Merge pull request #29 from maxibor/fix_index_error

Fix IndexError

.github/workflows/publish_pypi.yml

@@ -13,7 +13,7 @@ jobs:
       - name: Setup Python
         uses: actions/setup-python@v3
         with:
-          python-version: "3.9"
+          python-version: "3.10"
       - name: Build pydamage
         run: |
           pip install wheel

.github/workflows/pydamage_ci.yml

@@ -10,26 +10,26 @@ jobs:
     if: "!contains(github.event.head_commit.message, '[skip_ci]')"
     steps:
       - uses: actions/checkout@v2
-      - uses: conda-incubator/setup-miniconda@v3
+      - uses: mamba-org/setup-micromamba@v2
         with:
-          auto-update-conda: true
-          mamba-version: "*"
-          channels: conda-forge,bioconda,defaults
-          channel-priority: true
           environment-file: environment.yml
-          activate-environment: pydamage
+          environment-name: pydamage
+          init-shell: >-
+            bash
+          cache-environment: true
+          post-cleanup: 'all'
       - name: Test with pytest
-        shell: bash -l {0}
+        shell: bash -el {0}
         run: |
           pip install -e .
           pip install pytest
           pytest
       - name: Check pydamage help message
-        shell: bash -l {0}
+        shell: bash -el {0}
         run: |
           pydamage --help
       - name: Check pydamage on test data
-        shell: bash -l {0}
+        shell: bash -el {0}
         run: |
           pydamage analyze --verbose tests/data/aligned.bam
           pydamage filter pydamage_results/pydamage_results.csv

environment.yml

@@ -2,7 +2,6 @@ name: pydamage
 channels:
   - conda-forge
   - bioconda
-  - defaults
 dependencies:
   - click
   - numpy

pydamage/__init__.py

@@ -1,4 +1,4 @@
-__version__ = "0.80"
+__version__ = "0.90"
 from pydamage.main import pydamage_analyze
 import logging
 

pydamage/damage.py

@@ -121,14 +121,24 @@ def compute_damage(self):
         # All conserved C and G
         no_mut_pos, no_mut_counts = sort_count_array_dict(np.array(self.no_mut, dtype="uint32"))
 
+
         CT_damage_amount = np.zeros(self.wlen)
-        CT_damage_amount[CT_pos] = CT_counts / C_counts[CT_pos]
+        C_pos_dict = {pos: i for i, pos in enumerate(C_pos)}
+        CT_pos_indices = [C_pos_dict[pos] for pos in CT_pos]
+        CT_damage_amount[CT_pos] = CT_counts / C_counts[CT_pos_indices]
 
         GA_damage_amount = np.zeros(self.wlen)
-        GA_damage_amount[GA_pos] = GA_counts / G_counts[GA_pos]
+        G_pos_dict = {pos: i for i, pos in enumerate(G_pos)}
+        GA_pos_indices = [G_pos_dict[pos] for pos in GA_pos]
+
+        GA_damage_amount[GA_pos] = GA_counts / G_counts[GA_pos_indices]
+
 
         damage_amount = np.zeros(self.wlen)
-        damage_amount[damage_bases_pos] = damage_bases_counts / C_G_bases_counts[damage_bases_pos]
+        CG_pos_dict = {pos: i for i, pos in enumerate(C_G_bases_pos)}
+        CG_pos_indices = [CG_pos_dict[pos] for pos in damage_bases_pos]
+        damage_amount[damage_bases_pos] = damage_bases_counts / C_G_bases_counts[CG_pos_indices]
+
 
         _ = np.zeros(self.wlen, dtype="uint32")
         _[damage_bases_pos] = damage_bases_counts
@@ -251,4 +261,4 @@ def test_damage(ref, bam, mode, wlen, g2a, subsample, show_al, process, verbose)
                 f" - reflen: {reflen}\n"
             )
         al_handle.close()
-        return False
+        return False, read_dict

pydamage/main.py

@@ -76,6 +76,8 @@ def pydamage_analyze(
     #         bam=bam,
     #         ref=ref,
     #         wlen=wlen,
+    #         g2a=g2a,
+    #         subsample=subsample,
     #         show_al=show_al,
     #         mode=mode,
     #         process=process,