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Commit a8b804ad authored by Amandine PERRIN's avatar Amandine PERRIN
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adapt func test to new pangenome filename

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Pipeline #50226 passed
Stage: test
Stage: coverage
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test/test_functional/test_pangenome.py
+ 34
− 47
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...@@ -68,28 +68,26 @@ def test_main_from_parse(): ...@@ -68,28 +68,26 @@ def test_main_from_parse():
assert os.path.isfile(prtbank) assert os.path.isfile(prtbank)
# Check presence of tmp folder # Check presence of tmp folder
tmp_base = os.path.join(GENEPATH, "tmp_testFromParsePAN4.All.prt_0.8-mode1_*") tmp_base = os.path.join(GENEPATH, "tmp_testFromParsePAN4.All.prt_0.8-mode1")
assert len(glob.glob(tmp_base)) == 1 assert os.path.isdir(tmp_base)
# check presence of mmseq cluster files # check presence of mmseq cluster files
cluster = os.path.join(GENEPATH, name + ".All.prt-clust-0.8-mode1_*") cluster = os.path.join(GENEPATH, name + ".All.prt-clust-0.8-mode1*")
clust_files = glob.glob(cluster) clust_files = glob.glob(cluster)
assert len(clust_files) == 4 assert len(clust_files) == 4
# Check presence of pangenome files (pangenome, matrices, summary) # Check presence of pangenome files (pangenome, matrices, summary)
pan_files = glob.glob(os.path.join(GENEPATH, "PanGenome-testFromParsePAN4*")) pan_files = glob.glob(os.path.join(GENEPATH, "PanGenome-testFromParsePAN4*"))
to_check = [".tsv.lst", ".tsv.lst.quali.txt", ".tsv.lst.quanti.txt", ".tsv.lst.summary.txt"] to_check = [".lst", ".lst.quali.txt", ".lst.quanti.txt", ".lst.summary.txt"]
found = [] found = []
pangenome_file = ""
for f in pan_files: for f in pan_files:
for c in to_check: for c in to_check:
if f.endswith(c): if f.endswith(c):
found.append(c) found.append(c)
if f.endswith(".tsv.lst"): panfile = os.path.join(GENEPATH, "PanGenome-testFromParsePAN4.All.prt-clust-0.8-mode1.lst")
pangenome_file = f
assert set(found) == set(to_check) assert set(found) == set(to_check)
# Check content of pangenome # Check content of pangenome
exp_pan = os.path.join(EXP_FILES, "exp_pangenome-4genomes.lst") exp_pan = os.path.join(EXP_FILES, "exp_pangenome-4genomes.lst")
# Check that all families are as expected. Compare lines without the family number # Check that all families are as expected. Compare lines without the family number
with open(exp_pan, "r") as ep, open(pangenome_file, "r") as panf: with open(exp_pan, "r") as ep, open(panfile, "r") as panf:
lines_exp = [] lines_exp = []
lines_out = [] lines_out = []
for line_exp in ep: for line_exp in ep:
...@@ -116,30 +114,27 @@ def test_main(caplog): ...@@ -116,30 +114,27 @@ def test_main(caplog):
used_dbpath = os.path.join(GENEPATH, "database") used_dbpath = os.path.join(GENEPATH, "database")
# copy db_path folder to output folder, as it will modify it # copy db_path folder to output folder, as it will modify it
shutil.copytree(DBPATH, used_dbpath) shutil.copytree(DBPATH, used_dbpath)
out_panfile = os.path.join(outdir, "PanGenome-testPAN4.All.prt-clust-0.8-mode1_") out_panfile = os.path.join(outdir, "PanGenome-testPAN4.All.prt-clust-0.8-mode1.lst")
assert pan.main(cmd, lstinfo, name, used_dbpath, min_id, outdir, clust_mode, assert pan.main(cmd, lstinfo, name, used_dbpath, min_id, outdir, clust_mode,
spe_dir, threads, verbose=2).startswith(out_panfile) spe_dir, threads, verbose=2) == out_panfile
# Checl creation of prt bank # Checl creation of prt bank
prtbank = os.path.join(used_dbpath, "testPAN4.All.prt") prtbank = os.path.join(used_dbpath, "testPAN4.All.prt")
assert os.path.isfile(prtbank) assert os.path.isfile(prtbank)
# Check presence of tmp folder # Check presence of tmp folder
tmp_base = os.path.join(outdir, "tmp_testPAN4.All.prt_0.8-mode1_*") tmp_base = os.path.join(outdir, "tmp_testPAN4.All.prt_0.8-mode1")
assert len(glob.glob(tmp_base)) == 1 assert os.path.isdir(tmp_base)
# Check presence of pangenome files (pangenome, matrices, summary) # Check presence of pangenome files (pangenome, matrices, summary)
pan_files = glob.glob(os.path.join(GENEPATH, "PanGenome-testPAN4*")) pan_files = glob.glob(os.path.join(GENEPATH, "PanGenome-testPAN4*"))
to_check = [".tsv.lst", ".tsv.lst.quali.txt", ".tsv.lst.quanti.txt", ".tsv.lst.summary.txt"] to_check = [".lst", ".lst.quali.txt", ".lst.quanti.txt", ".lst.summary.txt"]
found = [] found = []
pangenome_file = ""
for f in pan_files: for f in pan_files:
for c in to_check: for c in to_check:
if f.endswith(c): if f.endswith(c):
found.append(c) found.append(c)
if f.endswith(".tsv.lst"):
pangenome_file = f
assert set(found) == set(to_check) assert set(found) == set(to_check)
# Check content of pangenome # Check content of pangenome
exp_pan = os.path.join(EXP_FILES, "exp_pangenome-4genomes.lst") exp_pan = os.path.join(EXP_FILES, "exp_pangenome-4genomes.lst")
with open(exp_pan, "r") as ep, open(pangenome_file, "r") as panf: with open(exp_pan, "r") as ep, open(out_panfile, "r") as panf:
lines_exp = [] lines_exp = []
lines_out = [] lines_out = []
for line_exp in ep: for line_exp in ep:
...@@ -182,9 +177,9 @@ def test_main_prt_exist(caplog): ...@@ -182,9 +177,9 @@ def test_main_prt_exist(caplog):
dest_prt_bank = os.path.join(used_dbpath, "test2PAN4.All.prt") dest_prt_bank = os.path.join(used_dbpath, "test2PAN4.All.prt")
shutil.copyfile(src_prt_bank, dest_prt_bank) shutil.copyfile(src_prt_bank, dest_prt_bank)
out_panfile = os.path.join(outdir, "PanGenome-test2PAN4.All.prt-clust-0.8-mode1_") out_panfile = os.path.join(outdir, "PanGenome-test2PAN4.All.prt-clust-0.8-mode1.lst")
assert pan.main(cmd, lstinfo, name, used_dbpath, min_id, outdir, clust_mode, spe_dir, assert pan.main(cmd, lstinfo, name, used_dbpath, min_id, outdir, clust_mode, spe_dir,
threads, verbose=15).startswith(out_panfile) threads, verbose=15) == out_panfile
# Check presence of mmseq DB files # Check presence of mmseq DB files
msdb = os.path.join(GENEPATH, "test2PAN4.All.prt-msDB") msdb = os.path.join(GENEPATH, "test2PAN4.All.prt-msDB")
...@@ -194,27 +189,24 @@ def test_main_prt_exist(caplog): ...@@ -194,27 +189,24 @@ def test_main_prt_exist(caplog):
assert os.path.isfile(msdb + "_h") assert os.path.isfile(msdb + "_h")
assert os.path.isfile(msdb + "_h.index") assert os.path.isfile(msdb + "_h.index")
# Check presence of mmseq cluster files # Check presence of mmseq cluster files
cluster = os.path.join(outdir, "test2PAN4.All.prt-clust-0.8-mode1_*") cluster = os.path.join(outdir, "test2PAN4.All.prt-clust-0.8-mode1*")
clust_files = glob.glob(cluster) clust_files = glob.glob(cluster)
assert len(clust_files) == 4 assert len(clust_files) == 4
# Check presence of pangenome files (pangenome, matrices, summary) # Check presence of pangenome files (pangenome, matrices, summary)
pan_files = glob.glob(os.path.join(GENEPATH, "PanGenome-test2PAN4*")) pan_files = glob.glob(os.path.join(GENEPATH, "PanGenome-test2PAN4*"))
to_check = [".tsv.lst", ".tsv.lst.quali.txt", ".tsv.lst.quanti.txt", ".tsv.lst.summary.txt"] to_check = [".lst", ".lst.quali.txt", ".lst.quanti.txt", ".lst.summary.txt"]
found = [] found = []
pangenome_file = ""
for f in pan_files: for f in pan_files:
for c in to_check: for c in to_check:
if f.endswith(c): if f.endswith(c):
found.append(c) found.append(c)
if f.endswith(".tsv.lst"):
pangenome_file = f
assert set(found) == set(to_check) assert set(found) == set(to_check)
# Check presence of tmp folder # Check presence of tmp folder
tmp_base = os.path.join(outdir, "tmp_test2PAN4.All.prt_0.8-mode1_*") tmp_base = os.path.join(outdir, "tmp_test2PAN4.All.prt_0.8-mode1")
assert len(glob.glob(tmp_base)) == 1 assert os.path.isdir(tmp_base)
# Check content of pangenome # Check content of pangenome
exp_pan = os.path.join(EXP_FILES, "exp_pangenome-4genomes.lst") exp_pan = os.path.join(EXP_FILES, "exp_pangenome-4genomes.lst")
with open(exp_pan, "r") as ep, open(pangenome_file, "r") as panf: with open(exp_pan, "r") as ep, open(out_panfile, "r") as panf:
lines_exp = [] lines_exp = []
lines_out = [] lines_out = []
for line_exp in ep: for line_exp in ep:
...@@ -253,9 +245,9 @@ def test_main_spedir(caplog): ...@@ -253,9 +245,9 @@ def test_main_spedir(caplog):
# copy db_path folder to output folder, as it will modify it # copy db_path folder to output folder, as it will modify it
shutil.copytree(DBPATH, used_dbpath) shutil.copytree(DBPATH, used_dbpath)
out_panfile = os.path.join(outdir, "PanGenome-test3PAN4.All.prt-clust-0.8-mode1_") out_panfile = os.path.join(outdir, "PanGenome-test3PAN4.All.prt-clust-0.8-mode1.lst")
assert pan.main(cmd, lstinfo, name, used_dbpath, min_id, outdir, clust_mode, spe_dir, assert pan.main(cmd, lstinfo, name, used_dbpath, min_id, outdir, clust_mode, spe_dir,
threads, verbose=15).startswith(out_panfile) threads, verbose=15) == out_panfile
# Checl creation of prt bank # Checl creation of prt bank
prtbank = os.path.join(spe_dir, "test3PAN4.All.prt") prtbank = os.path.join(spe_dir, "test3PAN4.All.prt")
assert os.path.isfile(prtbank) assert os.path.isfile(prtbank)
...@@ -267,27 +259,24 @@ def test_main_spedir(caplog): ...@@ -267,27 +259,24 @@ def test_main_spedir(caplog):
assert os.path.isfile(msdb + "_h") assert os.path.isfile(msdb + "_h")
assert os.path.isfile(msdb + "_h.index") assert os.path.isfile(msdb + "_h.index")
# Check presence of mmseq cluster files # Check presence of mmseq cluster files
cluster = os.path.join(outdir, "test3PAN4.All.prt-clust-0.8-mode1_*") cluster = os.path.join(outdir, "test3PAN4.All.prt-clust-0.8-mode1*")
clust_files = glob.glob(cluster) clust_files = glob.glob(cluster)
assert len(clust_files) == 4 assert len(clust_files) == 4
# Check presence of tmp folder # Check presence of tmp folder
tmp_base = os.path.join(outdir, "tmp_test3PAN4.All.prt_0.8-mode1_*") tmp_base = os.path.join(outdir, "tmp_test3PAN4.All.prt_0.8-mode1")
assert len(glob.glob(tmp_base)) == 1 assert os.path.isdir(tmp_base)
# Check presence of pangenome files (pangenome, matrices, summary) # Check presence of pangenome files (pangenome, matrices, summary)
pan_files = glob.glob(os.path.join(GENEPATH, "PanGenome-test3PAN4*")) pan_files = glob.glob(os.path.join(GENEPATH, "PanGenome-test3PAN4*"))
to_check = [".tsv.lst", ".tsv.lst.quali.txt", ".tsv.lst.quanti.txt", ".tsv.lst.summary.txt"] to_check = [".lst", ".lst.quali.txt", ".lst.quanti.txt", ".lst.summary.txt"]
found = [] found = []
pangenome_file = ""
for f in pan_files: for f in pan_files:
for c in to_check: for c in to_check:
if f.endswith(c): if f.endswith(c):
found.append(c) found.append(c)
if f.endswith(".tsv.lst"):
pangenome_file = f
assert set(found) == set(to_check) assert set(found) == set(to_check)
# Check content of pangenome # Check content of pangenome
exp_pan = os.path.join(EXP_FILES, "exp_pangenome-4genomes.lst") exp_pan = os.path.join(EXP_FILES, "exp_pangenome-4genomes.lst")
with open(exp_pan, "r") as ep, open(pangenome_file, "r") as panf: with open(exp_pan, "r") as ep, open(out_panfile, "r") as panf:
lines_exp = [] lines_exp = []
lines_out = [] lines_out = []
for line_exp in ep: for line_exp in ep:
...@@ -338,12 +327,12 @@ def test_main_outfile(caplog): ...@@ -338,12 +327,12 @@ def test_main_outfile(caplog):
assert os.path.isfile(msdb + "_h") assert os.path.isfile(msdb + "_h")
assert os.path.isfile(msdb + "_h.index") assert os.path.isfile(msdb + "_h.index")
# Check presence of mmseq cluster files # Check presence of mmseq cluster files
cluster = os.path.join(outdir, "test4PAN4.All.prt-clust-0.8-mode1_*") cluster = os.path.join(outdir, "test4PAN4.All.prt-clust-0.8-mode1*")
clust_files = glob.glob(cluster) clust_files = glob.glob(cluster)
assert len(clust_files) == 4 assert len(clust_files) == 4
# Check presence of tmp folder # Check presence of tmp folder
tmp_base = os.path.join(outdir, "tmp_test4PAN4.All.prt_0.8-mode1_*") tmp_base = os.path.join(outdir, "tmp_test4PAN4.All.prt_0.8-mode1")
assert len(glob.glob(tmp_base)) == 1 assert os.path.isdir(tmp_base)
# Check presence of pangenome files (pangenome, matrices, summary) # Check presence of pangenome files (pangenome, matrices, summary)
outf = os.path.join(outdir, outfile) outf = os.path.join(outdir, outfile)
assert os.path.isfile(outf) assert os.path.isfile(outf)
...@@ -402,23 +391,21 @@ def test_pangenome_all(): ...@@ -402,23 +391,21 @@ def test_pangenome_all():
assert os.path.isfile(msdb + "_h") assert os.path.isfile(msdb + "_h")
assert os.path.isfile(msdb + "_h.index") assert os.path.isfile(msdb + "_h.index")
# Check presence of mmseq cluster files # Check presence of mmseq cluster files
cluster = os.path.join(outdir, "testAllPAN4.All.prt-clust-0.8-mode1_*") cluster = os.path.join(outdir, "testAllPAN4.All.prt-clust-0.8-mode1*")
clust_files = glob.glob(cluster) clust_files = glob.glob(cluster)
assert len(clust_files) == 4 assert len(clust_files) == 4
# Check presence of tmp folder # Check presence of tmp folder
tmp_base = os.path.join(outdir, "tmp_testAllPAN4.All.prt_0.8-mode1_*") tmp_base = os.path.join(outdir, "tmp_testAllPAN4.All.prt_0.8-mode1")
assert len(glob.glob(tmp_base)) == 1 assert os.path.isdir(tmp_base)
# Check presence of pangenome files (pangenome, matrices, summary) # Check presence of pangenome files (pangenome, matrices, summary)
pan_files = glob.glob(os.path.join(GENEPATH, "PanGenome-testAllPAN4*")) pan_files = glob.glob(os.path.join(GENEPATH, "PanGenome-testAllPAN4*"))
to_check = [".tsv.lst", ".tsv.lst.quali.txt", ".tsv.lst.quanti.txt", ".tsv.lst.summary.txt"] to_check = [".lst", ".lst.quali.txt", ".lst.quanti.txt", ".lst.summary.txt"]
found = [] found = []
pangenome_file = "" pangenome_file = os.path.join(outdir, "PanGenome-testAllPAN4.All.prt-clust-0.8-mode1.lst")
for f in pan_files: for f in pan_files:
for c in to_check: for c in to_check:
if f.endswith(c): if f.endswith(c):
found.append(c) found.append(c)
if f.endswith(".tsv.lst"):
pangenome_file = f
assert set(found) == set(to_check) assert set(found) == set(to_check)
# Check content of pangenome # Check content of pangenome
exp_pan = os.path.join(EXP_FILES, "exp_pangenome-4genomes.lst") exp_pan = os.path.join(EXP_FILES, "exp_pangenome-4genomes.lst")
......
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