Merge pull request #90 from RIVM-bioinformatics/dev

Update AmpliGone & resolve pandas FutureWarning
RIVM-bioinformatics · Mar 22, 2024 · 7578111 · 7578111
2 parents 9109a5c + 18e4ffb
commit 7578111
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Showing 3 changed files with 4 additions and 4 deletions.
diff --git a/ViroConstrictor/workflow/envs/Clean.yaml b/ViroConstrictor/workflow/envs/Clean.yaml
@@ -6,7 +6,7 @@ channels:
   - nodefaults
 dependencies:
   - python>=3.8
-  - ampligone==1.2.1
+  - ampligone==1.3.0
   - pandas>=1.3
   - minimap2==2.24
   - mappy==2.24

diff --git a/ViroConstrictor/workflow/envs/Consensus.yaml b/ViroConstrictor/workflow/envs/Consensus.yaml
@@ -5,10 +5,10 @@ channels:
   - intel
   - nodefaults
 dependencies:
-  - python=3.7
+  - python=3.8
   - libffi==3.3
   - pandas==1.3.5
-  - pysam=0.15
+  - pysam=0.16
   - pysamstats==1.1.2
   - biopython==1.79
   - parmap==1.5.3

diff --git a/ViroConstrictor/workflow/scripts/boc.py b/ViroConstrictor/workflow/scripts/boc.py
@@ -12,5 +12,5 @@
 
 with open(output, "w") as f:
     f.write(
-        f"{samplename}\t{100-(int(df[df < 1 ].count())/a)*100}\t{100-(int(df[df < 5 ].count())/a)*100}\t{100-(int(df[df < 10 ].count())/a)*100}\t{100-(int(df[df < 50 ].count())/a)*100}\t{100-(int(df[df < 100 ].count())/a)*100}\n"
+        f"{samplename}\t{100-(int(df[df < 1].count().iloc[0])/a)*100}\t{100-(int(df[df < 5].count().iloc[0])/a)*100}\t{100-(int(df[df < 10].count().iloc[0])/a)*100}\t{100-(int(df[df < 50].count().iloc[0])/a)*100}\t{100-(int(df[df < 100].count().iloc[0])/a)*100}\n"
     )