Contributing cyvcf2 get mean allele length fork

tasks/cyvcf2_count_alterations/data/.gitignore

@@ -0,0 +1 @@
+# Add large files here that should not be committed to the repository

tasks/cyvcf2_count_alterations/implementation.py

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+def cyvcf2_count_alterations(
+    input_vcf: str = "/mount/input/SRR2058984_zc.vcf",
+    reference_nucleotide: str = "A",
+    alternate_nucleotide: str = "C",
+) -> dict:
+    """
+        Use the cyvcf2 to parse through VCF file containing detected sequence variants to identify the number of single
+    nucleotide polymorphisms (SNPs) from a specific reference nucleotide to a specific alternate nucleotide.
+
+        Args:
+            input_vcf: Path to the input VCF file
+            reference_nucleotide: The reference nucleotide to compare against ("A", "C", "G", or "T")
+            alternate_nucleotide: The alternate nucleotide to compare against ("A", "C", "G", or "T")
+
+        Returns:
+            dict with the following structure:
+            {
+              'num_snps': int  # The number of SNPs that are altered from reference `reference_nucleotide` to
+    `alternate_nucleotide`.
+            }
+    """
+    from cyvcf2 import VCF
+
+    # Initialize counters
+    num_snps = 0
+
+    # Iterate over each variant
+    for variant in VCF(input_vcf):
+        if (
+            variant.is_snp
+            and variant.REF == reference_nucleotide
+            and variant.ALT
+            and variant.ALT[0] == alternate_nucleotide
+        ):
+            num_snps += 1
+
+    return {"num_snps": num_snps}

tasks/cyvcf2_count_alterations/install.sh

@@ -0,0 +1,9 @@
+#! /bin/bash
+set -e
+
+git clone https://github.com/brentp/cyvcf2 /workspace/cyvcf2
+cd /workspace/cyvcf2 && git checkout main && git checkout 541ab16
+
+# Insert commands here to install dependencies and setup the environment...
+pip install cyvcf2
+pip install numpy 

tasks/cyvcf2_count_alterations/task.yaml

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+name: cyvcf2_count_alterations
+repo:
+  name: cyvcf2
+  url: "https://github.com/brentp/cyvcf2" 
+  commit: 541ab16 
+  branch: main 
+  env: []
+papers: [pedersen2017cyvcf2] 
+category: genomics_proteomics
+requires: cpu 
+description: Use cyvcf2 to parse through VCF file containing detected sequence variants to identify the number of single nucleotide polymorphisms (SNPs) from a specific reference nucleotide to a specific alternate nucleotide.
+arguments:
+  - name: input_vcf
+    description: Path to the input VCF file
+    type: str
+  - name: reference_nucleotide
+    description: The reference nucleotide to compare against ("A", "C", "G", or "T")
+    type: str
+  - name: alternate_nucleotide
+    description: The alternate nucleotide to compare against ("A", "C", "G", or "T")
+    type: str
+returns:
+  - name: num_snps
+    description: The number of SNPs that are altered from reference `reference_nucleotide` to `alternate_nucleotide`.
+    type: int
+example:
+  arguments:
+    - name: input_vcf
+      value: /mount/input/SRR2058984_zc.vcf
+    - name: reference_nucleotide
+      value: "A"
+    - name: alternate_nucleotide
+      value: "C"
+  mount:
+    - source: SRR2058984_zc.vcf
+      target: SRR2058984_zc.vcf
+test_invocations:
+  - name: SRR2058985
+    arguments:
+      - name: input_vcf
+        value: /mount/input/SRR2058985_zc.vcf
+      - name: reference_nucleotide
+        value: "A"
+      - name: alternate_nucleotide
+        value: "T"
+    mount:
+      - source: SRR2058985_zc.vcf
+        target: SRR2058985_zc.vcf
+  - name: SRR2058987
+    arguments:
+      - name: input_vcf
+        value: /mount/input/SRR2058987_zc.vcf
+      - name: reference_nucleotide
+        value: "T"
+      - name: alternate_nucleotide
+        value: "C"
+    mount:
+      - source: SRR2058987_zc.vcf
+        target: SRR2058987_zc.vcf
+  - name: SRR2058988
+    arguments:
+      - name: input_vcf
+        value: /mount/input/SRR2058988_zc.vcf
+      - name: reference_nucleotide
+        value: "T"
+      - name: alternate_nucleotide
+        value: "A"
+    mount:
+      - source: SRR2058988_zc.vcf
+        target: SRR2058988_zc.vcf
+  - name: SRR2058989
+    arguments:
+      - name: input_vcf
+        value: /mount/input/SRR2058989_zc.vcf
+      - name: reference_nucleotide
+        value: "T"
+      - name: alternate_nucleotide
+        value: "G"
+    mount:
+      - source: SRR2058989_zc.vcf
+        target: SRR2058989_zc.vcf

tasks/cyvcf2_count_alterations/tests.py

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+import pytest
+from pytest_lazy_fixtures import lf
+from tasks.utils import initialize, parametrize_invocation
+from toolarena.run import ToolRunResult
+
+initialize()
+
+
+@parametrize_invocation("SRR2058985", "SRR2058987", "SRR2058988", "SRR2058989")
+def test_status(invocation: ToolRunResult):
+    assert invocation.status == "success"
+
+
+@pytest.mark.parametrize(
+    "invocation,expected_num_snps",
+    [
+        (lf("SRR2058985"), 0),
+        (lf("SRR2058987"), 13),
+        (lf("SRR2058988"), 1),
+        (lf("SRR2058989"), 4),
+    ],
+)
+def test_num_snps(invocation: ToolRunResult, expected_num_snps: int):
+    assert invocation.result["num_snps"] == expected_num_snps

tasks/papers.bib

@@ -1,3 +1,15 @@
+@article{pedersen2017cyvcf2,
+  author  = {Pedersen, Brent S and Quinlan, Aaron R},
+  title   = {cyvcf2: fast, flexible variant analysis with Python},
+  year    = {2017},
+  month   = {02},
+  journal = {Bioinformatics},
+  volume  = {33},
+  number  = {12},
+  pages   = {1867-1869},
+  issn    = {1367-4803},
+}
+
 @article{isensee2020nnunet,
   author    = {Isensee,  Fabian and Jaeger,  Paul F. and Kohl,  Simon A. A. and Petersen,  Jens and Maier-Hein,  Klaus H.},
   title     = {nnU-Net: a self-configuring method for deep learning-based biomedical image segmentation},

tasks/papers.yaml

@@ -24,3 +24,4 @@ yuksekgonul2024textgrad: "https://arxiv.org/abs/2406.07496"
 neidlinger2025eagle: "https://arxiv.org/abs/2502.13027"
 wasserthal2023totalsegmentator: "https://pubs.rsna.org/doi/10.1148/ryai.230024"
 zigutyte2024mopadi: "https://www.biorxiv.org/content/10.1101/2024.10.29.620913v2"
+pedersen2017cyvcf2: "https://academic.oup.com/bioinformatics/article/33/12/1867/2971439"