get samples from bam suffix

snakePipes/common_functions.py

@@ -172,6 +172,19 @@ def get_sample_names_bam(infiles, bamExt):
         s.append(x)
     return sorted(list(set(s)))
 
+def get_sample_names_suffix_bam(infiles, bamExt):
+    """
+    Get sample names without file extensions
+    """
+    bamSuff = [x + bamExt for x in ["genome1","genome2","unassigned","allele_flagged"]]
+    s = []
+    for x in infiles:
+        for y in bamSuff:
+            if y in os.path.basename(x):
+                x = os.path.basename(x).replace(y, "")
+                s.append(x)
+    return sorted(list(set(s)))
+
 
 def is_paired(infiles, ext, reads):
     """

snakePipes/workflows/mRNA-seq/internals.snakefile

@@ -37,7 +37,10 @@ if not fromBAM:
     pairedEnd = cf.is_paired(infiles, ext, reads)
 else:
     infiles = sorted(glob.glob(os.path.join(str(indir or ''), '*' + bamExt)))
-    samples = cf.get_sample_names_bam(infiles, bamExt)
+    if mode in "allelic-counting":
+        samples = cf.get_sample_names_suffix_bam(infiles, bamExt)
+    else:
+        samples = cf.get_sample_names_bam(infiles, bamExt)
 
 if formula and not sampleSheet:
     print("In order to apply custom formula, please provide a sample sheet!")

snakePipes/workflows/mRNA-seq/mRNA-seq

@@ -173,6 +173,7 @@ def main():
     if "allelic-counting" in modeTemp and not args.fromBAM:
         warnings.warn("--fromBAM is required with allelic-counting mode. Setting to True.")
         args.fromBAM = True
+        args.aligner = "EXTERNAL_BAM"
     if args.rMats and not args.sampleSheet:
         sys.exit("--rMats flag requires a sampleSheet (specified with --sampleSheet).\n")
     if "three_prime_seq" in mode: