codeply-cli 0.3.0 → 0.4.0

package/skills/scientific-pkg-gget/SKILL.md

@@ -1,167 +1,167 @@
----
-name: gget
-description: gget CLI and Python workflow for quick genomic database queries, sequence lookup, BLAST-style searches, enrichment checks, and reproducible bioinformatics evidence logs.
-metadata:
-  origin: community
----
-
-# gget
-
-Use this skill when a task needs quick bioinformatics lookup across genomic
-reference databases with the `gget` CLI or Python package.
-
-## When to Use
-
-- Finding Ensembl IDs, gene metadata, transcript details, or sequences.
-- Running quick BLAST or BLAT lookups without building a full local pipeline.
-- Fetching reference genome links and annotations from Ensembl.
-- Querying protein structure, pathway, cancer, expression, or disease-association
-  modules through a single interface.
-- Creating a reproducible first-pass evidence log before moving to heavier
-  tools such as Biopython, Snakemake, Nextflow, BLAST+, or database-specific
-  clients.
-
-Use a dedicated workflow instead of `gget` when the task requires regulated
-clinical interpretation, high-throughput production pipelines, or fine-grained
-control over database versions and local indexes.
-
-## Installation
-
-Use a clean Python environment.
-
-```bash
-python -m venv .venv
-. .venv/bin/activate
-python -m pip install --upgrade pip
-python -m pip install --upgrade gget
-gget --help
-```
-
-If `uv` is available:
-
-```bash
-uv venv
-. .venv/bin/activate
-uv pip install gget
-```
-
-Before relying on an older environment, upgrade `gget` and re-check the module
-docs. The upstream databases queried by `gget` change over time.
-
-## Basic Patterns
-
-CLI shape:
-
-```bash
-gget <module> [arguments] [options]
-```
-
-Python shape:
-
-```python
-import gget
-
-result = gget.search(["BRCA1"], species="human")
-print(result)
-```
-
-Common workflow:
-
-1. Identify the species, assembly, gene ID type, and database needed.
-2. Check the current module documentation for arguments.
-3. Run a small query first.
-4. Save output with an explicit filename and date.
-5. Record module name, version, arguments, and database assumptions.
-
-## Common Modules
-
-Use current upstream docs for exact arguments. These modules are common first
-choices:
-
-- `gget search`: find Ensembl IDs from search terms.
-- `gget info`: retrieve metadata for Ensembl, UniProt, or related IDs.
-- `gget seq`: fetch nucleotide or amino-acid sequences.
-- `gget ref`: retrieve reference genome download links.
-- `gget blast`: run a quick BLAST query.
-- `gget blat`: locate a sequence against supported genome assemblies.
-- `gget muscle`: run multiple sequence alignment.
-- `gget diamond`: run local sequence alignment against reference sequences.
-- `gget alphafold` and `gget pdb`: inspect protein-structure references.
-- `gget enrichr`, `gget opentargets`, `gget archs4`, `gget bgee`, `gget cbio`,
-  and `gget cosmic`: explore enrichment, target, expression, cancer, and disease
-  association data.
-
-Do not assume every module supports every Python version or dependency set.
-Some optional scientific dependencies have narrower version support than the
-core package.
-
-## Quick Examples
-
-Find genes:
-
-```bash
-gget search -s human brca1 dna repair -o brca1-search.json
-```
-
-Fetch gene metadata:
-
-```bash
-gget info ENSG00000012048 -o brca1-info.json
-```
-
-Fetch a sequence:
-
-```bash
-gget seq ENSG00000012048 -o brca1-seq.fa
-```
-
-Run a small BLAST query:
-
-```bash
-gget blast "MEEPQSDPSVEPPLSQETFSDLWKLLPEN" -l 10 -o blast-results.json
-```
-
-Python example:
-
-```python
-import gget
-
-genes = gget.search(["BRCA1", "DNA repair"], species="human")
-info = gget.info(["ENSG00000012048"])
-sequence = gget.seq("ENSG00000012048")
-```
-
-## Reproducibility Log
-
-For scientific outputs, include enough metadata to replay the query.
-
-```markdown
-| Date | gget version | Module | Query | Species/assembly | Output | Notes |
-| --- | --- | --- | --- | --- | --- | --- |
-| 2026-05-11 | `gget --version` | search | `BRCA1 DNA repair` | human | `brca1-search.json` | Docs checked before run |
-```
-
-Also record:
-
-- Python version and environment manager.
-- Any optional dependency installed through `gget setup`.
-- Database-specific identifiers returned by the query.
-- Whether output is JSON, CSV, FASTA, or a DataFrame export.
-- Any failures that were resolved by upgrading `gget`.
-
-## Review Checklist
-
-- Did you upgrade or verify the installed `gget` version?
-- Did you check the current upstream module docs before using arguments?
-- Is the species or assembly explicit?
-- Are identifiers preserved exactly, including Ensembl/UniProt prefixes?
-- Is the result labeled as database output rather than clinical interpretation?
-- Is the query reproducible from the saved command or Python snippet?
-- Are optional dependencies installed in an isolated environment?
-
-## References
-
-- [gget documentation](https://pachterlab.github.io/gget/)
-- [gget updates](https://pachterlab.github.io/gget/en/updates.html)
-- [gget GitHub repository](https://github.com/pachterlab/gget)
-- [gget Bioinformatics paper](https://doi.org/10.1093/bioinformatics/btac836)
+---
+name: gget
+description: gget CLI and Python workflow for quick genomic database queries, sequence lookup, BLAST-style searches, enrichment checks, and reproducible bioinformatics evidence logs.
+metadata:
+  origin: community
+---
+
+# gget
+
+Use this skill when a task needs quick bioinformatics lookup across genomic
+reference databases with the `gget` CLI or Python package.
+
+## When to Use
+
+- Finding Ensembl IDs, gene metadata, transcript details, or sequences.
+- Running quick BLAST or BLAT lookups without building a full local pipeline.
+- Fetching reference genome links and annotations from Ensembl.
+- Querying protein structure, pathway, cancer, expression, or disease-association
+  modules through a single interface.
+- Creating a reproducible first-pass evidence log before moving to heavier
+  tools such as Biopython, Snakemake, Nextflow, BLAST+, or database-specific
+  clients.
+
+Use a dedicated workflow instead of `gget` when the task requires regulated
+clinical interpretation, high-throughput production pipelines, or fine-grained
+control over database versions and local indexes.
+
+## Installation
+
+Use a clean Python environment.
+
+```bash
+python -m venv .venv
+. .venv/bin/activate
+python -m pip install --upgrade pip
+python -m pip install --upgrade gget
+gget --help
+```
+
+If `uv` is available:
+
+```bash
+uv venv
+. .venv/bin/activate
+uv pip install gget
+```
+
+Before relying on an older environment, upgrade `gget` and re-check the module
+docs. The upstream databases queried by `gget` change over time.
+
+## Basic Patterns
+
+CLI shape:
+
+```bash
+gget <module> [arguments] [options]
+```
+
+Python shape:
+
+```python
+import gget
+
+result = gget.search(["BRCA1"], species="human")
+print(result)
+```
+
+Common workflow:
+
+1. Identify the species, assembly, gene ID type, and database needed.
+2. Check the current module documentation for arguments.
+3. Run a small query first.
+4. Save output with an explicit filename and date.
+5. Record module name, version, arguments, and database assumptions.
+
+## Common Modules
+
+Use current upstream docs for exact arguments. These modules are common first
+choices:
+
+- `gget search`: find Ensembl IDs from search terms.
+- `gget info`: retrieve metadata for Ensembl, UniProt, or related IDs.
+- `gget seq`: fetch nucleotide or amino-acid sequences.
+- `gget ref`: retrieve reference genome download links.
+- `gget blast`: run a quick BLAST query.
+- `gget blat`: locate a sequence against supported genome assemblies.
+- `gget muscle`: run multiple sequence alignment.
+- `gget diamond`: run local sequence alignment against reference sequences.
+- `gget alphafold` and `gget pdb`: inspect protein-structure references.
+- `gget enrichr`, `gget opentargets`, `gget archs4`, `gget bgee`, `gget cbio`,
+  and `gget cosmic`: explore enrichment, target, expression, cancer, and disease
+  association data.
+
+Do not assume every module supports every Python version or dependency set.
+Some optional scientific dependencies have narrower version support than the
+core package.
+
+## Quick Examples
+
+Find genes:
+
+```bash
+gget search -s human brca1 dna repair -o brca1-search.json
+```
+
+Fetch gene metadata:
+
+```bash
+gget info ENSG00000012048 -o brca1-info.json
+```
+
+Fetch a sequence:
+
+```bash
+gget seq ENSG00000012048 -o brca1-seq.fa
+```
+
+Run a small BLAST query:
+
+```bash
+gget blast "MEEPQSDPSVEPPLSQETFSDLWKLLPEN" -l 10 -o blast-results.json
+```
+
+Python example:
+
+```python
+import gget
+
+genes = gget.search(["BRCA1", "DNA repair"], species="human")
+info = gget.info(["ENSG00000012048"])
+sequence = gget.seq("ENSG00000012048")
+```
+
+## Reproducibility Log
+
+For scientific outputs, include enough metadata to replay the query.
+
+```markdown
+| Date | gget version | Module | Query | Species/assembly | Output | Notes |
+| --- | --- | --- | --- | --- | --- | --- |
+| 2026-05-11 | `gget --version` | search | `BRCA1 DNA repair` | human | `brca1-search.json` | Docs checked before run |
+```
+
+Also record:
+
+- Python version and environment manager.
+- Any optional dependency installed through `gget setup`.
+- Database-specific identifiers returned by the query.
+- Whether output is JSON, CSV, FASTA, or a DataFrame export.
+- Any failures that were resolved by upgrading `gget`.
+
+## Review Checklist
+
+- Did you upgrade or verify the installed `gget` version?
+- Did you check the current upstream module docs before using arguments?
+- Is the species or assembly explicit?
+- Are identifiers preserved exactly, including Ensembl/UniProt prefixes?
+- Is the result labeled as database output rather than clinical interpretation?
+- Is the query reproducible from the saved command or Python snippet?
+- Are optional dependencies installed in an isolated environment?
+
+## References
+
+- [gget documentation](https://pachterlab.github.io/gget/)
+- [gget updates](https://pachterlab.github.io/gget/en/updates.html)
+- [gget GitHub repository](https://github.com/pachterlab/gget)
+- [gget Bioinformatics paper](https://doi.org/10.1093/bioinformatics/btac836)