From 3af6f093f052d29431ff46ab827fe62bfc75caf9 Mon Sep 17 00:00:00 2001
From: Keith Cheveralls <keith.chev@gmail.com>
Date: Thu, 25 Jan 2024 17:59:18 -0800
Subject: [PATCH] Ensure user-provided PDBs are used for clustering (#83)
* prioritize copy_pdbs
* exclude the input protids from the protids for which to download pdbs from alphafold
---
ProteinCartography/filter_uniprot_hits.py | 20 +++++++++++++++++++-
Snakefile | 9 +++++++--
2 files changed, 26 insertions(+), 3 deletions(-)
diff --git a/ProteinCartography/filter_uniprot_hits.py b/ProteinCartography/filter_uniprot_hits.py
index dca225c..1f4b3ce 100644
--- a/ProteinCartography/filter_uniprot_hits.py
+++ b/ProteinCartography/filter_uniprot_hits.py
@@ -30,6 +30,11 @@ def parse_args():
default="0",
help="maximum protein length of proteins to keep. If set to 0, no upper limit is applied.",
)
+ parser.add_argument(
+ "--excluded-protids",
+ nargs="*",
+ help="a list of protids to exclude from the results",
+ )
args = parser.parse_args()
return args
@@ -42,6 +47,7 @@ def filter_results(
filter_fragment=True,
min_length=0,
max_length=0,
+ excluded_protids=None,
):
"""
Takes an input uniprot_features.tsv file and filters the results based on fragment status,
@@ -78,6 +84,11 @@ def filter_results(
if max_length > 0:
filtered_df = filtered_df[filtered_df["Length"].astype(int) < max_length]
+ if excluded_protids is None:
+ excluded_protids = []
+
+ filtered_df = filtered_df[~filtered_df["protid"].isin(excluded_protids)]
+
with open(output_file, "w+") as f:
f.writelines([protid + "\n" for protid in filtered_df["protid"]])
@@ -88,6 +99,7 @@ def main():
args = parse_args()
input_file = args.input
output_file = args.output
+ excluded_protids = args.excluded_protids
try:
min_length = int(args.min_length)
@@ -98,7 +110,13 @@ def main():
except (TypeError, ValueError):
max_length = 0
- filter_results(input_file, output_file, min_length=min_length, max_length=max_length)
+ filter_results(
+ input_file,
+ output_file,
+ min_length=min_length,
+ max_length=max_length,
+ excluded_protids=excluded_protids,
+ )
if __name__ == "__main__":
diff --git a/Snakefile b/Snakefile
index 087267f..b1b492f 100644
--- a/Snakefile
+++ b/Snakefile
@@ -125,7 +125,7 @@ rule make_pdb:
input:
cds=input_dir / "{protid}.fasta",
output:
- pdb=input_dir / "{protid}.pdb",
+ pdb=pdb_download_dir / "{protid}.pdb",
benchmark:
output_dir / benchmarks_dir / "{protid}.make_pdb.txt"
conda:
@@ -150,6 +150,11 @@ rule copy_pdb:
"""
+# first try to copy any user-provided PDB files from the input directory;
+# if they don't exist, generate them using make_pdb
+ruleorder: copy_pdb > make_pdb
+
+
rule run_blast:
"""
Using files located in the input directory, run `blastp` using the remote BLAST API.
@@ -348,7 +353,7 @@ rule filter_uniprot_hits:
"envs/pandas.yml"
shell:
"""
- python ProteinCartography/filter_uniprot_hits.py -i {input} -o {output} -m {params.min_length} -M {params.max_length}
+ python ProteinCartography/filter_uniprot_hits.py -i {input} -o {output} -m {params.min_length} -M {params.max_length} --excluded-protids {PROTID}
"""