# HG changeset patch
# User galaxy-australia
# Date 1665613520 0
# Node ID c0e71cb2bd1b9415c6af69e0d74a8af39001676b
# Parent 7fbec959cf2b87c93b312aad0411d1ed4e224cbd
planemo upload for repository https://github.com/usegalaxy-au/tools-au commit 830b5bbf9c5375e714e1b7b9a3e8eec1e584e6b2
diff -r 7fbec959cf2b -r c0e71cb2bd1b alphafold.xml
--- a/alphafold.xml Fri Sep 16 06:14:06 2022 +0000
+++ b/alphafold.xml Wed Oct 12 22:25:20 2022 +0000
@@ -2,7 +2,7 @@
- AI-guided 3D structural prediction of proteins
2.1.2
- 3
+ 4
topic_0082
diff -r 7fbec959cf2b -r c0e71cb2bd1b gen_extra_outputs.py
--- a/gen_extra_outputs.py Fri Sep 16 06:14:06 2022 +0000
+++ b/gen_extra_outputs.py Wed Oct 12 22:25:20 2022 +0000
@@ -35,6 +35,7 @@
action="store_true"
)
parser.add_argument(
+ "-m",
"--multimer",
help="parse output from AlphaFold multimer",
action="store_true"
@@ -51,6 +52,12 @@
def __init__(self, settings: Settings):
self.settings = settings
+ def get_model_key(self, ix):
+ """Return json key for model index."""
+ if self.settings.is_multimer:
+ return f'model_{ix}_multimer'
+ return f'model_{ix}'
+
@property
def ranking_debug(self) -> str:
return f'{self.settings.workdir}/ranking_debug.json'
@@ -110,7 +117,7 @@
pklfile = model_pkls[i]
with open(pklfile, 'rb') as fp:
data = pickle.load(fp)
- plddts[f'model_{i+1}'] = [
+ plddts[self.context.get_model_key(i+1)] = [
float(f'{x:.2f}')
for x in data['plddt']
]
@@ -121,20 +128,25 @@
"""generates the output data we are interested in creating"""
def __init__(self, loader: FileLoader):
self.loader = loader
+ self.context = loader.context
def gen_conf_scores(self):
mapping = self.loader.get_model_mapping()
scores = self.loader.get_conf_scores()
ranked = list(scores.items())
ranked.sort(key=lambda x: x[1], reverse=True)
- return {f'model_{mapping[name]}': score
- for name, score in ranked}
+ return {
+ self.context.get_model_key(mapping[name]): score
+ for name, score in ranked
+ }
def gen_residue_scores(self) -> Dict[str, List[float]]:
mapping = self.loader.get_model_mapping()
model_plddts = self.loader.get_model_plddts()
- return {f'model_{mapping[name]}': plddts
- for name, plddts in model_plddts.items()}
+ return {
+ self.context.get_model_key(mapping[name]): plddts
+ for name, plddts in model_plddts.items()
+ }
class OutputWriter: