study was deleted

McTavishLab · Nov 13, 2019 · 57370eb · 57370eb
1 parent 7ee8afd
commit 57370eb
Showing 1 changed file with 26 additions and 46 deletions.
diff --git a/tests/test_unmapped_taxa.py b/tests/test_unmapped_taxa.py
@@ -5,7 +5,7 @@
 from dendropy import DnaCharacterMatrix
 
 #Use OpenTree phylesystem identifiers to get study and tree
-study_id = "ot_350"
+study_id = "pg_873"
 tree_id = "tree1679"
 seqaln = "tests/data/minitest.fas"
 mattype = "fasta"
@@ -15,52 +15,32 @@
 configfi = "tests/data/test.config"
 
 def test_0():
-    if os.path.isfile("tests/data/precooked/otol_scraper.p"):
-        # physcraper.debug(os.getcwd())
-        conf = physcraper.ConfigObj(configfi, interactive=False)
-        # physcraper.debug("conf")
-        conf.unmapped = 'keep'
-        # physcraper.debug("set unmapped")
-        data_obj = pickle.load(open("tests/data/precooked/otol_tiny_dataobj.p", 'rb'))
-        data_obj.workdir = absworkdir
-        # physcraper.debug("dataobj loaded")
-        ids = physcraper.IdDicts(conf, workdir=data_obj.workdir)
-        ids.acc_ncbi_dict = pickle.load(open("tests/data/precooked/otol_tiny_gi_map.p", "rb"))
-        # physcraper.debug("ids loaded")
-        scraper = pickle.load(open("tests/data/precooked/otol_scraper.p", "rb"))
-        # physcraper.debug("scraper loaded")
-        # scraper2 = pickle.load(open("tests/data/precooked/otol_scraper.p", "rb"))
-        num_keep = len(scraper.data.aln.taxon_namespace)
-        # physcraper.debug('num_keep')
-
-        # physcraper.debug(num_keep)
-    # except:
-    else:
-        sys.stdout.write("\n\n No files present\n\n")
-        conf = physcraper.ConfigObj(configfi)
-        conf.unmapped = 'keep'
-        aln = DnaCharacterMatrix.get(path=seqaln, schema=mattype)
-        data_obj = physcraper.generate_ATT_from_phylesystem(aln=aln,
-                                    workdir=workdir,
-                                    config_obj=conf,
-                                    study_id = study_id,
-                                    tree_id = tree_id,
-                                    phylesystem_loc = conf.phylesystem_loc)
-        # physcraper.debug(len(data_obj.aln.taxon_namespace))
-        data_obj.workdir = absworkdir
+
+    sys.stdout.write("\n\n No files present\n\n")
+    conf = physcraper.ConfigObj(configfi)
+    conf.unmapped = 'keep'
+    aln = DnaCharacterMatrix.get(path=seqaln, schema=mattype)
+    data_obj = physcraper.generate_ATT_from_phylesystem(aln=aln,
+                                workdir=workdir,
+                                config_obj=conf,
+                                study_id = study_id,
+                                tree_id = tree_id,
+                                phylesystem_loc = conf.phylesystem_loc)
+    # physcraper.debug(len(data_obj.aln.taxon_namespace))
+    data_obj.workdir = absworkdir
 
-        pickle.dump(data_obj, open("tests/data/precooked/otol_tiny_dataobj.p", "wb" ))
-        ids =  physcraper.IdDicts(conf, workdir=workdir)
-        # physcraper.debug(os.getcwd())
-        pickle.dump(ids.acc_ncbi_dict, open("tests/data/precooked/otol_tiny_gi_map.p", "wb"))
-        data_obj.write_files()
-        scraper = physcraper.PhyscraperScrape(data_obj, ids)
-        # physcraper.debug(len(scraper.data.aln.taxon_namespace))
-        # physcraper.debug("scraper obj made")
-        pickle.dump(scraper.config, open("tests/data/precooked/otol_conf.p", "wb"))
-        pickle.dump(scraper, open("tests/data/precooked/otol_scraper.p", "wb"))
-        num_keep = len(scraper.data.aln.taxon_namespace)
-        # physcraper.debug(num_keep)
+    pickle.dump(data_obj, open("tests/data/precooked/otol_tiny_dataobj.p", "wb" ))
+    ids =  physcraper.IdDicts(conf, workdir=workdir)
+    # physcraper.debug(os.getcwd())
+    pickle.dump(ids.acc_ncbi_dict, open("tests/data/precooked/otol_tiny_gi_map.p", "wb"))
+    data_obj.write_files()
+    scraper = physcraper.PhyscraperScrape(data_obj, ids)
+    # physcraper.debug(len(scraper.data.aln.taxon_namespace))
+    # physcraper.debug("scraper obj made")
+    pickle.dump(scraper.config, open("tests/data/precooked/otol_conf.p", "wb"))
+    pickle.dump(scraper, open("tests/data/precooked/otol_scraper.p", "wb"))
+    num_keep = len(scraper.data.aln.taxon_namespace)
+    # physcraper.debug(num_keep)