tips subcommand for starting mini tree workflow, unit tests

ghosttree/tips/cluster.py

@@ -0,0 +1,17 @@
+import skbio
+from skbio import BiologicalSequence
+
+
+""" takes 97_OTUs (at "species" level) and clusters them at a lower level of
+similarity using swarm.
+"""
+
+
+def preprocess_tip_sequences(species_level_otus_f):
+    for seq in skbio.read(species_level_otus_f, format="fasta"):
+        if "-" not in seq.id:
+            new_seq_id = str(seq.id) + "_1"
+        seq = BiologicalSequence(seq.sequence, id=new_seq_id)
+        yield seq
+
+# swarmdir = "/Users/jenniferfouquier/dev/ghost-tree/swarm"

ghosttree/tips/tests/test_cluster.py

@@ -0,0 +1,25 @@
+import unittest
+from StringIO import StringIO
+
+from skbio import BiologicalSequence
+
+from ghosttree.tips.cluster import preprocess_tip_sequences
+
+
+# Fix input OTU level sequence files (unnecessary characters and other
+# requirements set forth by SWARM software)
+class TestClusterTipSequences(unittest.TestCase):
+    def setUp(self):
+        self.tips_with_returns = StringIO(tips_with_returns)
+
+    def test_tip_sequences_with_returns(self):
+        result = preprocess_tip_sequences(self.tips_with_returns)
+        self.assertEqual(list(result), [BiologicalSequence("ATC",
+                                                           id="SSS456_1")])
+
+tips_with_returns = """>SSS456
+ATC
+"""
+
+if __name__ == "__main__":
+    unittest.main()

scripts/ghost-tree

@@ -6,7 +6,7 @@ import skbio
 # library code imports
 from ghosttree.silva.filter import fungi_from_fasta
 from ghosttree.util import compare_tip_to_tip_distances
-
+from ghosttree.tips.cluster import preprocess_tip_sequences
 
 @click.group()
 def cli():
@@ -43,5 +43,18 @@ def extract_fungi(fasta_file, accession_file, taxonomy_file, output_file):
     skbio.write(fungi_from_fasta(fasta_file, accession_file, taxonomy_file), into=output_file, format="fasta")
 
 
+@cli.group()
+def tips():
+    pass
+
+@tips.command("group-tips")
+@click.argument("species-level-otus-file", type=click.File("U"))
+@click.argument("fixed-species-level-otus-file", type=click.File("w"))
+def group_tips(species_level_otus_file, fixed_species_level_otus_file):
+    skbio.write(preprocess_tip_sequences(species_level_otus_file), into=fixed_species_level_otus_file, format="fasta")
+
+
+
+
 if __name__ == "__main__":
     cli()