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Commit 7e6447e8 authored by Amandine  PERRIN's avatar Amandine PERRIN
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test when all files are already ok

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>GEN2.1017.00001.i0002_00005 834 amiD | N-acetylmuramoyl-L-alanine amidase AmiD | 3.5.1.28 | similar to AA sequence:UniProtKB:P75820
MMKALLWLVGLALLLTGCASEKGIIDKEGYQLDTRHRAQAAYPRIKVLVIHYTAENFDVS
LATLTGRNVSSHYLIPATPPLYGGKPRIWQLVPEQDQAWHAGVSFWRGATRLNDTSIGIE
LENRGWRMSGGVKSFAPFESAQIQALIPLAKDIIARYDIKPQNVVAHADIAPQRKDDPGP
RFPWRELAAQGIGAWPDAQRVAFYLAGRAPYTPVDTATVLALLSRYGYEVKADMTAREQQ
RVIMAFQMHFRPAQWNGIADAETQAIAEALLEKYGQD
>GEN4.1111.00001.b0001_00001 831 amiD | N-acetylmuramoyl-L-alanine amidase AmiD | 3.5.1.28 | similar to AA sequence:UniProtKB:P75820
-MKALLWLVGLALLLTGCASEKGIIDKEGYQLDTRHRAQAAYPRIKVLVIHYTAENFDVS
LATLTGRNVSSHYLIPATPPLYGGKPRIWQLVPEQDQAWHAGVSFWRGATRLNDTSIGIE
LENRGWRMSGGVKSFAPFESAQIQALIPLAKDIIARYDIKPQNVVAHADIAPQRKDDPGP
RFPWRELAAQGIGAWPDAQRVAFYLAGRAPYTPVDTATVLALLSRYGYEVKADMTAREQQ
RVIMAFQMHFRPAQWNGIADAETQAIAEALLEKYGQD
>GENO.1017.00001.b0001_00002 831 amiD | N-acetylmuramoyl-L-alanine amidase AmiD | 3.5.1.28 | similar to AA sequence:UniProtKB:P75820
-MKALLWLVGLALLLTGCASEKGIIDKEGYQLDTRHRAQAAYPRIKVLVIHYTAENFDVS
LATLTGRNVSSHYLIPATPPLYGGKPRIWQLVPEQDQAWHAGVSFWRGATRLNDTSIGIE
LENRGWRMSGGVKSFAPFESAQIQALIPLAKDIIARYNIKPQNVVAHADIAPQRKDDPGP
RFPWRELAAQGISAWPDAQRVAFYLAGRAPYTPVDTATVLALLSRYGYEVKADMTAREQQ
RVIMAFQMHFRPAQWNGIADAETQAIAEALLEKYGQD
>GENO.1216.00002
-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
...@@ -57,7 +57,8 @@ def test_main(): ...@@ -57,7 +57,8 @@ def test_main():
threads = 1 threads = 1
force = False force = False
cmd = "cmd" cmd = "cmd"
al.main(cmd, corepers, list_genomes, dname, dbpath, outdir, threads, force) prot_ali = False
al.main(cmd, corepers, list_genomes, dname, dbpath, outdir, prot_ali, threads, force)
# Check creation of the 3 subdirectories # Check creation of the 3 subdirectories
aldir = os.path.join(outdir, "Align-" + dname) aldir = os.path.join(outdir, "Align-" + dname)
listdir = os.path.join(outdir, "List-" + dname) listdir = os.path.join(outdir, "List-" + dname)
...@@ -78,11 +79,11 @@ def test_main(): ...@@ -78,11 +79,11 @@ def test_main():
assert os.path.isfile(os.path.join(aldir, f'{dname}-current.{fam}.miss.lst')) 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-align.{fam}.aln'))
assert os.path.isfile(os.path.join(aldir, f'{dname}-mafft-prt2nuc.{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") out_concat = os.path.join(aldir, dname + "-complete.nucl.cat.aln")
exp_concat = os.path.join(EXPPATH, "exp_pers4genome-complete.cat.aln") exp_concat = os.path.join(EXPPATH, "exp_pers4genome-complete.cat.aln")
assert tutil.compare_order_content(out_concat, exp_concat) assert tutil.compare_order_content(out_concat, exp_concat)
# Check content of treedir # Check content of treedir
out_grp = os.path.join(treedir, dname + ".grp.aln") out_grp = os.path.join(treedir, dname + ".nucl.grp.aln")
exp_grp = os.path.join(EXPPATH, "exp_pers4genomes.grp.aln") exp_grp = os.path.join(EXPPATH, "exp_pers4genomes.grp.aln")
assert tutil.compare_order_content(out_grp, exp_grp) assert tutil.compare_order_content(out_grp, exp_grp)
# Check presence of log files, and log.err is empty # Check presence of log files, and log.err is empty
...@@ -123,6 +124,7 @@ def test_main_exist_ok(): ...@@ -123,6 +124,7 @@ def test_main_exist_ok():
threads = 1 threads = 1
force = False force = False
cmd = "cmd test_main_exist_ok" cmd = "cmd test_main_exist_ok"
prot_ali = False
# Create output directories and files # Create output directories and files
aldir = os.path.join(outdir, "Align-" + dname) aldir = os.path.join(outdir, "Align-" + dname)
listdir = os.path.join(outdir, "List-" + dname) listdir = os.path.join(outdir, "List-" + dname)
...@@ -143,6 +145,8 @@ def test_main_exist_ok(): ...@@ -143,6 +145,8 @@ def test_main_exist_ok():
# Create content of aldir # Create content of aldir
ex_aldir = os.path.join(EXPPATH, "exp_aldir-pers") ex_aldir = os.path.join(EXPPATH, "exp_aldir-pers")
fams = [1, 4, 6, 8, 10, 11, 13, 14] fams = [1, 4, 6, 8, 10, 11, 13, 14]
fams_ok = [1, 6, 10, 11, 13, 14] # families with already all 4 genomes
fams_miss = [4, 8] # families with missing genomes
for fam in fams: for fam in fams:
outgen = os.path.join(aldir, f'{dname}-current.{fam}.gen') outgen = os.path.join(aldir, f'{dname}-current.{fam}.gen')
refgen = os.path.join(ex_aldir, f"current.{fam}.gen") refgen = os.path.join(ex_aldir, f"current.{fam}.gen")
...@@ -153,21 +157,28 @@ def test_main_exist_ok(): ...@@ -153,21 +157,28 @@ def test_main_exist_ok():
outmiss = os.path.join(aldir, f'{dname}-current.{fam}.miss.lst') outmiss = os.path.join(aldir, f'{dname}-current.{fam}.miss.lst')
refmiss = os.path.join(ex_aldir, f"current.{fam}.miss.lst") refmiss = os.path.join(ex_aldir, f"current.{fam}.miss.lst")
shutil.copyfile(refmiss, outmiss) 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') outbtr = os.path.join(aldir, f'{dname}-mafft-prt2nuc.{fam}.aln')
refbtr = os.path.join(ex_aldir, f"mafft-prt2nuc.{fam}.aln") refbtr = os.path.join(ex_aldir, f"mafft-prt2nuc.{fam}.aln")
shutil.copyfile(refbtr, outbtr) shutil.copyfile(refbtr, outbtr)
outcat = os.path.join(aldir, dname + "-complete.cat.aln") for fam in fams_ok:
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)
for fam in fams_miss:
outaln = os.path.join(aldir, f'{dname}-mafft-align.{fam}.aln')
refaln = os.path.join(ex_aldir, f"mafft-align.{fam}-completed.aln")
shutil.copyfile(refaln, outaln)
outcat = os.path.join(aldir, dname + "-complete.nucl.cat.aln")
refcat = os.path.join(EXPPATH, "exp_pers4genome-complete.cat.aln") refcat = os.path.join(EXPPATH, "exp_pers4genome-complete.cat.aln")
shutil.copyfile(refcat, outcat) shutil.copyfile(refcat, outcat)
# Create content of treedir # Create content of treedir
outgrp = os.path.join(treedir, dname + ".grp.aln") outgrp = os.path.join(treedir, dname + ".nucl.grp.aln")
refgrp = os.path.join(EXPPATH, "exp_pers4genomes.grp.aln") refgrp = os.path.join(EXPPATH, "exp_pers4genomes.grp.aln")
shutil.copyfile(refgrp, outgrp) shutil.copyfile(refgrp, outgrp)
# Run align module
al.main(cmd, corepers, list_genomes, dname, dbpath, outdir, threads, force) # RUN align module
al.main(cmd, corepers, list_genomes, dname, dbpath, outdir, prot_ali, threads, force, verbose=2)
# Check logs # Check logs
logfile = os.path.join(outdir, "PanACoTA-align_TEST4exists.log.details") logfile = os.path.join(outdir, "PanACoTA-align_TEST4exists.log.details")
with open(logfile, "r") as lc: with open(logfile, "r") as lc:
......
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