fix bugs

pyrpipe/mapping.py

@@ -291,7 +291,7 @@ def __init__(self,*args,index=None,genome=None,threads=None,**kwargs):
         self.resolve_parameter("--genomeDir",index,index,'index')
 
         #check index
-        if not pu.check_starindex(self.index):
+        if not self.check_index():
             if not (pu.check_files_exist(self.genome)):
                 pu.print_boldred("STAR index '{}' not found; New index could not be created as genome file '{}' not found.".format(self.index,self.genome))
                 raise ValueError("Please provide a valid STAR index, or a valid fasta file to generate the index")
@@ -488,13 +488,13 @@ def __init__(self,*args,index=None,genome=None,threads=None,**kwargs):
         self.resolve_parameter("-x",index,index,'index')
 
         #if index is passed, update the passed arguments
-        if not pu.check_bowtie2index(index):
+        if not self.check_index():
             if not (pu.check_files_exist(self.genome)):
                 pu.print_boldred("Bowtie2 index '{}' not found; New index could not be created as genome file '{}' not found.".format(self.index,self.genome))
                 raise ValueError("Please provide a valid Bowtie2 index, or a valid fasta file to generate the index")
             else:
                 #call build index to generate index
-                self.build_index(index,self.genome)
+                self.build_index(self.index,self.genome)
 
 
     def build_index(self,index_path,genome,objectid="NA"):

pyrpipe/pyrpipe_utils.py

@@ -190,7 +190,7 @@ def check_hisatindex(index):
     return True
 
 def check_kallistoindex(index):
-    """Function to check if salmon index is valid and exists.
+    """Function to check if kallisto index is valid and exists.
     
     Parameters
     ----------

pyrpipe/quant.py

@@ -66,7 +66,7 @@ def __init__(self,*args,index=None,transcriptome=None,threads=None,**kwargs):
 
         #check index
         #kallisto index is a single file
-        if not pu.check_files_exist(index):
+        if not self.check_index():
             if not (pu.check_files_exist(self.transcriptome)):
                 pu.print_boldred("Kallisto index '{}' not found; New index could not be created as transcriptome file '{}' not found.".format(self.index,self.transcriptome))
                 raise ValueError("Please provide a valid Kallisto index, or a valid fasta file to generate the index")
@@ -244,7 +244,7 @@ def __init__(self,*args,index=None,transcriptome=None,threads=None,**kwargs):
         self.resolve_parameter("-i",index,index,'index')
 
         #check index
-        if not pu.check_salmonindex(index):
+        if not self.check_index():
             if not (pu.check_files_exist(self.transcriptome)):
                 pu.print_boldred("Salmon index '{}' not found; New index could not be created as transcriptome file '{}' not found.".format(self.index,self.transcriptome))
                 raise ValueError("Please provide a valid Salmon index, or a valid fasta file to generate the index")