fix: change bwa to bwa-aln-interactive

fulcrumgenomics · Sep 20, 2024 · 9ca141c · 9ca141c
1 parent 9cf576a
commit 9ca141c
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Showing 4 changed files with 26 additions and 32 deletions.
diff --git a/.github/workflows/tests.yml b/.github/workflows/tests.yml
@@ -32,10 +32,19 @@ jobs:
         with:
           python-version: ${{ matrix.PYTHON_VERSION }}
 
+      - name: Install poetry
+        run: |
+          python -m pip install --upgrade pip
+          python -m pip install poetry==${{env.POETRY_VERSION}}
+
+      - name: Configure poetry
+        shell: bash
+        run: poetry config virtualenvs.in-project true
+
       - name: Set up miniconda
         uses: conda-incubator/setup-miniconda@v3
         with:
-          miniforge-variant: Mambaforge
+          miniforge-variant: Miniforge
           miniforge-version: latest
           channels: conda-forge,bioconda
           activate-environment: prymer
@@ -45,29 +54,6 @@ jobs:
           auto-activate-base: false
           python-version: ${{ matrix.PYTHON_VERSION }}
 
-      - name: Install fulcrumgenomics/bwa
-        shell: bash -l {0}
-        run: |
-          conda activate prymer
-          pushd bwa
-          make -j $(nproc)
-          cp bwa ${CONDA_PREFIX}/bin
-          popd
-
-      - name: Configure poetry and check lock file
-        shell: bash -l {0}
-        run: |
-          conda activate prymer
-          poetry config virtualenvs.in-project false
-          poetry check --lock
-
-      - name: Poetry install
-        shell: bash -l {0}
-        run: |
-          conda activate prymer
-          poetry lock --no-update
-          poetry install --with dev
-
       - name: Unit tests (with doctest and coverage)
         shell: bash -l {0}
         run: |

diff --git a/prymer.yml b/prymer.yml
@@ -2,7 +2,6 @@ name: prymer
 channels:
   - bioconda
   - conda-forge
-  - defaults
 dependencies:
   - bioconda::bwa-aln-interactive=0.7.18
   - bioconda::primer3=2.6.1

diff --git a/prymer/offtarget/bwa.py b/prymer/offtarget/bwa.py
@@ -15,7 +15,13 @@
 hits in the "XA" tag than the total number hits reported in the "HN".  This occurs when BWA finds more
 hits than `max_hits` (see `bwt aln -X`).
 
- ## Example
+Use of this module requires installation of a custom version of BWA named `bwa-aln-interactive`.
+See:
+
+    - https://github.com/fulcrumgenomics/bwa/tree/interactive_aln
+    - https://bioconda.github.io/recipes/bwa-aln-interactive/README.html
+
+## Example
 
 ```python
 >>> from pathlib import Path
@@ -193,7 +199,10 @@ class BwaAlnInteractive(ExecutableRunner):
     the process running and be able to send it chunks of reads periodically and get alignments
     back without waiting for a full batch of reads to be sent.
 
-    See: https://github.com/fulcrumgenomics/bwa/tree/interactive_aln
+    See:
+        - https://bioconda.github.io/recipes/bwa-aln-interactive/README.html
+        - https://github.com/fulcrumgenomics/bwa/tree/interactive_aln
+
 
     Attributes:
         max_hits: the maximum number of hits to report - if more than this number of seed hits
@@ -207,7 +216,7 @@ def __init__(
         self,
         ref: Path,
         max_hits: int,
-        executable: str | Path = "bwa",
+        executable: str | Path = "bwa-aln-interactive",
         max_mismatches: int = 3,
         max_mismatches_in_seed: int = 3,
         max_gap_opens: int = 0,
@@ -222,7 +231,7 @@ def __init__(
             ref: the path to the reference FASTA, which must be indexed with bwa.
             max_hits: the maximum number of hits to report - if more than this number of seed hits
                       are found, report only the count and not each hit.
-            executable: string or Path representation of the `bwa` executable path
+            executable: string or Path representation of the `bwa-aln-interactive` executable path
             max_mismatches: the maximum number of mismatches allowed in the full query sequence
             max_mismatches_in_seed: the maximum number of mismatches allowed in the seed region
             max_gap_opens: the maximum number of gap opens allowed in the full query sequence
@@ -252,7 +261,7 @@ def __init__(
             else:
                 message = "BWA index file does not exist:\n\t"
             message += "\t\n".join(f"{p}" for p in missing_aux_paths)
-            raise FileNotFoundError(f"{message}\nPlease index with: `bwa index {ref}`")
+            raise FileNotFoundError(f"{message}\nPlease index with: `{executable_path} index {ref}`")
 
         # -N = non-iterative mode: search for all n-difference hits (slooow)
         # -S = output SAM (run samse)

diff --git a/prymer/offtarget/offtarget_detector.py b/prymer/offtarget/offtarget_detector.py
@@ -123,7 +123,7 @@ class OffTargetResult:
 
 class OffTargetDetector:
     """A class for detecting off-target mappings of primers and primer pairs that uses a custom
-    version of "bwa aln".
+    version of "bwa aln" named "bwa-aln-interactive".
 
     The off-target detection is faster and more sensitive than traditional isPCR and in addition can
     correctly detect primers that are repetitive and contain many thousands or millions of mappings
@@ -146,7 +146,7 @@ def __init__(
         threads: Optional[int] = None,
         keep_spans: bool = True,
         keep_primer_spans: bool = True,
-        executable: str | Path = "bwa",
+        executable: str | Path = "bwa-aln-interactive",
     ) -> None:
         """
         Args: