From 728445dd84f8b5d159c97371ee828ea8761ea938 Mon Sep 17 00:00:00 2001
From: Amandine PERRIN <amandine.perrin@pasteur.fr>
Date: Mon, 10 Jul 2023 11:01:57 +0200
Subject: [PATCH] Add option anysymbol to mafft
---
PanACoTA/align_module/alignment.py | 2 +-
test/test_functional/test_align.py | 2 +-
test/test_unit/test_align/test_alignment.py | 10 +++++-----
3 files changed, 7 insertions(+), 7 deletions(-)
diff --git a/PanACoTA/align_module/alignment.py b/PanACoTA/align_module/alignment.py
index bd3f05a1..1618f4a8 100755
--- a/PanACoTA/align_module/alignment.py
+++ b/PanACoTA/align_module/alignment.py
@@ -557,7 +557,7 @@ def mafft_align(num_fam, prt_file, mafft_file, nbfprt, logger):
False otherwise
"""
logger.log(utils.detail_lvl(), f"Aligning family {num_fam}")
- cmd = f"mafft --auto {prt_file}"
+ cmd = f"mafft --auto --anysymbol {prt_file}"
error = f"Problem while trying to align fam {num_fam}"
stdout = open(mafft_file, "w")
stderr = open(mafft_file + ".log", "w")
diff --git a/test/test_functional/test_align.py b/test/test_functional/test_align.py
index cf49b2e9..586b6b2d 100755
--- a/test/test_functional/test_align.py
+++ b/test/test_functional/test_align.py
@@ -106,7 +106,7 @@ def test_main():
for fam in fams:
assert f"Checking extractions for family {fam}" in " ".join(log_content)
assert f"Aligning family {fam}" in " ".join(log_content)
- assert ("Mafft command: mafft --auto "
+ assert ("Mafft command: mafft --auto --anysymbol "
"test/data/align/generated_by_func_tests/"
f"Align-TEST4/TEST4-current.{fam}.prt") in " ".join(log_content)
assert f"Back-translating family {fam}" in " ".join(log_content)
diff --git a/test/test_unit/test_align/test_alignment.py b/test/test_unit/test_align/test_alignment.py
index f597c8a5..8260be8a 100755
--- a/test/test_unit/test_align/test_alignment.py
+++ b/test/test_unit/test_align/test_alignment.py
@@ -470,7 +470,7 @@ def test_family_align_mafftempty_btrempty(caplog):
"in test/data/align/exp_files/exp_aldir-pers/current.8.prt (3) and proteins aligned "
"in existing test/data/align/generated_by_unit-tests/test_fam_align.8.aln") in caplog.text
assert "Aligning family 8" in caplog.text
- assert "Mafft command: mafft --auto test/data/align/exp_files/exp_aldir-pers/current.8.prt" in caplog.text
+ assert "Mafft command: mafft --auto --anysymbol test/data/align/exp_files/exp_aldir-pers/current.8.prt" in caplog.text
assert "Back-translating family 8" in caplog.text
# Check content of mafft and btr files
exp_mafft = os.path.join(EXPPATH, "exp_aldir-pers", "mafft-align.8.aln")
@@ -577,7 +577,7 @@ def test_family_align_nomafft_btrempty_errormafft(caplog):
ngenomes, logger)
assert "Checking extractions for family 8" in caplog.text
assert "Aligning family 8" in caplog.text
- assert ("command '>mafft --auto test/data/align/exp_files/exp_aldir-pers/current.8.prt' "
+ assert ("command '>mafft --auto --anysymbol test/data/align/exp_files/exp_aldir-pers/current.8.prt' "
"is not possible") in caplog.text
# Check content of mafft and btr files
assert not os.path.isfile(mafft_file)
@@ -808,7 +808,7 @@ def test_handle_family_true():
q.put(None)
assert "Checking extractions for family 8" in q.get().message
assert "Aligning family 8" in q.get().message
- assert ("mafft --auto test/data/align/generated_by_unit-tests/aldir/"
+ assert ("mafft --auto --anysymbol test/data/align/generated_by_unit-tests/aldir/"
"TESThandlefam-current.8.prt") in q.get().message
assert "Back-translating family 8" in q.get().message
# Writes it twice: 1 for nucleic and one for aa
@@ -849,7 +849,7 @@ def test_handle_family_true_nomiss():
q.put(None)
assert "Checking extractions for family 8" in q.get().message
assert "Aligning family 8" in q.get().message
- assert ("mafft --auto test/data/align/generated_by_unit-tests/aldir/"
+ assert ("mafft --auto --anysymbol test/data/align/generated_by_unit-tests/aldir/"
"TESThandlefam-current.8.prt") in q.get().message
assert "Back-translating family 8" in q.get().message
assert not q.get()
@@ -894,7 +894,7 @@ def test_handle_family_emptyaln_true():
"and proteins aligned in existing "
"test/data/align/generated_by_unit-tests/aldir/TESThandlefam-mafft-align.8.aln") in q.get().message
assert "Aligning family 8" in q.get().message
- assert ("mafft --auto test/data/align/generated_by_unit-tests/aldir/"
+ assert ("mafft --auto --anysymbol test/data/align/generated_by_unit-tests/aldir/"
"TESThandlefam-current.8.prt") in q.get().message
assert "Back-translating family 8" in q.get().message
assert "Adding missing genomes for family 8 in protein alignment" in q.get().message
--
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