create nonexistant outbase parent directories if necessary

matsengrp · Aug 26, 2024 · 357cc61 · 357cc61
1 parent ee0bc22
commit 357cc61
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diff --git a/gctree/cli.py b/gctree/cli.py
@@ -15,6 +15,7 @@
 import random
 import ete3
 import itertools
+from pathlib import Path
 
 
 def test(args):
@@ -164,6 +165,9 @@ def isotype_add(forest):
             isotype_names=args.isotype_names,
         )
 
+    # Make parent directory of output file base string if it doesn't exist
+    Path(args.outbase).parent.mkdir(parents=True, exist_ok=True)
+
     if len(args.infiles) == 2:
         forest = bp.CollapsedForest(
             pp.parse_outfile(args.infiles[0], args.infiles[1], args.root)

diff --git a/tests/smalltest.sh b/tests/smalltest.sh
@@ -14,7 +14,7 @@ wget -O $substitutions https://bitbucket.org/kleinstein/shazam/raw/ba4b30fc6791e
 
 # testing backward compatibility:
 
-gctree infer tests/small_outfile tests/abundances.csv --outbase tests/smalltest_output/gctree.infer --root GL --frame 1 --verbose --idlabel --idmapfile tests/idmap.txt --isotype_mapfile tests/isotypemap.txt --mutability HS5F_Mutability.csv --substitution HS5F_Substitution.csv --ranking_coeffs 1 1 0 --use_old_mut_parsimony --branching_process_ranking_coeff 0 
+gctree infer tests/small_outfile tests/abundances.csv --outbase tests/smalltest_output/nonexistant_dir/gctree.infer --root GL --frame 1 --verbose --idlabel --idmapfile tests/idmap.txt --isotype_mapfile tests/isotypemap.txt --mutability HS5F_Mutability.csv --substitution HS5F_Substitution.csv --ranking_coeffs 1 1 0 --use_old_mut_parsimony --branching_process_ranking_coeff 0 
 
 gctree infer tests/smalltest_output/gctree.infer.inference.parsimony_forest.p --outbase tests/smalltest_output/gctree.infer --root GL --frame 1 --verbose --idlabel --idmapfile tests/idmap.txt --isotype_mapfile tests/isotypemap.txt --mutability HS5F_Mutability.csv --substitution HS5F_Substitution.csv --ranking_coeffs 1 -1 0 --use_old_mut_parsimony