small fixes to several modules

pgpipe/vcf_bed_to_seq.py

@@ -322,7 +322,8 @@ def get_model_sequences_from_region(vcf=None,popmodel=None,
 
     if called_from_run or out != None: #write/append sequences to a file 
         if out == None:
-            out = os.path.dirname(vcffile) + "//ppp_vcf_to_sequences.out"
+            assert not isinstance(vcf,vf.VcfReader) # vcf should be a file
+            out = os.path.dirname(vcf) + "//ppp_vcf_to_sequences.out"
         if called_from_run == False and os.path.exists(out):
             f = open(out,'a')
         else:
@@ -403,10 +404,10 @@ def get_model_sequences(vcf=None,model_file = None,modelname=None,
     if popmodel and (model_file or modelname):
         raise Exception("must specify _either_ popmodel or both model_file and modelname")
     if xor(model_file,modelname):
-        raise Eception("both model_file and modelname must be given, unless popmodel is being used")
+        raise Exception("both model_file and modelname must be given, unless popmodel is being used")
     if not popmodel:
         popmodels = read_model_file(model_file)
-        popmodel = popmodels[model]
+        popmodel = popmodels[modelname]
     # make an instance of VcfReader 
     vcf_reader = vf.VcfReader(vcf,popmodel=popmodel)
     with open(BED_filename,'r') as bf:
@@ -495,7 +496,8 @@ def run (**kwargs):
 if __name__ == "__main__":
     initLogger()
     run(**parser())
-    exit()
+    sys.exit()
+    # clumsy way of passing arguments for debugging,  for use with idle 
     debugargs = ['--vcf','..//jhtests//pan_example.vcf.gz','--fasta-reference',
                  "..//jhtests//pan_example_ref.fa",
             '--model-file',"..//jhtests//panmodels.model",'--modelname',"4Pop",

pgpipe/vcf_to_dadi.py

@@ -304,8 +304,9 @@ def run (**kwargs):
 if __name__ == "__main__":
     initLogger()
     run(**dadisnp_parser())
-    exit()
-
+
+    sys.exit()
+    # clumsy way of passing arguments for debugging,  for use with idle                   
     debugargs = ['--vcf','..//jhtests//pan_example.vcf.gz','--model-file',
                  "..//jhtests//panmodels.model",
                  '--modelname',"4Pop",'--out','../jhtests/results/vcf_dadisnp_bedfile_test.out',

pgpipe/vcf_to_fastsimcoal.py

@@ -348,7 +348,8 @@ def run (**kwargs):
 if __name__ == "__main__":
     initLogger()
     run(**fscmsfs_parser)
-    exit()
+    sys.exit()
+    # clumsy way of passing arguments for debugging,  for use with idle 
     debugargs=['--vcf',"..//jhtests//pan_example.vcf.gz",
                '--model-file',"..//jhtests//panmodels.model",'--modelname','3Pop',
            '--dim','1','2','m','--basename','../jhtests/results/vcf_fsc1']#,'--folded']

pgpipe/vcf_to_gphocs.py

@@ -263,6 +263,7 @@ def run (**kwargs):
     sys.exit()
     # test using a vcf file
     debugargs = """--vcf //home//jodyhey//temp//PPP//tests//input//pan_example.vcf.gz --reference //home//jodyhey//temp//PPP//tests//input//pan_example_ref.fa  --model-file //home//jodyhey//temp//PPP//tests//input//panmodels.model  --modelname 4Pop             --bed-file //home//jodyhey//temp//PPP//tests//input//pan_example_regions.bed  --out ..//jhtests//results//vcf_gphocs_test.out  """
+    # clumsy way of passing arguments for debugging,  for use with idle 
     # debugargs = ['--vcf','//home//jodyhey//temp//PPP//tests//input//pan_example.vcf.gz',
             # '--reference',"//home//jodyhey//temp//PPP//tests//input//pan_example_ref.fa",
             # '--model-file',"//home//jodyhey//temp//PPP//tests//input//panmodels.model",

pgpipe/vcf_to_sfs.py

@@ -646,9 +646,9 @@ def run (**kwargs):
 
 if __name__ == "__main__":
     initLogger()
-    run(**sfs_parcer())
-    exit()
-
+    run(**sfs_parser())
+    sys.exit()
+    # clumsy way of passing arguments for debugging,  for use with idle 
     debugargs=['--vcf',"..//jhtests//pan_example2.vcf.gz",
                '--model-file',"..//jhtests//panmodels.model",'--modelname','4Pop',
                '--downsamplesizes','3','3','3','4',

pgpipe/vcf_to_treemix.py

@@ -84,6 +84,7 @@
 
 
 import os
+import sys
 import logging
 import argparse
 import subprocess
@@ -309,17 +310,18 @@ def run (**kwargs):
 if __name__ == "__main__":
     initLogger()
     run(**treemix_parser())
-    exit()
+    sys.exit()
+    # clumsy way of passing arguments for debugging,  for use with idle 
     debugargs = ['--vcf','../jhtests/pan_example.vcf.gz','--model-file',
             "../jhtests/panmodels.model",'--modelname',"4Pop",
             '--out','../jhtests/results/vcf_treemixtest1','--bed-file',"../jhtests/pan_example_regions.bed",'--kblock','1000']
     run(**debugargs)
-    exit()
+    sys.exit()
     debugargs = ['--vcf','../jhtests/pan_example.vcf.gz','--model-file',
             "../jhtests/panmodels.model",'--modelname',"4Pop",
             '--out','../jhtests/results/vcf_treemixtest2']
     run(debugargs)
-    exit()
+    sys.exit()
 
 
 

tests/tests_jody.py

@@ -294,6 +294,3 @@ def test_vcf_to_dadi3(self):
 
 if __name__ == "__main__":
     unittest.main(verbosity = 2)
-
-
-