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,
study_id=study_id,
tree_id=tree_id,
phylesystem_loc=conf.phylesystem_loc)
# physcraper.debug(len(data_obj.aln.taxon_namespace))
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)
def test_unmapped():
conf = physcraper.ConfigObj(configfi, interactive=False)
conf.unmapped = 'remove'
data_obj = pickle.load(
open("tests/data/precooked/otol_tiny_dataobj.p", 'rb'))
data_obj.workdir = absworkdir
ids = physcraper.IdDicts(conf, workdir=data_obj.workdir)
scraper2 = physcraper.PhyscraperScrape(data_obj, ids)
num_remove = len(scraper2.data.aln.taxon_namespace)
dict_id = 0
for tax in scraper.data.aln.taxon_namespace:
if '^ot:ottId' in scraper.data.otu_dict[tax.label]:
dict_id = dict_id + 1
# print(num_remove, num_keep, dict_id)
assert num_remove <= num_keep - 1
assert num_keep == dict_id
print "1. {}".format(conf.email)
aln = DnaCharacterMatrix.get(path=seqaln, schema=mattype)
data_obj = physcraper.generate_ATT_from_phylesystem(aln=aln,
workdir=workdir,
study_id = study_id,
tree_id = tree_id,
phylesystem_loc = conf.phylesystem_loc)
ids = physcraper.IdDicts(conf, workdir=workdir)
print "3. {}".format(ids.config.email)
data_obj.prune_short()
assert len(data_obj.aln) == 9
data_obj.write_files()
try:
scraper = physcraper.PhyscraperScrape(data_obj, ids)
scraper.run_blast_wrapper()
scraper.read_blast_wrapper()
scraper.remove_identical_seqs()
scraper.generate_streamed_alignment()
sys.stdout.write("\nTest opentree_scrape.py (round 1) passed\n")
except:
sys.stdout.write("\nTest opentree_scrape.py (round 1) FAILED'\n")