Merge pull request #13 from holtgrewe/feature/config-arg

Users can now specify the config INI file

Thanks for getting to this. I've been extremely busy over the past weeks.

Author: dantaki

sv2/sv2.py

@@ -40,6 +40,7 @@
   -b, -bed    ...     bed files(s) of SVs
   -snv        ...     snv vcf files(s), must be bgzipped and tabixed
   -p, -ped    ...     ped files(s)
+  -ini        ...     configuration INI file (the default one lives in the sv2 package)
 
 genotype arguments: github.com/dantaki/SV2/wiki/Options#genotype-arguments
 
@@ -84,6 +85,7 @@ def main():
 	inArgs.add_argument('-v','-vcf',type=str,default=None,nargs='*')
 	inArgs.add_argument('-snv',type=str,default=None,nargs='*')
 	inArgs.add_argument('-p','-ped',type=str,default=None,nargs='*')
+	genoArgs.add_argument('-ini',required=False,default=None,type=str)
 	genoArgs.add_argument('-g','-genome',required=False,default='hg19',type=str)
 	genoArgs.add_argument('-pcrfree',required=False,default=False,action="store_true")
 	genoArgs.add_argument('-M',default=False,required=False,action="store_true")
@@ -105,7 +107,7 @@ def main():
 	optArgs.add_argument('-O','-odir',required=False,default=os.getcwd(),type=str)
 	optArgs.add_argument('-h','-help',required=False,action="store_true",default=False)
 	args = parser.parse_args()
-	bams,bed,vcf,snv,ped = args.i,args.b,args.v,args.snv,args.p
+	bams,bed,vcf,snv,ped,ini = args.i,args.b,args.v,args.snv,args.p,args.ini
 	gen,pcrfree,legacy_m,merge_flag,min_ovr,anno_flag= args.g,args.pcrfree,args.M,args.merge,args.min_ovr,args.no_anno
 	predir,featsdir = args.pre,args.feats
 	clfLoad, classifier_name = args.load_clf,args.clf
@@ -124,6 +126,7 @@ def main():
 	olog = logfh
 	if olog == None: olog = 'STDOUT'
 	print 'sv2 version:{}    report bugs to <dantaki at ucsd dot edu>       error messages located in {}'.format(__version__,olog)
+	Config.ini=ini
 	Confs=Config()
 	if clfLoad!=None:
 		Confs.load_clf(clfLoad)
@@ -236,4 +239,4 @@ def main():
 	output(SV,SVs,Peds,ids,gen,outdir+ofh,anno_flag,tmp_dir)
 	shutil.rmtree(tmp_dir)
 	if logfh!=None: lfh.close()
-	report_time(init_time,'GENOTYPING COMPLETE')
+	report_time(init_time,'GENOTYPING COMPLETE')

sv2/sv2Config.py

@@ -7,7 +7,10 @@
 __resource_url__ = 'https://github.com/dantaki/SV2/releases/download/sv2v1.4.0/sv2_resources.zip'
 class Config():
 	def __init__(self):
-		self.fh=get_path()+'/config/sv2.ini'
+		if Config.ini:
+			self.fh = Config.ini
+		else:
+			self.fh=get_path()+'/config/sv2.ini'
 		self.json=get_path()+'/config/sv2_clf.json'
 		self.fasta_chr_flag=False
 		self.clfs=None
@@ -180,4 +183,7 @@ def write_config(self,hg19=None,hg38=None,mm10=None):
 				conf.set('FASTA_PATHS','mm10',mm10)
 			if self.resource != None:
 				conf.set('RESOURCE_DIR','sv2_resource',self.resource)
-			with open(self.fh,'w') as conf_fh: conf.write(conf_fh)
+			with open(self.fh,'w') as conf_fh: conf.write(conf_fh)
+
+# Path to INI file, if any.
+Config.ini = None

sv2/sv2_train.py

@@ -38,6 +38,7 @@
   -b, -bed    ...     bed files(s) of SVs
   -snv        ...     snv vcf files(s), must be bgzipped and tabixed
   -p, -ped    ...     ped files(s)
+  -ini        ...     path to configuration INI file, default lives in sv2 package
 
 genotype arguments: github.com/dantaki/SV2/wiki/Options#genotype-arguments
 
@@ -67,6 +68,7 @@ def main():
 	inArgs.add_argument('-v','-vcf',type=str,default=None,nargs='*')
 	inArgs.add_argument('-snv',type=str,default=None,nargs='*')
 	inArgs.add_argument('-p','-ped',type=str,default=None,nargs='*')
+	inArgs.add_argument('-ini',type=str,default=None)
 	genoArgs.add_argument('-g','-genome',required=False,default='hg19',type=str)
 	genoArgs.add_argument('-pcrfree',required=False,default=False,action="store_true")
 	genoArgs.add_argument('-M',default=False,required=False,action="store_true")
@@ -79,7 +81,7 @@ def main():
 	optArgs.add_argument('-O','-odir',required=False,default=os.getcwd(),type=str)
 	optArgs.add_argument('-h','-help',required=False,action="store_true",default=False)
 	args = parser.parse_args()
-	bams,bed,vcf,snv,ped = args.i,args.b,args.v,args.snv,args.p
+	bams,bed,vcf,snv,ped,ini = args.i,args.b,args.v,args.snv,args.p,args.ini
 	gen,pcrfree,legacy_m,predir,featsdir= args.g,args.pcrfree,args.M,args.pre,args.feats
 	logfh, tmp_dir, seed, ofh, odir = args.L,args.T,args.s,args.o,args.O
 	_help = args.h
@@ -94,6 +96,7 @@ def main():
 	olog = logfh
 	if olog == None: olog = 'STDOUT'
 	print 'sv2 version:{}    report bugs to <dantaki at ucsd dot edu>       error messages located in {}'.format(__version__,olog)
+	Config.ini=ini
 	Confs=Config()
 	if bams==None and predir==None and featsdir==None:
 		print 'FATAL ERROR: No BAM file specified <-i, -bam  FILE ...>'
@@ -183,4 +186,4 @@ def main():
 	sv2_train_output(feats,Peds,gen,train_dir+ofh)
 	shutil.rmtree(tmp_dir)
 	lfh.close()
-	report_time(init_time,'FEATURE EXTRACTION COMPLETE')
+	report_time(init_time,'FEATURE EXTRACTION COMPLETE')