update numeric indexing to suppress pandas warning, remove debug prin…

…t output
pinellolab · Oct 2, 2023 · 1a218af · 1a218af
1 parent ee0e4e2
commit 1a218af
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Showing 3 changed files with 5 additions and 8 deletions.
diff --git a/bean/mapping/GuideEditCounter.py b/bean/mapping/GuideEditCounter.py
@@ -371,13 +371,13 @@ def _count_guide_edits(
     def _get_strand_offset_from_guide_index(self, guide_idx: int) -> Tuple[int, int]:
         """Returns guide starnd and offset for a given guide index."""
         if self.guides_has_strands:
-            strand = self.screen.guides.strand[guide_idx]
+            strand = self.screen.guides.strand.iloc[guide_idx]
             if strand in strand_str_to_int:
                 guide_strand = strand_str_to_int[strand]
                 offset = _get_stranded_guide_offset(
                     strand=guide_strand,
-                    start_pos=self.screen.guides.start_pos[guide_idx],
-                    guide_len=self.screen.guides.guide_len[guide_idx],
+                    start_pos=self.screen.guides.start_pos.iloc[guide_idx],
+                    guide_len=self.screen.guides.guide_len.iloc[guide_idx],
                 )
             else:
                 guide_strand = 1
@@ -448,7 +448,7 @@ def _count_reporter_edits(
         single_base_qual_cutoff: Ignore this base if the Phread quality score is less than this threshold
         guide_allele: Allele from baseedit in gRNA spacer sequence when paired with guide allele.
         """
-        ref_reporter_seq = self.screen.guides.reporter[matched_guide_idx]
+        ref_reporter_seq = self.screen.guides.reporter.iloc[matched_guide_idx]
         read_reporter_seq, read_reporter_qual = self.get_reporter_seq_qual(R2_record)
 
         guide_strand, offset = self._get_strand_offset_from_guide_index(

diff --git a/bean/model/model.py b/bean/model/model.py
@@ -74,9 +74,6 @@ def NormalModel(
     with replicate_plate2:
         with pyro.plate("guide_plate3", data.n_guides, dim=-1):
             a = get_alpha(expected_guide_p, data.size_factor, data.sample_mask, data.a0)
-            print(a)
-            print(a.max())
-            print(a.min())
             a_bcmatch = get_alpha(
                 expected_guide_p,
                 data.size_factor_bcmatch,

diff --git a/setup.py b/setup.py
@@ -8,7 +8,7 @@
 
 setup(
     name="crispr-bean",
-    version="0.2.6",
+    version="0.2.7",
     python_requires=">=3.8.0",
     author="Jayoung Ryu",
     author_email="[email protected]",