Skip to content

Commit

Permalink
Update test update files
Browse files Browse the repository at this point in the history
  • Loading branch information
@nickjcroucher
nickjcroucher committed Oct 10, 2024
1 parent 35fc89d commit 9feb957
Show file tree
Hide file tree
Showing 2 changed files with 59 additions and 61 deletions.
2 changes: 0 additions & 2 deletions test/rfile3.txt
View file
Original file line number Diff line number Diff line change
@@ -1,4 +1,2 @@
12754_5#71 12754_5#71.contigs_velvet.fa
12754_5#55 12754_5#55.contigs_velvet.fa
12754_5#16 12754_5#16.contigs_velvet.fa
12754_5#88 12754_5#88.contigs_velvet.fa
118 changes: 59 additions & 59 deletions test/test-update.py
View file
Original file line number Diff line number Diff line change
Expand Up @@ -65,62 +65,62 @@ def old_get_seq_tuples(rows,cols):

for lineage_option_string in [" "," --count-unique-distances ", " --reciprocal-only "," --count-unique-distances --reciprocal-only "]:

if lineage_option_string != " ":
print("\n*** Now running tests with lineage option" + lineage_option_string + "***\n")

# Check distances after one query

# Check that order is the same after doing 1 + 2 with --update-db, as doing all of 1 + 2 together
subprocess.run(python_cmd + " ../poppunk-runner.py --create-db --r-files rfile12.txt --output batch12 --overwrite", shell=True, check=True)
subprocess.run(python_cmd + " ../poppunk-runner.py --fit-model lineage --ref-db batch12 --ranks 1,2 --overwrite" + lineage_option_string,shell=True, check=True)
print(" ../poppunk-runner.py --fit-model lineage --ref-db batch12 --ranks 1,2 --overwrite\n\n")
subprocess.run(python_cmd + " ../poppunk-runner.py --create-db --r-files rfile1.txt --output batch1 --overwrite", shell=True, check=True)
subprocess.run(python_cmd + " ../poppunk-runner.py --fit-model lineage --ref-db batch1 --ranks 1,2 --overwrite" + lineage_option_string, shell=True, check=True)
print("../poppunk-runner.py --fit-model lineage --ref-db batch1 --ranks 1,2 --overwrite\n\n")
subprocess.run(python_cmd + " ../poppunk_assign-runner.py --db batch1 --query rfile2.txt --output batch2 --update-db --overwrite --max-a-dist 1", shell=True, check=True)
print(" ../poppunk_assign-runner.py --db batch1 --query rfile2.txt --output batch2 --update-db --overwrite --max-a-dist 1\n\n")

# Load updated distance order
with open("batch2/batch2.dists.pkl", 'rb') as pickle_file:
rlist2, qlist, self = pickle.load(pickle_file)

# Check sparse distances after one query
with open("batch12/batch12.dists.pkl", 'rb') as pickle_file:
rlist1, qlist1, self = pickle.load(pickle_file)
S1 = scipy.sparse.load_npz("batch12/batch12_rank_2_fit.npz")
S2 = scipy.sparse.load_npz("batch2/batch2_rank_2_fit.npz")
sys.stderr.write("Comparing sparse matrices at rank 2 after first query calculated with options " + lineage_option_string + "\n")
compare_sparse_matrices(S1,S2,rlist1,rlist2)

# Check rank 1
S3 = scipy.sparse.load_npz("batch12/batch12_rank_1_fit.npz")
S4 = scipy.sparse.load_npz("batch2/batch2_rank_1_fit.npz")
sys.stderr.write("Comparing sparse matrices at rank 1 after first query calculated with options " + lineage_option_string + "\n")
compare_sparse_matrices(S3,S4,rlist1,rlist2)

# Check distances after second query

# Check that order is the same after doing 1 + 2 + 3 with --update-db, as doing all of 1 + 2 + 3 together
subprocess.run(python_cmd + " ../poppunk-runner.py --create-db --r-files rfile123.txt --output batch123 --overwrite", shell=True, check=True)
subprocess.run(python_cmd + " ../poppunk-runner.py --fit-model lineage --ref-db batch123 --ranks 1,2 --overwrite" + lineage_option_string, shell=True, check=True)
print("../poppunk-runner.py --fit-model lineage --ref-db batch123 --ranks 1,2 --overwrite\n\n")
subprocess.run(python_cmd + " ../poppunk_assign-runner.py --db batch2 --query rfile3.txt --output batch3 --update-db --overwrite", shell=True, check=True)
print(python_cmd + " ../poppunk_assign-runner.py --db batch2 --query rfile3.txt --output batch3 --update-db --overwrite\n\n")

# Load updated distances order
with open("batch3/batch3.dists.pkl", 'rb') as pickle_file:
rlist4, qlist, self = pickle.load(pickle_file)

# Check sparse distances after second query
with open("batch123/batch123.dists.pkl", 'rb') as pickle_file:
rlist3, qlist, self = pickle.load(pickle_file)
S5 = scipy.sparse.load_npz("batch123/batch123_rank_2_fit.npz")
S6 = scipy.sparse.load_npz("batch3/batch3_rank_2_fit.npz")
sys.stderr.write("Comparing sparse matrices at rank 2 after second query calculated with options " + lineage_option_string + "\n")
compare_sparse_matrices(S5,S6,rlist3,rlist4)

# Check rank 1
S7 = scipy.sparse.load_npz("batch123/batch123_rank_1_fit.npz")
S8 = scipy.sparse.load_npz("batch3/batch3_rank_1_fit.npz")
sys.stderr.write("Comparing sparse matrices at rank 1 after second query calculated with options " + lineage_option_string + "\n")
compare_sparse_matrices(S7,S8,rlist3,rlist4)
if lineage_option_string != " ":
print("\n*** Now running tests with lineage option" + lineage_option_string + "***\n")

# Check distances after one query

# Check that order is the same after doing 1 + 2 with --update-db, as doing all of 1 + 2 together
subprocess.run(python_cmd + " ../poppunk-runner.py --create-db --r-files rfile12.txt --output batch12 --overwrite", shell=True, check=True)
subprocess.run(python_cmd + " ../poppunk-runner.py --fit-model lineage --ref-db batch12 --ranks 1,2 --overwrite" + lineage_option_string,shell=True, check=True)
print(" ../poppunk-runner.py --fit-model lineage --ref-db batch12 --ranks 1,2 --overwrite\n\n")
subprocess.run(python_cmd + " ../poppunk-runner.py --create-db --r-files rfile1.txt --output batch1 --overwrite", shell=True, check=True)
subprocess.run(python_cmd + " ../poppunk-runner.py --fit-model lineage --ref-db batch1 --ranks 1,2 --overwrite" + lineage_option_string, shell=True, check=True)
print("../poppunk-runner.py --fit-model lineage --ref-db batch1 --ranks 1,2 --overwrite\n\n")
subprocess.run(python_cmd + " ../poppunk_assign-runner.py --db batch1 --query rfile2.txt --output batch2 --update-db --overwrite --max-a-dist 1", shell=True, check=True)
print(" ../poppunk_assign-runner.py --db batch1 --query rfile2.txt --output batch2 --update-db --overwrite --max-a-dist 1\n\n")

# Load updated distance order
with open("batch2/batch2.dists.pkl", 'rb') as pickle_file:
rlist2, qlist, self = pickle.load(pickle_file)

# Check sparse distances after one query
with open("batch12/batch12.dists.pkl", 'rb') as pickle_file:
rlist1, qlist1, self = pickle.load(pickle_file)
S1 = scipy.sparse.load_npz("batch12/batch12_rank_2_fit.npz")
S2 = scipy.sparse.load_npz("batch2/batch2_rank_2_fit.npz")
sys.stderr.write("Comparing sparse matrices at rank 2 after first query calculated with options " + lineage_option_string + "\n")
compare_sparse_matrices(S1,S2,rlist1,rlist2)

# Check rank 1
S3 = scipy.sparse.load_npz("batch12/batch12_rank_1_fit.npz")
S4 = scipy.sparse.load_npz("batch2/batch2_rank_1_fit.npz")
sys.stderr.write("Comparing sparse matrices at rank 1 after first query calculated with options " + lineage_option_string + "\n")
compare_sparse_matrices(S3,S4,rlist1,rlist2)

# Check distances after second query

# Check that order is the same after doing 1 + 2 + 3 with --update-db, as doing all of 1 + 2 + 3 together
subprocess.run(python_cmd + " ../poppunk-runner.py --create-db --r-files rfile123.txt --output batch123 --overwrite", shell=True, check=True)
subprocess.run(python_cmd + " ../poppunk-runner.py --fit-model lineage --ref-db batch123 --ranks 1,2 --overwrite" + lineage_option_string, shell=True, check=True)
print("../poppunk-runner.py --fit-model lineage --ref-db batch123 --ranks 1,2 --overwrite\n\n")
subprocess.run(python_cmd + " ../poppunk_assign-runner.py --db batch2 --query rfile3.txt --output batch3 --update-db --overwrite", shell=True, check=True)
print(python_cmd + " ../poppunk_assign-runner.py --db batch2 --query rfile3.txt --output batch3 --update-db --overwrite\n\n")

# Load updated distances order
with open("batch3/batch3.dists.pkl", 'rb') as pickle_file:
rlist4, qlist, self = pickle.load(pickle_file)

# Check sparse distances after second query
with open("batch123/batch123.dists.pkl", 'rb') as pickle_file:
rlist3, qlist, self = pickle.load(pickle_file)
S5 = scipy.sparse.load_npz("batch123/batch123_rank_2_fit.npz")
S6 = scipy.sparse.load_npz("batch3/batch3_rank_2_fit.npz")
sys.stderr.write("Comparing sparse matrices at rank 2 after second query calculated with options " + lineage_option_string + "\n")
compare_sparse_matrices(S5,S6,rlist3,rlist4)

# Check rank 1
S7 = scipy.sparse.load_npz("batch123/batch123_rank_1_fit.npz")
S8 = scipy.sparse.load_npz("batch3/batch3_rank_1_fit.npz")
sys.stderr.write("Comparing sparse matrices at rank 1 after second query calculated with options " + lineage_option_string + "\n")
compare_sparse_matrices(S7,S8,rlist3,rlist4)

0 comments on commit 9feb957

Please sign in to comment.