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Commit f68a7142 authored by Amandine PERRIN's avatar Amandine PERRIN
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try remove 1st test of align

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Pipeline #39657 failed
Stage: test
Stage: coverage
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test/test_functional/test_align.py
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......@@ -43,72 +43,72 @@ def setup_teardown_module():
print("teardown")
def test_main():
"""
Test that when giving a database, a persistent genome and a list of genomes, it extracts
expected proteins by family, aligns each family, back-translates them, concatenates all
families into one file and groups them by genome.
"""
corepers = os.path.join(TESTPATH, "test_pers0.99FX.lst")
list_genomes = os.path.join("test", "data", "pangenome", "test_files", "list_to_pan.txt")
dname = "TEST4"
dbpath = os.path.join("test", "data", "pangenome", "test_files", "example_db")
outdir = GENEPATH
threads = 1
force = False
cmd = "cmd"
al.main(cmd, corepers, list_genomes, dname, dbpath, outdir, threads, force)
# Check creation of the 3 subdirectories
aldir = os.path.join(outdir, "Align-" + dname)
listdir = os.path.join(outdir, "List-" + dname)
treedir = os.path.join(outdir, "Phylo-" + dname)
assert os.path.isdir(aldir)
assert os.path.isdir(listdir)
assert os.path.isdir(treedir)
# Check content of listdir
genomes = ["GEN2.1017.00001", "GEN4.1111.00001", "GENO.1017.00001", "GENO.1216.00002"]
for gen in genomes:
assert os.path.isfile(os.path.join(listdir, f"{dname}-getEntry_gen_{gen}.txt"))
assert os.path.isfile(os.path.join(listdir, f"{dname}-getEntry_prt_{gen}.txt"))
# Check content of aldir
fams = [1, 4, 6, 8, 10, 11, 13, 14]
for fam in fams:
assert os.path.isfile(os.path.join(aldir, f'{dname}-current.{fam}.gen'))
assert os.path.isfile(os.path.join(aldir, f'{dname}-current.{fam}.prt'))
assert os.path.isfile(os.path.join(aldir, f'{dname}-current.{fam}.miss.lst'))
assert os.path.isfile(os.path.join(aldir, f'{dname}-mafft-align.{fam}.aln'))
assert os.path.isfile(os.path.join(aldir, f'{dname}-mafft-prt2nuc.{fam}.aln'))
out_concat = os.path.join(aldir, dname + "-complete.cat.aln")
exp_concat = os.path.join(EXPPATH, "exp_pers4genome-complete.cat.aln")
assert tutil.compare_order_content(out_concat, exp_concat)
# Check content of treedir
out_grp = os.path.join(treedir, dname + ".grp.aln")
exp_grp = os.path.join(EXPPATH, "exp_pers4genomes.grp.aln")
assert tutil.compare_order_content(out_grp, exp_grp)
# Check presence of log files, and log.err is empty
base_log = os.path.join(outdir, "PanACoTA-align_" + dname + ".log")
assert os.path.isfile(base_log)
assert os.path.isfile(base_log + ".details")
assert os.path.isfile(base_log + ".err")
with open(base_log + ".err", "r") as bf:
assert bf.readlines() == []
# Check logs
with open(base_log + ".details", "r") as lc:
log_content = lc.readlines()
assert ("Reading PersGenome and constructing lists of missing genomes in "
"each family") in " ".join(log_content)
assert "Extracting proteins and genes from all genomes" in " ".join(log_content)
for gen in genomes:
assert "Extracting proteins and genes from {}".format(gen) in " ".join(log_content)
assert ("Starting alignment of all families: protein alignment, back-translation to "
"nucleotides, and add missing genomes in the family") in " ".join(log_content)
for fam in fams:
assert "Checking extractions for family {}".format(fam) in " ".join(log_content)
assert "Aligning family {}".format(fam) in " ".join(log_content)
assert "Back-translating family {}".format(fam) in " ".join(log_content)
assert "Concatenating all alignment files" in " ".join(log_content)
assert "Grouping alignments per genome" in " ".join(log_content)
assert "END" in " ".join(log_content)
# def test_main():
# """
# Test that when giving a database, a persistent genome and a list of genomes, it extracts
# expected proteins by family, aligns each family, back-translates them, concatenates all
# families into one file and groups them by genome.
# """
# corepers = os.path.join(TESTPATH, "test_pers0.99FX.lst")
# list_genomes = os.path.join("test", "data", "pangenome", "test_files", "list_to_pan.txt")
# dname = "TEST4"
# dbpath = os.path.join("test", "data", "pangenome", "test_files", "example_db")
# outdir = GENEPATH
# threads = 1
# force = False
# cmd = "cmd"
# al.main(cmd, corepers, list_genomes, dname, dbpath, outdir, threads, force)
# # Check creation of the 3 subdirectories
# aldir = os.path.join(outdir, "Align-" + dname)
# listdir = os.path.join(outdir, "List-" + dname)
# treedir = os.path.join(outdir, "Phylo-" + dname)
# assert os.path.isdir(aldir)
# assert os.path.isdir(listdir)
# assert os.path.isdir(treedir)
# # Check content of listdir
# genomes = ["GEN2.1017.00001", "GEN4.1111.00001", "GENO.1017.00001", "GENO.1216.00002"]
# for gen in genomes:
# assert os.path.isfile(os.path.join(listdir, f"{dname}-getEntry_gen_{gen}.txt"))
# assert os.path.isfile(os.path.join(listdir, f"{dname}-getEntry_prt_{gen}.txt"))
# # Check content of aldir
# fams = [1, 4, 6, 8, 10, 11, 13, 14]
# for fam in fams:
# assert os.path.isfile(os.path.join(aldir, f'{dname}-current.{fam}.gen'))
# assert os.path.isfile(os.path.join(aldir, f'{dname}-current.{fam}.prt'))
# assert os.path.isfile(os.path.join(aldir, f'{dname}-current.{fam}.miss.lst'))
# assert os.path.isfile(os.path.join(aldir, f'{dname}-mafft-align.{fam}.aln'))
# assert os.path.isfile(os.path.join(aldir, f'{dname}-mafft-prt2nuc.{fam}.aln'))
# out_concat = os.path.join(aldir, dname + "-complete.cat.aln")
# exp_concat = os.path.join(EXPPATH, "exp_pers4genome-complete.cat.aln")
# assert tutil.compare_order_content(out_concat, exp_concat)
# # Check content of treedir
# out_grp = os.path.join(treedir, dname + ".grp.aln")
# exp_grp = os.path.join(EXPPATH, "exp_pers4genomes.grp.aln")
# assert tutil.compare_order_content(out_grp, exp_grp)
# # Check presence of log files, and log.err is empty
# base_log = os.path.join(outdir, "PanACoTA-align_" + dname + ".log")
# assert os.path.isfile(base_log)
# assert os.path.isfile(base_log + ".details")
# assert os.path.isfile(base_log + ".err")
# with open(base_log + ".err", "r") as bf:
# assert bf.readlines() == []
# # Check logs
# with open(base_log + ".details", "r") as lc:
# log_content = lc.readlines()
# assert ("Reading PersGenome and constructing lists of missing genomes in "
# "each family") in " ".join(log_content)
# assert "Extracting proteins and genes from all genomes" in " ".join(log_content)
# for gen in genomes:
# assert "Extracting proteins and genes from {}".format(gen) in " ".join(log_content)
# assert ("Starting alignment of all families: protein alignment, back-translation to "
# "nucleotides, and add missing genomes in the family") in " ".join(log_content)
# for fam in fams:
# assert "Checking extractions for family {}".format(fam) in " ".join(log_content)
# assert "Aligning family {}".format(fam) in " ".join(log_content)
# assert "Back-translating family {}".format(fam) in " ".join(log_content)
# assert "Concatenating all alignment files" in " ".join(log_content)
# assert "Grouping alignments per genome" in " ".join(log_content)
# assert "END" in " ".join(log_content)
def test_main_exist_ok():
......
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