trim2 test

tests/run_tests.sh

@@ -21,6 +21,6 @@ py.test tests/test_addLocal.py
 py.test tests/test_reconcile.py
 py.test tests/test_trim.py
 py.test tests/test_unmapped_taxa.py
-
+python tests/test_trim2.py
 
 py.test tests/test_blacklist.py

tests/test_trim2.py

@@ -0,0 +1,51 @@
+from dendropy import Tree, \
+      DnaCharacterMatrix, \
+      DataSet, \
+      datamodel
+from physcraper import wrappers, generate_ATT_from_files, AlignTreeTax, OtuJsonDict, IdDicts, ConfigObj
+import os
+import json
+
+
+
+seqaln= "tests/data/Senecioneae_ets_update/Senecioneae_ets2.fas"
+mattype="fasta"
+treefile= "tests/data/Senecioneae_ets_update/2taxon.tre"
+schema_trf = "newick"
+workdir="tests/output/test_trim2"
+configfi = "tests/data/localblast.config"
+id_to_spn = r"tests/data/Senecioneae_ets_update/nicespl.csv"
+otu_jsonfi = "{}/otu_dict.json".format(workdir)
+
+
+
+if not os.path.exists("{}".format(workdir)):
+        os.makedirs("{}".format(workdir))
+
+conf = ConfigObj(configfi, interactive=False)
+ids = IdDicts(conf, workdir=workdir)
+
+if os.path.exists(otu_jsonfi):
+    print("load json")
+    otu_json = json.load(open(otu_jsonfi))
+else:
+    otu_json = OtuJsonDict(id_to_spn, ids)
+    json.dump(otu_json, open(otu_jsonfi,"w"))
+
+
+data_obj = generate_ATT_from_files(seqaln=seqaln, 
+                                 mattype=mattype, 
+                                 workdir=workdir,
+                                 treefile=treefile,
+                                 schema_trf = schema_trf,
+                                 otu_json=otu_jsonfi,
+                                 ingroup_mrca=None)
+
+for tax, seq in data_obj.aln.items():
+	len_start = len(seq)
+	next
+data_obj.trim()
+for tax, seq in data_obj.aln.items():
+	len_end = len(seq)
+
+assert len_start != len_end