Skip to content

Fixed warnings from reproducibility audit #99

New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Open
braebigge wants to merge 1 commit into
base: main
Choose a base branch
from
+4 −3
Open

Fixed warnings from reproducibility audit #99

Show file tree
Hide file tree
Changes from all commits
Commits
Show all changes
1 commit
Select commit
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
4 changes: 3 additions & 1 deletion README.md
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -74,6 +74,8 @@ The pipeline supports two modes: **Search** and **Cluster**. Both modes are impl

In this mode, the pipeline starts with a set of input proteins of interest in PDB and FASTA format and performs broad BLAST and Foldseek searches to identify hits. The pipeline aggregates all hits, downloads PDBs, and builds a map.

Note: Search mode depends on live external APIs (Foldseek, BLAST, UniProt, and AlphaFold database). These services may change, experience downtime, or enforce rate limits, so results may not be fully reproducible across runs separated by significant time.

![search-mode-rulegraph](rulegraph-search-mode.png)

#### Inputs
Expand Down Expand Up @@ -135,7 +137,7 @@ In this mode, the pipeline starts with a folder containing PDBs of interest and
- `output`: directory where all pipeline outputs are placed.
- `analysis_name`: nickname for the analysis, appended to important output files.
- `features_file`: path to features file (described below).
- (Optional) `keyids`: a list of one or more key `protid` corresponding to the proteins to highlight in the output plots (similar to how the input proteins are highlighted in 'search' mode). Note: if not provided, the output directory `key_protid_tmscore_results` will be empty, as will the `protein_features/key_protid_tmscore_features.tsv` file.
- (Optional) `keyids`: a list of one or more key `protid` corresponding to the proteins to highlight in the output plots (similar to how the input proteins are highlighted in 'search' mode). Note: if not provided, the output directory `key_protid_tmscore_results` will be empty, as will the `protein_features/key_protid_tmscore_features.tsv` file. If `keyids` is provided, the pipeline will make Foldseek API calls for each key protein, so an internet connection is still required even in cluster mode.
- See [`config.yml`](config.yml) for additional parameters.
- Features file with protein metadata.
- Usually, we call this file `uniprot_features.tsv` but you can use any name.
Expand Down
3 changes: 1 addition & 2 deletions setup.py
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -2,7 +2,7 @@

setup(
name="ProteinCartography",
url="https://github.com/Arcadia-Science/ProteinCartography-private",
url="https://github.com/Arcadia-Science/ProteinCartography",
author="Dennis Sun",
author_email="dennis.sun@arcadiascience.com",
packages=["ProteinCartography"],
Expand All @@ -16,7 +16,6 @@
"ProteinCartography/esmfold_apiquery.py",
"ProteinCartography/extract_blast_hits.py",
"ProteinCartography/extract_foldseek_hits.py",
"ProteinCartography/extract_input_protein_distances.py",
"ProteinCartography/fetch_accession.py",
"ProteinCartography/foldseek_apiquery.py",
"ProteinCartography/foldseek_clustering.py",
Expand Down
Loading