,
                 make_unique=make_unique,
-                max_ec_size=max_ec_size
+                max_ec_size=max_ec_size,
+                temp_dir=temp_dir
             )
         elif n == 1:
             index_result = kallisto_index(
@@ -999,7 +1005,8 @@ def ref_nac(
                 dlist=dlist,
                 dlist_overhang=dlist_overhang,
                 make_unique=make_unique,
-                max_ec_size=max_ec_size
+                max_ec_size=max_ec_size,
+                temp_dir=temp_dir
             )
         else:
             cdna_index_result = kallisto_index(
@@ -1010,7 +1017,8 @@ def ref_nac(
                 dlist=dlist,
                 dlist_overhang=dlist_overhang,
                 make_unique=make_unique,
-                max_ec_size=max_ec_size
+                max_ec_size=max_ec_size,
+                temp_dir=temp_dir
             )
             if n == 2:
                 intron_index_result = kallisto_index(
@@ -1021,7 +1029,8 @@ def ref_nac(
                     dlist=dlist,
                     dlist_overhang=dlist_overhang,
                     make_unique=make_unique,
-                    max_ec_size=max_ec_size
+                    max_ec_size=max_ec_size,
+                    temp_dir=temp_dir
                 )
                 index_result = {
                     'indices': [
@@ -1213,15 +1222,15 @@ def ref_lamanno(
         # if n > 2, make n indices, one for spliced, another n - 1 for unspliced
         if n == 1:
             index_result = kallisto_index(
-                combined_path, index_path, k=k or 31, threads=threads
+                combined_path, index_path, k=k or 31, threads=threads, temp_dir=temp_dir
             )
         else:
             cdna_index_result = kallisto_index(
-                cdna_path, f'{index_path}_cdna', k=k or 31
+                cdna_path, f'{index_path}_cdna', k=k or 31, temp_dir=temp_dir
             )
             if n == 2:
                 intron_index_result = kallisto_index(
-                    intron_path, f'{index_path}_intron', k=k or 31
+                    intron_path, f'{index_path}_intron', k=k or 31, temp_dir=temp_dir
                 )
                 index_result = {
                     'indices': [