From 2e48b5d15b673b89a988999566a6e7562a56b5ff Mon Sep 17 00:00:00 2001
From: Stefan Bienert <stefan.bienert@unibas.ch>
Date: Wed, 16 Mar 2022 09:20:44 +0100
Subject: [PATCH] Prepare for AF2 2.2.0
---
CHANGELOG.md | 10 +++++++++-
run_af2/bin/submit-af2 | 6 ------
run_af2/src/run_af2/_shared.py | 20 --------------------
run_af2/src/run_af2/run_singularity.py | 11 -----------
4 files changed, 9 insertions(+), 38 deletions(-)
diff --git a/CHANGELOG.md b/CHANGELOG.md
index d3ddb5a..9e98c05 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -1,8 +1,16 @@
+Changes in Release 3.0.0
+=================================================================================
+
+* `run_af2` Python package:
+ * Prepare to run AF2 pipeline 2.2.0
+ * Remove option `--is-prokaryote-list`
+
+
Changes in Release 2.2.0
=================================================================================
* `run_af2` Python package:
- * add command line options `--use-precomputed-msas`, `--no-run-relax` and
+ * Add command line options `--use-precomputed-msas`, `--no-run-relax` and
`--use-gpu-relax`
diff --git a/run_af2/bin/submit-af2 b/run_af2/bin/submit-af2
index 014b8b8..1108268 100755
--- a/run_af2/bin/submit-af2
+++ b/run_af2/bin/submit-af2
@@ -29,7 +29,6 @@ if test $# -lt 2; then
echo "usage: submit-af2 [--use-gpu]"
echo " [--db-preset {reduced_dbs,full_dbs}]"
echo " [--model-preset {monomer,monomer_casp14,monomer_ptm,multimer}]"
- echo " [--is-prokaryote-list <bool>,<bool>,...]"
echo " [--max-template-date YYYY-MM-DD]"
echo " <OUTPUT DIR> <FASTA FILE> [<FASTA FILE> ...]"
exit 1
@@ -56,11 +55,6 @@ for i in 1 2 3 4 5; do
shift
AF_PIPELINE_PARAM="${AF_PIPELINE_PARAM} --model-preset ${1}"
shift
- else if test x"${1}" = x"--is-prokaryote-list"; then
- shift
- AF_PIPELINE_PARAM="${AF_PIPELINE_PARAM} --is-prokaryote-list ${1}"
- shift
- fi
fi
fi
fi
diff --git a/run_af2/src/run_af2/_shared.py b/run_af2/src/run_af2/_shared.py
index 577ec12..5671bb3 100644
--- a/run_af2/src/run_af2/_shared.py
+++ b/run_af2/src/run_af2/_shared.py
@@ -110,16 +110,6 @@ def parse_af2_arguments(parser):
+ "AF2 pipeline.",
default="monomer",
)
- af2_group.add_argument(
- "-i",
- "--is-prokaryote-list",
- type=str,
- help="For the multimer model, declare sequences to by prokaryotic or "
- + "not. Goes by true/ false, needs to be listed for every input FASTA "
- + "as a list.",
- metavar="<true|false>,<true|false>,...",
- default=None,
- )
af2_group.add_argument(
"--use-precomputed-msas",
action="store_true",
@@ -254,16 +244,6 @@ def parse_af2_arguments(parser):
flush=True,
)
- # check that --is-prokaryote-list has as many values as sequence files
- if opts.is_prokaryote_list is not None:
- if opts.is_prokaryote_list.count(",") + 1 != len(opts.fasta_files):
- print(
- "Number of values for '--is-prokaryote-list' does not match "
- + "the number of FASTA files. Aborting.",
- file=sys.stderr,
- )
- sys.exit(1)
-
if opts.singularity_image is not None:
if not os.path.exists(opts.singularity_image):
print(
diff --git a/run_af2/src/run_af2/run_singularity.py b/run_af2/src/run_af2/run_singularity.py
index 24af0d0..66b5542 100644
--- a/run_af2/src/run_af2/run_singularity.py
+++ b/run_af2/src/run_af2/run_singularity.py
@@ -116,7 +116,6 @@ def _assemble_singularity_call( # pylint: disable=too-many-arguments
use_gpu,
db_preset,
model_preset,
- is_prokaryote_list,
use_precomputed_msas,
no_run_relax,
use_gpu_relax,
@@ -156,8 +155,6 @@ def _assemble_singularity_call( # pylint: disable=too-many-arguments
"--logtostderr",
]
)
- if is_prokaryote_list is not None:
- snglrty_cmd.append(f"--is_prokaryote_list={is_prokaryote_list}")
bool_args = {
"use_precomputed_msas": use_precomputed_msas,
@@ -208,7 +205,6 @@ def run_af2_singularity_image( # pylint: disable=too-many-arguments
use_gpu=False,
db_preset="full_dbs",
model_preset="monomer",
- is_prokaryote_list=None,
use_precomputed_msas=False,
no_run_relax=False,
use_gpu_relax=True,
@@ -273,11 +269,6 @@ def run_af2_singularity_image( # pylint: disable=too-many-arguments
:param model_preset: Model configuration - corresponds to the model_preset
parameter in AF2.
:type model_preset: :class:`str`
- :param is_prokaryote_list: For the multimer model, mark sequences as
- prokaryotic. Corresponds to the
- is_prokaryote_list parameter in AF2.
- :type is_prokaryote_list: :class:`str` like needed by AF2, e.g.
- "true,false,true"
:param use_precomputed_msas: Use existing MSAs from cwd. Corresponds to the
use_precomputed_msas parameter in AF2.
:type use_precomputed_msas: :class:`bool`
@@ -416,7 +407,6 @@ def run_af2_singularity_image( # pylint: disable=too-many-arguments
use_gpu,
db_preset,
model_preset,
- is_prokaryote_list,
use_precomputed_msas,
no_run_relax,
use_gpu_relax,
@@ -488,7 +478,6 @@ def main():
opts.use_gpu,
opts.db_preset,
opts.model_preset,
- opts.is_prokaryote_list,
opts.use_precomputed_msas,
opts.no_run_relax,
opts.use_gpu_relax,
--
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