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Commit 45a7d392 authored by Amandine PERRIN's avatar Amandine PERRIN
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Try removing first tests of align

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Pipeline #39663 failed
Stage: test
Stage: coverage
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test/test_functional/test_align.py
+ 92
− 92
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......@@ -111,98 +111,98 @@ def setup_teardown_module():
# assert "END" in " ".join(log_content)
def test_main_exist_ok():
"""
Test main all files exist and are ok, no force -> end without error, with warnings on re-use
"""
corepers = os.path.join(TESTPATH, "test_pers0.99FX.lst")
list_genomes = os.path.join("test", "data", "pangenome", "test_files", "list_to_pan.txt")
dname = "TEST4exists"
dbpath = os.path.join("test", "data", "pangenome", "test_files", "example_db")
outdir = os.path.join(GENEPATH, "test_main_exist_ok")
threads = 1
force = False
cmd = "cmd test_main_exist_ok"
# Create output directories and files
aldir = os.path.join(outdir, "Align-" + dname)
listdir = os.path.join(outdir, "List-" + dname)
treedir = os.path.join(outdir, "Phylo-" + dname)
os.makedirs(aldir)
os.makedirs(listdir)
os.makedirs(treedir)
# Create content of listdir
ex_listdir = os.path.join(EXPPATH, "exp_listdir-pers")
genomes = ["GEN2.1017.00001", "GEN4.1111.00001", "GENO.1017.00001", "GENO.1216.00002"]
for gen in genomes:
outgen = os.path.join(listdir, f"{dname}-getEntry_gen_{gen}.txt")
refgen = os.path.join(ex_listdir, f"getEntry_gen_{gen}")
shutil.copyfile(refgen, outgen)
outprt = os.path.join(listdir, f"{dname}-getEntry_prt_{gen}.txt")
refprt = os.path.join(ex_listdir, f"getEntry_prt_{gen}")
shutil.copyfile(refprt, outprt)
# Create content of aldir
ex_aldir = os.path.join(EXPPATH, "exp_aldir-pers")
fams = [1, 4, 6, 8, 10, 11, 13, 14]
for fam in fams:
outgen = os.path.join(aldir, f'{dname}-current.{fam}.gen')
refgen = os.path.join(ex_aldir, f"current.{fam}.gen")
shutil.copyfile(refgen, outgen)
outprt = os.path.join(aldir, f'{dname}-current.{fam}.prt')
refprt = os.path.join(ex_aldir, f"current.{fam}.prt")
shutil.copyfile(refprt, outprt)
outmiss = os.path.join(aldir, f'{dname}-current.{fam}.miss.lst')
refmiss = os.path.join(ex_aldir, f"current.{fam}.miss.lst")
shutil.copyfile(refmiss, outmiss)
outaln = os.path.join(aldir, f'{dname}-mafft-align.{fam}.aln')
refaln = os.path.join(ex_aldir, f"mafft-align.{fam}.aln")
shutil.copyfile(refaln, outaln)
outbtr = os.path.join(aldir, f'{dname}-mafft-prt2nuc.{fam}.aln')
refbtr = os.path.join(ex_aldir, f"mafft-prt2nuc.{fam}.aln")
shutil.copyfile(refbtr, outbtr)
outcat = os.path.join(aldir, dname + "-complete.cat.aln")
refcat = os.path.join(EXPPATH, "exp_pers4genome-complete.cat.aln")
shutil.copyfile(refcat, outcat)
# Create content of treedir
outgrp = os.path.join(treedir, dname + ".grp.aln")
refgrp = os.path.join(EXPPATH, "exp_pers4genomes.grp.aln")
shutil.copyfile(refgrp, outgrp)
# Run align module
al.main(cmd, corepers, list_genomes, dname, dbpath, outdir, threads, force)
# Check logs
logfile = os.path.join(outdir, "PanACoTA-align_TEST4exists.log.details")
with open(logfile, "r") as lc:
log_content = lc.readlines()
assert ("Reading PersGenome and constructing lists of missing genomes in "
"each family") in " ".join(log_content)
for gen in genomes:
assert (f"For genome {gen}, test/data/align/generated_by_func_tests/test_main_exist_ok/"
f"List-TEST4exists/TEST4exists-getEntry_prt_{gen}.txt and test/data/align/"
"generated_by_func_tests/test_main_exist_ok/List-TEST4exists/"
f"TEST4exists-getEntry_gen_{gen}.txt already exist. The program "
"will use them to extract proteins and genes. If you prefer to rewrite "
"them, use option -F ") 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 ("Alignment already done for family {}. The program will use it for next "
"steps").format(fam) in " ".join(log_content)
assert ("All extraction files already existing (see detailed log for more "
"information)") in " ".join(log_content)
assert ("All prt and gene files for all families already exist. The program will use them "
"for the next step. If you want to re-extract a given family, remove its prt and "
"gen extraction files. If you want to re-extract all families, use option -F "
"(or --force).") in " ".join(log_content)
assert ("Alignments already concatenated in "
"test/data/align/generated_by_func_tests/test_main_exist_ok/Align-TEST4exists/"
"TEST4exists-complete.cat.aln. Program will "
"use it for next steps. If you want to redo it, remove it before "
"running.") in " ".join(log_content)
assert ("Alignments already grouped by genome in "
"test/data/align/generated_by_func_tests/test_main_exist_ok/Phylo-TEST4exists/"
"TEST4exists.grp.aln. Program will "
"end.") in " ".join(log_content)
assert "END" in " ".join(log_content)
# def test_main_exist_ok():
# """
# Test main all files exist and are ok, no force -> end without error, with warnings on re-use
# """
# corepers = os.path.join(TESTPATH, "test_pers0.99FX.lst")
# list_genomes = os.path.join("test", "data", "pangenome", "test_files", "list_to_pan.txt")
# dname = "TEST4exists"
# dbpath = os.path.join("test", "data", "pangenome", "test_files", "example_db")
# outdir = os.path.join(GENEPATH, "test_main_exist_ok")
# threads = 1
# force = False
# cmd = "cmd test_main_exist_ok"
# # Create output directories and files
# aldir = os.path.join(outdir, "Align-" + dname)
# listdir = os.path.join(outdir, "List-" + dname)
# treedir = os.path.join(outdir, "Phylo-" + dname)
# os.makedirs(aldir)
# os.makedirs(listdir)
# os.makedirs(treedir)
# # Create content of listdir
# ex_listdir = os.path.join(EXPPATH, "exp_listdir-pers")
# genomes = ["GEN2.1017.00001", "GEN4.1111.00001", "GENO.1017.00001", "GENO.1216.00002"]
# for gen in genomes:
# outgen = os.path.join(listdir, f"{dname}-getEntry_gen_{gen}.txt")
# refgen = os.path.join(ex_listdir, f"getEntry_gen_{gen}")
# shutil.copyfile(refgen, outgen)
# outprt = os.path.join(listdir, f"{dname}-getEntry_prt_{gen}.txt")
# refprt = os.path.join(ex_listdir, f"getEntry_prt_{gen}")
# shutil.copyfile(refprt, outprt)
# # Create content of aldir
# ex_aldir = os.path.join(EXPPATH, "exp_aldir-pers")
# fams = [1, 4, 6, 8, 10, 11, 13, 14]
# for fam in fams:
# outgen = os.path.join(aldir, f'{dname}-current.{fam}.gen')
# refgen = os.path.join(ex_aldir, f"current.{fam}.gen")
# shutil.copyfile(refgen, outgen)
# outprt = os.path.join(aldir, f'{dname}-current.{fam}.prt')
# refprt = os.path.join(ex_aldir, f"current.{fam}.prt")
# shutil.copyfile(refprt, outprt)
# outmiss = os.path.join(aldir, f'{dname}-current.{fam}.miss.lst')
# refmiss = os.path.join(ex_aldir, f"current.{fam}.miss.lst")
# shutil.copyfile(refmiss, outmiss)
# outaln = os.path.join(aldir, f'{dname}-mafft-align.{fam}.aln')
# refaln = os.path.join(ex_aldir, f"mafft-align.{fam}.aln")
# shutil.copyfile(refaln, outaln)
# outbtr = os.path.join(aldir, f'{dname}-mafft-prt2nuc.{fam}.aln')
# refbtr = os.path.join(ex_aldir, f"mafft-prt2nuc.{fam}.aln")
# shutil.copyfile(refbtr, outbtr)
# outcat = os.path.join(aldir, dname + "-complete.cat.aln")
# refcat = os.path.join(EXPPATH, "exp_pers4genome-complete.cat.aln")
# shutil.copyfile(refcat, outcat)
# # Create content of treedir
# outgrp = os.path.join(treedir, dname + ".grp.aln")
# refgrp = os.path.join(EXPPATH, "exp_pers4genomes.grp.aln")
# shutil.copyfile(refgrp, outgrp)
# # Run align module
# al.main(cmd, corepers, list_genomes, dname, dbpath, outdir, threads, force)
# # Check logs
# logfile = os.path.join(outdir, "PanACoTA-align_TEST4exists.log.details")
# with open(logfile, "r") as lc:
# log_content = lc.readlines()
# assert ("Reading PersGenome and constructing lists of missing genomes in "
# "each family") in " ".join(log_content)
# for gen in genomes:
# assert (f"For genome {gen}, test/data/align/generated_by_func_tests/test_main_exist_ok/"
# f"List-TEST4exists/TEST4exists-getEntry_prt_{gen}.txt and test/data/align/"
# "generated_by_func_tests/test_main_exist_ok/List-TEST4exists/"
# f"TEST4exists-getEntry_gen_{gen}.txt already exist. The program "
# "will use them to extract proteins and genes. If you prefer to rewrite "
# "them, use option -F ") 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 ("Alignment already done for family {}. The program will use it for next "
# "steps").format(fam) in " ".join(log_content)
# assert ("All extraction files already existing (see detailed log for more "
# "information)") in " ".join(log_content)
# assert ("All prt and gene files for all families already exist. The program will use them "
# "for the next step. If you want to re-extract a given family, remove its prt and "
# "gen extraction files. If you want to re-extract all families, use option -F "
# "(or --force).") in " ".join(log_content)
# assert ("Alignments already concatenated in "
# "test/data/align/generated_by_func_tests/test_main_exist_ok/Align-TEST4exists/"
# "TEST4exists-complete.cat.aln. Program will "
# "use it for next steps. If you want to redo it, remove it before "
# "running.") in " ".join(log_content)
# assert ("Alignments already grouped by genome in "
# "test/data/align/generated_by_func_tests/test_main_exist_ok/Phylo-TEST4exists/"
# "TEST4exists.grp.aln. Program will "
# "end.") in " ".join(log_content)
# assert "END" in " ".join(log_content)
def test_main_exist_emptygrp(capsys):
......
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