def test_sp_seq_d():
absworkdir = os.path.abspath(workdir)
conf = ConfigObj(configfi, interactive=False)
data_obj = pickle.load(open("tests/data/precooked/tiny_dataobj.p", 'rb'))
data_obj.workdir = absworkdir
ids = IdDicts(conf, workdir=data_obj.workdir)
ids.acc_ncbi_dict = pickle.load(
open("tests/data/precooked/tiny_acc_map.p", "rb"))
filteredScrape = PhyscraperScrape(data_obj, ids)
filteredScrape._blasted = 1
blast_dir = "tests/data/precooked/fixed/tte_blast_files"
# filteredScrape.acc_list_mrca = pickle.load(open("tests/data/precooked/acc_list_mrca.p", 'rb'))
filteredScrape.read_blast_wrapper(blast_dir=blast_dir)
filteredScrape.remove_identical_seqs()
filteredScrape.sp_dict(downtorank)
filteredScrape.seq_filter = [
'deleted', 'subsequence,', 'not', "removed", "deleted,"
]
gi_sp_d = []
sp_d = filteredScrape.make_sp_dict()
for key in sp_d:
v = sp_d[key]
for v2 in v:
v2 = filteredScrape.data.otu_dict[v2]
if '^physcraper:status' in v2:
not_added = ['deleted', 'subsequence,', 'not']
if v2['^physcraper:status'].split(' ')[0] not in not_added:
if '^ncbi:gi' in v2:
gi_sp_d.append(v2['^ncbi:accession'])
user_sp_d = []
for v in filteredScrape.sp_d.values():
for v2 in v:
v2 = filteredScrape.data.otu_dict[v2]
if '^physcraper:status' in v2 or u'^physcraper:status' in v2:
if v2['^physcraper:status'].split(
' ')[0] not in filteredScrape.seq_filter:
if v2['^physcraper:last_blasted'] != '1800/01/01':
if '^user:TaxonName' in v2:
user_sp_d.append(v2['^user:TaxonName'])
elif '^ot:ottTaxonName' in v2:
user_sp_d.append(v2['^ot:ottTaxonName'])
filteredScrape.make_sp_seq_dict()
gi_sp_seq_d = []
ott_sp_seq_d = []
for v in filteredScrape.sp_seq_d.values():
for k in v.keys():
# print(k)
if len(k.split('.')) >= 2:
# if type(k) == int:
gi_sp_seq_d.append(k)
else:
# if type(k) == str or type(k) == unicode:
ott_sp_seq_d.append(k)
# print(len(ott_sp_seq_d), len(user_sp_d), len(gi_sp_seq_d), len(gi_sp_d))
assert len(ott_sp_seq_d) == len(user_sp_d)
assert len(gi_sp_seq_d) == len(gi_sp_d)
def test_read_local_blast():
conf = physcraper.ConfigObj(configfi, interactive=False)
data_obj = pickle.load(open("tests/data/precooked/tiny_dataobj.p", 'rb'))
data_obj.workdir = absworkdir
ids = physcraper.IdDicts(conf, workdir=data_obj.workdir)
ids.acc_ncbi_dict = pickle.load(
open("tests/data/precooked/tiny_acc_map.p", "rb"))
filteredScrape = PhyscraperScrape(data_obj, ids)
filteredScrape._blasted = 1
blast_dir = "tests/data/precooked/fixed/tte_blast_files"
# filteredScrape.acc_list_mrca = pickle.load(open("tests/data/precooked/acc_list_mrca.p", 'rb'))
filteredScrape.read_blast_wrapper(blast_dir=blast_dir)
filteredScrape.remove_identical_seqs()
filteredScrape.sp_dict(downtorank)
filteredScrape.make_sp_seq_dict()
# print("prepare test")
for taxonID in filteredScrape.sp_d:
if len(filteredScrape.sp_seq_d[taxonID]) > treshold:
# print(taxonID)
blast_seq = filteredScrape.sp_seq_d[taxonID].keys()[0]
seq = filteredScrape.sp_seq_d[taxonID][blast_seq]
local_blast.write_filterblast_query(filteredScrape.workdir,
taxonID,
seq,
fn=str(taxonID))
# print(filteredScrape.sp_seq_d[taxonID].keys()[1:] )
blast_db = [
item for item in filteredScrape.sp_seq_d[taxonID].keys()[1:]
if len(item.split(".")) >= 2
]
# print(blast_db)
for blast_key in blast_db:
seq = filteredScrape.sp_seq_d[taxonID][blast_key]
local_blast.write_filterblast_db(filteredScrape.workdir,
blast_key,
seq,
fn=str(taxonID))
break
# print(taxonID)
blast_db = taxonID
blast_seq = taxonID
key = taxonID
local_blast.run_filter_blast(filteredScrape.workdir, blast_seq, blast_db)
local_blast.read_filter_blast(filteredScrape.workdir,
filteredScrape.sp_seq_d[key], blast_db)
blast_out = "{}/blast/output_{}_tobeblasted.xml".format(workdir, key)
if os.path.exists(blast_out):
with open(blast_out) as f:
first_line = f.readline()
assert len(first_line.strip()) != 0
