Merge pull request #563 from gagneurlab/external_bam

Minor changes and bug fixes

.readthedocs.yaml

@@ -0,0 +1,22 @@
+# Read the Docs configuration file for Sphinx projects
+# See https://docs.readthedocs.io/en/stable/config-file/v2.html for details
+
+# Required
+version: 2
+
+# Set the OS, Python version and other tools you might need
+build:
+  os: ubuntu-22.04
+  tools:
+    python: "3.12"
+
+# Build documentation in the "docs/" directory with Sphinx
+sphinx:
+  configuration: docs/conf.py
+  fail_on_warning: true
+
+# Optionally build your docs in additional formats such as PDF and ePub
+formats:
+   - pdf
+   - epub
+

README.md

@@ -1,5 +1,5 @@
 # Detection of RNA Outlier Pipeline
-[![DROP pipeline status](https://github.com/gagneurlab/drop/workflows/Build/badge.svg?branch=master)](https://github.com/gagneurlab/drop/actions?query=workflow%3ABuild)
+[![DROP pipeline status](https://github.com/gagneurlab/drop/workflows/Build/badge.svg)](https://github.com/gagneurlab/drop/actions?query=workflow%3ABuild)
 [![Version](https://img.shields.io/github/v/release/gagneurlab/drop?include_prereleases)](https://github.com/gagneurlab/drop/releases)
 [![Version](https://readthedocs.org/projects/gagneurlab-drop/badge/?version=latest)](https://gagneurlab-drop.readthedocs.io/en/latest)
 

drop/config/SampleAnnotation.py

@@ -48,10 +48,6 @@ def parse(self, sep='\t'):
 
         annotationTable = pd.read_csv(self.file, sep=sep, index_col=False)
 
-        # FRASER cannot handle a mixture of stranded and unstranded samples, raise error in such cases
-        if (annotationTable['STRAND'] == 'no').any() & ((annotationTable['STRAND'] == 'reverse').any() | (annotationTable['STRAND'] == 'yes').any()):
-            raise ValueError("Data contains a mix of stranded and unstranded samples. Please analyze them separately.\n")
-
         if annotationTable['STRAND'].isnull().values.any():
             raise ValueError("STRAND is not provided for some samples. All samples should have STRAND value in the sample annotation file.\n")
 

drop/config/SampleParams.py

@@ -6,6 +6,8 @@
 import shutil
 
 
+pd.set_option("future.no_silent_downcasting", True)
+
 
 class ParamHelper:
     def __init__(self,include,sampleAnnotationColumns,group,path):

drop/config/submodules/AberrantSplicing.py

@@ -27,10 +27,11 @@ def __init__(self, config, sampleAnnotation, processedDataDir, processedResultsD
             if len(set(self.rnaIDs[g]) & set(self.rnaExIDs[g])) > 0:
                 raise ValueError(f"{set(self.rnaIDs[g]) & set(self.extRnaIDs[g])} has both BAM and external count file \
                 please fix in sample annotation table to only have either external count or BAM processing\n")
-
+   
         all_ids = self.sampleAnnotation.subsetGroups(self.groups, assay=["RNA", "SPLICE_COUNT"])
         self.checkSubset(all_ids)
-
+        self.checkStrandSpecificity()
+
     def setDefaultKeys(self, dict_):
         super().setDefaultKeys(dict_)
         setKey = utils.setKey
@@ -109,3 +110,15 @@ def getPsiTypeAssay(self):
         if(fraser_version == "FRASER2"):
             return "jaccard"
         return "theta"
+