various debug

cms/composite.py

@@ -167,7 +167,6 @@ def execute_ucsc_viz(args):
 		assert os.path.isfile(chromfile)
 		infile = open(chromfile, 'r')
 		if args.strip_header:
-			print("test")
 			infile.readline()
 		for line in infile:
 			entries = line.strip('\n').split()

cms/dists/scores_func.py

@@ -1,5 +1,5 @@
 ## helper functions for generating probability distributions for component scores as part of CMS 2.0.
-## last updated: 09.10.16 vitti@broadinstitute.org
+## last updated: 09.15.16 vitti@broadinstitute.org
 
 from math import fabs, sqrt
 from random import randint
@@ -14,7 +14,8 @@
 def calc_ihs(inputTped, outputFile, runProgram = "scans.py", numThreads = 7):
 	'''from func_clean.py'''
 	cmdStr = "python " + runProgram + " selscan_ihs " + inputTped + " " + outputFile + " --threads " + str(numThreads)
-	print(cmdStr)
+	#print(cmdStr)
+	subprocess.check_call( cmdStr.split() )
 	return
 def calc_delihh(readfilename, writefilename):
 	"""given a selscan iHS file, parses it and writes an analogous file with delIHH information"""
@@ -32,15 +33,16 @@ def calc_delihh(readfilename, writefilename):
 def calc_xpehh(inputTped, inputTped2, outputFile, runProgram = "scans.py", numThreads = 7):
 	'''from func_clean.py'''
 	cmdStr = "python " + runProgram + " selscan_xpehh " + inputTped + " " + outputFile + " " + inputTped2 + " --threads " + str(numThreads)
-	print(cmdStr)
+	#print(cmdStr)
+	subprocess.check_call( cmdStr.split() )
 	return	
 def calc_fst_deldaf(inputTped, inputTped2, recomFile, outputFile, modelpath):
 	if modelpath[-1] != "/":
 		modelpath += "/"
 	commandstring = modelpath + "calc_fst_deldaf"
 	argstring = inputTped + " " + inputTped2 + " " + recomFile + " " + outputFile
 	fullcommand = commandstring + " " + argstring
-	print(fullcommand)
+	#print(fullcommand)
 	subprocess.check_call( fullcommand.split() )
 	return
 def read_neut_normfile(neutNormfilename, scoretype ='ihs'):

cms/likes_from_model.py

@@ -1,6 +1,6 @@
 #!/usr/bin/env python
 ## top-level script for generating probability distributions for component scores as part of CMS 2.0. 
-## last updated: 09.13.16 vitti@broadinstitute.org
+## last updated: 09.16.16 vitti@broadinstitute.org
 
 from dists.likes_func import get_old_likes, read_likes_file, plot_likes, get_hist_bins
 from dists.freqbins_func import get_bin_strings, get_bins, check_bin_filled, check_make_dir, write_bin_paramfile
@@ -39,7 +39,7 @@ def full_parser_likes_from_model():
 	for snakemake_parser in [get_sel_trajs_parser, run_sel_sims_parser]:
 		snakemake_parser.add_argument('--cluster', action='store', help='if included: dispatch Snakemake to cluster to parallelize generation of replicates using supplied argument (e.g. qsub, sbatch)')
 		snakemake_parser.add_argument('--jobs', action='store', help='use at most this many cores in parallel')
-		snakemake_parser.add_argument('n', action='store', type=int, help='num replicates to run') #figure out where to store
+		snakemake_parser.add_argument('n', action='store', type=int, help='num replicates to run') 
 
 	##########################
 	### COSI - SHARED ARGS  ##
@@ -116,7 +116,7 @@ def execute_run_neut_sims(args):
 	neutRunDir = args.outputDir
 	if args.outputDir[-1] != "/":
 		neutRunDir += "/"
-	neutRunDir += "run_neut_sims"
+	neutRunDir += "neut_sims"
 	runDir = check_make_dir(neutRunDir)
 	runDir += "/"
 	print("running " + str(args.n) + " neutral simulates from model: " + args.inputParamFile)
@@ -127,7 +127,6 @@ def execute_run_neut_sims(args):
 	if args.dropSings is not None:
 		neutSimCommand += " --drop-singletons " + str(args.dropSings)
 	neutSimCommand += " -n "  + str(args.n) + " --tped " + runDir + "rep"
-
 	if args.printOnly:
 		print(neutSimCommand)
 	else:
@@ -350,8 +349,6 @@ def execute_visualize_likes(args):
 	# if called with no arguments, print help
 	if len(sys.argv)==1:
 		runparser.parse_args(['--help'])
-	elif len(sys.argv)==2:
-		runparser.parse_args([sys.argv[1], '--help'])
 
 	subcommand = sys.argv[1]
 	function_name = 'execute_' + subcommand + "(args)"

cms/model/calc_fst_deldaf.c

@@ -138,7 +138,7 @@ int main(int argc, char **argv) {
     fprintf(stderr, "skipped on: %d\n", nSkip);
     //fprintf(stderr, "fst_sum: %f\n", fst_sum);
     //fprintf(stderr, "nfst: %d\n", nfst);
-    fprintf(outf, "chrom ave Fst: %.8f\n", (fst_sum/nfst));
+    fprintf(stderr, "chrom ave Fst: %.8f\n", (fst_sum/nfst));
     return 0;
 }
 

cms/run_traj.py

@@ -1,6 +1,5 @@
 ## relaunches cosi command until a selection trajectory is created successully (i.e., resampling selection coefficients/sweep start times from specified distributions)
-## last updated: 08.15.16 	vitti@broadinstitute.org; phasing this out (redundant with Snakemake -- OR NOT?? needs drrma?)
-
+## last updated: 08.15.16 	vitti@broadinstitute.org
 import sys
 import subprocess
 

cms/scans.py

@@ -280,7 +280,7 @@ def main_selscan_ihs(args):
     metaData["ihs"] = args.outFile+".ihs.out"
     metaData["ihs_log"] = args.outFile+".ihs.log"
     jsonFilePath = os.path.abspath(args.inputTped).replace(".tped.gz",".metadata.json")
-    util.json_helpers.JSONHelper.annotate_json_file(jsonFilePath, metaData)
+    #util.json_helpers.JSONHelper.annotate_json_file(jsonFilePath, metaData)
 
     return 0
 __commands__.append(('selscan_ihs', parser_selscan_ihs))