Merge 9118da7 into 0bceac4

q2_shogun/_formats.py

@@ -6,6 +6,8 @@
 # The full license is in the file LICENSE, distributed with this software.
 # ----------------------------------------------------------------------------
 
+import itertools
+
 from qiime2.plugin import model
 
 
@@ -20,13 +22,24 @@ def _validate_(self, level):
 
 
 class Bowtie2IndexDirFmt(model.DirectoryFormat):
-    idx1 = model.File(r'.+(?<!\.rev)\.1\.bt2', format=Bowtie2IndexFileFormat)
-    idx2 = model.File(r'.+(?<!\.rev)\.2\.bt2', format=Bowtie2IndexFileFormat)
-    ref3 = model.File(r'.+\.3\.bt2', format=Bowtie2IndexFileFormat)
-    ref4 = model.File(r'.+\.4\.bt2', format=Bowtie2IndexFileFormat)
-    rev1 = model.File(r'.+\.rev\.1\.bt2', format=Bowtie2IndexFileFormat)
-    rev2 = model.File(r'.+\.rev\.2\.bt2', format=Bowtie2IndexFileFormat)
-
-    def get_name(self):
-        filename = str(self.idx1.path_maker().relative_to(self.path))
-        return filename.rsplit('.1.bt2')[0]
+    idx1 = model.File(r'.+(?<!\.rev)\.1\.bt2l?', format=Bowtie2IndexFileFormat)
+    idx2 = model.File(r'.+(?<!\.rev)\.2\.bt2l?', format=Bowtie2IndexFileFormat)
+    ref3 = model.File(r'.+\.3\.bt2l?', format=Bowtie2IndexFileFormat)
+    ref4 = model.File(r'.+\.4\.bt2l?', format=Bowtie2IndexFileFormat)
+    rev1 = model.File(r'.+\.rev\.1\.bt2l?', format=Bowtie2IndexFileFormat)
+    rev2 = model.File(r'.+\.rev\.2\.bt2l?', format=Bowtie2IndexFileFormat)
+
+    def get_basename(self):
+        paths = [str(x.relative_to(self.path)) for x in self.path.iterdir()]
+        prefix = _get_prefix(paths)
+        return prefix[:-1]  # trim trailing '.'
+
+
+# SO: https://stackoverflow.com/a/6718380/579416
+def _get_prefix(strings):
+    def all_same(x):
+        return all(x[0] == y for y in x)
+
+    char_tuples = zip(*strings)
+    prefix_tuples = itertools.takewhile(all_same, char_tuples)
+    return ''.join(x[0] for x in prefix_tuples)

q2_shogun/_shogun.py

@@ -38,13 +38,12 @@ def setup_database_dir(tmpdir, database, refseqs, reftaxa):
     reftaxa.to_csv(os.path.join(tmpdir, 'taxa.tsv'), sep='\t')
     shutil.copytree(str(database), os.path.join(tmpdir, BOWTIE_PATH),
                     copy_function=duplicate)
-    #        'bowtie2': os.path.join(BOWTIE_PATH, database.get_name())
     params = {
         'general': {
             'taxonomy': 'taxa.tsv',
             'fasta': 'refseqs.fna'
         },
-        'bowtie2': os.path.join(BOWTIE_PATH, 'genomes.small')
+        'bowtie2': os.path.join(BOWTIE_PATH, database.get_basename())
     }
     with open(os.path.join(tmpdir, 'metadata.yaml'), 'w') as fh:
         yaml.dump(params, fh, default_flow_style=False)
@@ -87,7 +86,6 @@ def minipipe(query: DNAFASTAFormat, reference_reads: DNAFASTAFormat,
              threads: int = 1, percent_id: float = 0.98) -> (
                      biom.Table, biom.Table, biom.Table, biom.Table):
     with tempfile.TemporaryDirectory() as tmpdir:
-        # database_dir = tmpdir.name
         setup_database_dir(tmpdir,
                            database, reference_reads, reference_taxonomy)