From aa893ae3d403fcc51d6390400ad79cc0690f607a Mon Sep 17 00:00:00 2001
From: Gabriel Studer <gabriel.studer@unibas.ch>
Date: Mon, 26 Apr 2021 18:13:10 +0200
Subject: [PATCH] apply black
---
docker/run_qmean.py | 59 +++++++++++++++++++++++++--------------------
1 file changed, 33 insertions(+), 26 deletions(-)
diff --git a/docker/run_qmean.py b/docker/run_qmean.py
index eb072d1..5092f69 100644
--- a/docker/run_qmean.py
+++ b/docker/run_qmean.py
@@ -254,7 +254,7 @@ def _seqanno(target_seq, workdir, uniclust30, do_disco, smtldir, datefilter):
with open(a3m) as fh:
a3m_content = hhblits3.ParseA3M(fh)
else:
- # hhblits prints stuff in stderr, let's setup yet another logger and
+ # hhblits prints stuff in stderr, let's setup yet another logger and
# swallow everything. Check later if something went wrong...
logger = _Logger()
ost.PushLogSink(logger)
@@ -268,7 +268,7 @@ def _seqanno(target_seq, workdir, uniclust30, do_disco, smtldir, datefilter):
logger = _Logger()
ost.PushLogSink(logger)
hhm = hh.A3MToProfile(a3m)
- ost.PopLogSink()
+ ost.PopLogSink()
prof = hhblits3.ParseHHM(open(hhm))
# data for PSIPREDHandler can be fetched from a3m_content
@@ -291,9 +291,7 @@ def _seqanno(target_seq, workdir, uniclust30, do_disco, smtldir, datefilter):
accpro_handler = ACCPROHandler(data)
if do_disco:
- dc = _get_dc(
- seqanno_workdir, target_seq, hh, a3m, smtldir, datefilter
- )
+ dc = _get_dc(seqanno_workdir, target_seq, hh, a3m, smtldir, datefilter)
else:
dc = None
@@ -436,25 +434,27 @@ class ModelScorer:
# the global scores are the same as QMEAN but the local ones change
settings = qmean_config.MembraneSettings()
peptide_sel = self.processed_model.Select("peptide=True")
- res = mqa_result_membrane.LocalMembraneResult.Create(peptide_sel,
- settings,
- False,
- psipred=psipred_handler_list,
- accpro=accpro_handler_list)
+ res = mqa_result_membrane.LocalMembraneResult.Create(
+ peptide_sel,
+ settings,
+ False,
+ psipred=psipred_handler_list,
+ accpro=accpro_handler_list,
+ )
for ch, s in zip(peptide_sel.chains, self.seqres_list):
score_list = list([None] * len(s))
local_scores[ch.GetName()] = score_list
- chain_name_idx = res.score_table.GetColIndex('chain')
- rnum_idx = res.score_table.GetColIndex('rnum')
- score_idx = res.score_table.GetColIndex('QMEAN')
+ chain_name_idx = res.score_table.GetColIndex("chain")
+ rnum_idx = res.score_table.GetColIndex("rnum")
+ score_idx = res.score_table.GetColIndex("QMEAN")
for r in res.score_table.rows:
chain_name = r[chain_name_idx]
rnum = r[rnum_idx]
score = r[score_idx]
- local_scores[chain_name][rnum-1] = NaN_To_None(score)
+ local_scores[chain_name][rnum - 1] = NaN_To_None(score)
else:
raise RuntimeError(f"Unknown scoring function {scoring_function}")
@@ -670,7 +670,7 @@ class ModelScorerContainer:
out_dict = dict()
out_dict["models"] = dict()
for m_idx, m in enumerate(self.models):
- identifier = str(m_idx+1)
+ identifier = str(m_idx + 1)
identifier = (3 - len(identifier)) * "0" + identifier
out_dict["models"]["model_" + identifier] = m.to_json()
return out_dict
@@ -783,7 +783,7 @@ def _check_smtl(args):
"seqres_data.dat",
"atomseq_data.dat",
"ca_pos_data.dat",
- "VERSION"
+ "VERSION",
]
for f in expected_files:
@@ -835,7 +835,7 @@ def _parse_args():
"--profiles",
nargs="+",
default=None,
- help="Precomputed HHblits sequence profile(s) in a3m format that match target sequence(s) provided in seqres - must contain psipred annotation"
+ help="Precomputed HHblits sequence profile(s) in a3m format that match target sequence(s) provided in seqres - must contain psipred annotation",
)
parser.add_argument(
"--workdir",
@@ -907,16 +907,22 @@ def _parse_args():
if not os.path.exists(p):
raise RuntimeError(f"specified path {p} does not exist")
a3m_content = hhblits3.ParseA3M(open(p))
- if a3m_content['ss_pred'] is None or a3m_content['ss_conf'] is None:
- raise RuntimeError(f"Sequence profile {p} must contain secondary structure annotation")
- trg_seq = a3m_content['msa'].GetSequence(0).GetGaplessString()
- trg_seq_hash = _get_seq_name(trg_seq)
+ if a3m_content["ss_pred"] is None or a3m_content["ss_conf"] is None:
+ raise RuntimeError(
+ f"Sequence profile {p} must contain secondary structure annotation"
+ )
+ trg_seq = a3m_content["msa"].GetSequence(0).GetGaplessString()
+ trg_seq_hash = _get_seq_name(trg_seq)
if trg_seq_hash not in seqres_hashes:
raise RuntimeError(f"Could not find matching SEQRES for {p}")
seqanno_workdir = os.path.join(args.workdir, trg_seq_hash)
os.makedirs(seqanno_workdir)
- shutil.copy(p, os.path.join(seqanno_workdir,
- hhblits3.HHblits.OUTPUT_PREFIX + '.a3m'))
+ shutil.copy(
+ p,
+ os.path.join(
+ seqanno_workdir, hhblits3.HHblits.OUTPUT_PREFIX + ".a3m"
+ ),
+ )
# Check for valid uniclust30 and report to logger
args.uniclust30 = _get_uniclust30()
@@ -952,11 +958,12 @@ def _main():
if args.seqres:
out["seqres_uploaded"] = list()
for s in args.seqres:
- out["seqres_uploaded"].append({"name": s.GetName(),
- "sequence": str(s)})
+ out["seqres_uploaded"].append(
+ {"name": s.GetName(), "sequence": str(s)}
+ )
out["smtl_version"] = None
if args.method == "QMEANDisCo":
- with open('/smtl/VERSION', 'r') as fh:
+ with open("/smtl/VERSION", "r") as fh:
out["smtl_version"] = fh.read().strip()
######################################
--
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