updated functions and tests with kwargs

pgpipe/bed_invert.py

@@ -53,13 +53,14 @@
 import pysam
 from pgpipe.genome_region import Region, RegionList, getIntervalsBetween
 import pgpipe.argparse_sets
+from pgpipe.misc import argprase_kwargs
 import argparse
 
 
 
 #Given a list of CDS intervals and optional buffer length,
 #Generate full set of intervals between regions.
-def createParser():
+def parseArguments(passed_arguments = []):
     parser = argparse.ArgumentParser(description=("Generates list of "
                 "intervals within a provided BED file with option "
                 "to pad intervals by a fixed amount"))
@@ -80,11 +81,14 @@ def createParser():
     cg.add_argument('--removechr',dest="remove_chr",action="store_true")
     parser.add_argument('--out', dest="output_name",
                         help="Output filename, default is stdout")
-    return parser
+    if passed_arguments:
+        return vars(parser.parse_args(passed_arguments))
+    else:
+        return vars(parser.parse_args())
 
 
 
-def get_intergenic(sysargs):
+def get_intergenic(**kwargs):
     """
     Creates a BED file with regions that are not covered in the input BED.
 
@@ -125,8 +129,11 @@ def get_intergenic(sysargs):
 
 
     """
-    parser = createParser()
-    args = parser.parse_args(sysargs)
+    #parser = createParser()
+    #args = parser.parse_args(sysargs)
+    if __name__ != "__main__":
+        kwargs = argprase_kwargs(kwargs, parseArguments)
+    args = argparse.Namespace(**kwargs)
     if args.region_name is None:
         raise Exception("BED input filename required")
     reg_list = RegionList(filename=args.region_name, colstr=args.colstr,
@@ -136,4 +143,4 @@ def get_intergenic(sysargs):
 
 if __name__ == "__main__":
     #initLogger()
-    get_intergenic(sys.argv[1:])
+    get_intergenic(**parseArguments())

pgpipe/get_nonmissing_chunks.py

@@ -4,8 +4,9 @@
 import io
 from pgpipe.vcf_reader_func import VcfReader
 from pgpipe.model import Model, read_single_model
+from pgpipe.misc import argprase_kwargs
 
-def createParser():
+def parseArguments(passed_arguments = []):
     parser = argparse.ArgumentParser(description=("Outputs windows in a "
                       "VCF file where all sites in the window have below"
                       " a set limit of missing data. Limit default "
@@ -35,7 +36,11 @@ def createParser():
                         "in model file if more than one is contained"))
     parser.add_argument("--tbi", dest="tabix_index", help="Path to bgzipped "
                         "file's index if name doesn't match VCF file")
-    return parser
+    if passed_arguments:
+        return vars(parser.parse_args(passed_arguments))
+    else:
+        return vars(parser.parse_args())
+    #return parser
 
 def getl(f,compressed=False):
     l = f.readline()
@@ -61,7 +66,7 @@ def outputLine(chrom,start_pos,end_pos,args):
     chrom = fixChromName(chrom,args.addchr,args.removechr)
     return chrom+'\t'+str(sp)+'\t'+str(ep)+'\n'
 
-def regionsWithData(sysargs):
+def regionsWithData(**kwargs):
     """Returns a BED file with regions where all SNPs contained have
     less than a given limit of missing data.
 
@@ -114,8 +119,11 @@ def regionsWithData(sysargs):
 
 
     """
-    parser = createParser()
-    args = parser.parse_args(sysargs)
+    #parser = createParser()
+    #args = parser.parse_args(sysargs)
+    if __name__ != "__main__":
+        kwargs = argprase_kwargs(kwargs, parseArguments)
+    args = argparse.Namespace(**kwargs)
     compressed_input = False
     #if args.vcfname is None:
     #    instream = sys.stdin
@@ -218,4 +226,4 @@ def regionsWithData(sysargs):
         pass
 
 if __name__ == '__main__':
-    regionsWithData(sys.argv[1:])
+    regionsWithData(**parseArguments())

pgpipe/vcf_four_gamete.py

@@ -104,6 +104,7 @@
 from pgpipe.logging_module import initLogger
 from pgpipe.genome_region import Region, RegionList
 from pgpipe.vcf_reader_func import getRecordList, vcfRegionName, getRecordsInRegion, VcfReader
+from pgpipe.misc import argprase_kwargs
 
 
 class BaseData():
@@ -516,7 +517,8 @@ def checkVcfRegion(self):
         self.seqs = [[base_list[row][col] for row in range(0, len(base_list))] for col in range(0, len(base_list[0]))]
 
 
-def createParser():
+#def createParser(passed_arguments = []):
+def parseArguments(passed_arguments = []):
     parser = argparse.ArgumentParser(description=("Given a file of aligned"
             "sequences or variable sites, will return intervals based"
             " on 4 gamete tests"))
@@ -542,7 +544,7 @@ def createParser():
             action='store_const', const="HandK85",help = "get a set of "
             "parsimonious intervals each containing at least 1 recombination"
             " event.  Follows appendix 2 of Hudson and Kaplan 1985")
-    intervaltype_group.add_argument("--4gcompat", dest="intervaltype",
+    intervaltype_group.add_argument("--fourgcompat", dest="intervaltype",
             action='store_const', const="CONTIG4GPASS",help = "get a set of "
             " intervals such that for each interval all the included bases are"
             " compatible with each other based on the 4 gamete test")
@@ -593,7 +595,12 @@ def createParser():
     #add checks for correct input type
     parser.add_argument('--tbi', dest="tabix_index",help=("Filepath for tabix "
                         "index file if using a single bgzipped VCF"))
-    return parser
+    parser.add_argument('--log', dest="log_name", help=("Filepath for log file"))
+    #return parser
+    if passed_arguments:
+        return vars(parser.parse_args(passed_arguments))
+    else:
+        return vars(parser.parse_args())
 
 def logArgs(args):
     logging.info('Arguments for vcf_region_write:')
@@ -775,7 +782,8 @@ def outputSubregion(args, interval, basedata, region=None, filename=None):
 
 
 
-def sample_fourgametetest_intervals(sys_args):
+#def sample_fourgametetest_intervals(sys_args):
+def sample_fourgametetest_intervals(**kwargs):
     """Returns interval(s) from aligned sequences or snps.
 
     Given a set of aligned sequences or a vcf file, this function
@@ -809,7 +817,7 @@ def sample_fourgametetest_intervals(sys_args):
     Tests (one required)
     --hk : bool
         Will find intervals that contain at least one recombination event
-    --4gcompat : bool
+    --fourgcompat : bool
         Will find intervals with zero recombination events in them
 
     Return options:
@@ -845,12 +853,18 @@ def sample_fourgametetest_intervals(sys_args):
         Extend region to overlapping informative sites
 
     """
-    parser = createParser()
+    #parser = createParser()
     # parser.print_help()
-    if len(sys_args) == 0:
-        parser.print_help()
-        sys.exit(1)
-    args = parser.parse_args(sys_args)
+    #if len(kwargs) == 0:
+        #parser.print_help()
+        #sys.exit(1)
+    #args = parser.parse_args(sys_args)
+    if __name__ != "__main__":
+        kwargs = argprase_kwargs(kwargs, parseArguments)
+
+    args = argparse.Namespace(**kwargs)
+    if args.log_name is not None:
+        initLogger(filename=log_name)
     logArgs(args)
     #argdic = vars(args)
     interval_list = []
@@ -953,7 +967,8 @@ def sample_fourgametetest_intervals(sys_args):
 
 
 if __name__ == '__main__':
-    initLogger()
+    #initLogger()
 
-    sample_fourgametetest_intervals(sys.argv[1:])
+    #sample_fourgametetest_intervals(sys.argv[1:])
+    sample_fourgametetest_intervals(**parseArguments())
 

pgpipe/vcf_split_pysam.py

@@ -8,17 +8,17 @@
 from pgpipe.genome_region import Region, RegionList
 import pgpipe.vcf_reader_func as vf
 from pgpipe.model import Model, read_model_file
+from pgpipe.misc import argprase_kwargs
 
-
-def createParser():
+def parseArguments(passed_arguments = []):
     parser= argparse.ArgumentParser(description=("Given a range or a file of "
                                 "ranges and a VCF file, will generate one or "
                                 "more VCF files with variants only from the "
                                 "region(s) specified. For regions, start and "
                                 "end coordinates required (default is zero-"
                                 "based, half-open intervals, chromosome "
                                 "optional unless VCF has more than one"))
-    parser.add_argument("vcfname", help="Input VCF name")
+    parser.add_argument("--vcf",dest="vcfname", help="Input VCF name")
     region_group = parser.add_mutually_exclusive_group()
     region_group.add_argument("--r", dest="gene_str", help=("Comma "
                               "separated string, formatted \"start,end,"
@@ -69,7 +69,11 @@ def createParser():
     subsamp_group.add_argument('--model-file',dest="modelname",help="Model file for selecting individuals for writing")
     parser.add_argument('--model',dest="poptag",help="If model file is used, will use model with this name")
     parser.add_argument("--forceempty",dest="forceempty",action="store_true",help=("Will create empty VCF if a region is empty rather than throw an error"))
-    return parser
+    if passed_arguments:
+        return vars(parser.parse_args(passed_arguments))
+    else:
+        return vars(parser.parse_args())
+    #return parser
 
 def logArgs(args):
     logging.info('Arguments for vcf_region_write:')
@@ -157,7 +161,7 @@ def writeFile(args, vcf_reader, filter_sites, remove_cpg, fasta_ref, header):
             outfile.write(rec)
 
 
-def vcf_region_write(sys_args):
+def vcf_region_write(**kwargs):
     """Returns a VCF file with variants from regions in a list
 
     Given a VCF file and gene region information (from either a file with one
@@ -226,11 +230,14 @@ def vcf_region_write(sys_args):
 
     """
 
-    parser = createParser()
-    if len(sys_args) == 0:
-        parser.print_help()
-        sys.exit(1)
-    args = parser.parse_args(sys_args)
+    #parser = createParser()
+    #if len(sys_args) == 0:
+    #    parser.print_help()
+    #    sys.exit(1)
+    #args = parser.parse_args(sys_args)
+    if __name__ != "__main__":
+        kwargs = argprase_kwargs(kwargs,parseArguments)
+    args = argparse.Namespace(**kwargs)
     logArgs(args)
     popmodel = None
     if args.modelname is not None:
@@ -318,5 +325,5 @@ def vcf_region_write(sys_args):
 
 
 if __name__ == '__main__':
-    initLogger()
-    vcf_region_write(sys.argv[1:])
+    #initLogger()
+    vcf_region_write(**parseArguments())

pgpipe/vcf_to_ima.py

@@ -111,6 +111,7 @@
 from pgpipe.genome_region import Region, RegionList
 from pgpipe.parse_functions import defaultsDictForFunction, getConfigFilename, makeRequiredList, getArgsWithConfig
 from pgpipe.model import Model, read_single_model
+from pgpipe.misc import argprase_kwargs
 #from tabix_wrapper import prepVcf
 
 #Input: VCF file, reference sequence, region list (possibly .bed file)
@@ -197,7 +198,7 @@ def writeHeader(self):
 
 
 
-def createParser():
+def parseArguments(passed_arguments = []):
     parser = argparse.ArgumentParser(description=("Generates an IMa input "
                                      "file from a VCF file, a reference"
                                      " genome, a list of gene regions, "
@@ -268,7 +269,10 @@ def createParser():
     parser.add_argument("--out-prefix",dest="multi_out",type=str,
                         help=("If output is fasta, generate one file"
                         "per loci."))
-    return parser
+    if passed_arguments:
+        return vars(parser.parse_args(passed_arguments))
+    else:
+        return vars(parser.parse_args())
 
 
 def checkArgs(args):
@@ -444,7 +448,7 @@ def hasMissingData(rec_list, indiv_idx):
     return False
 
 
-def vcf_to_ima(sys_args):
+def vcf_to_ima(**kwargs):
     """Returns an IMa input file given four-gamete filtered loci in one or 
     multiple VCFs.
 
@@ -532,13 +536,16 @@ def vcf_to_ima(sys_args):
         Will be named either '--out' value or (vcfinput).ima.u.
         Contains variants in designated loci for IMa run.
     """
-    parser = createParser()
-    if len(sys_args) == 0:
-        parser.print_help()
-        sys.exit(1)
-
-    required_args = ['vcfname','popname']
-    args = getArgsWithConfig(parser,sys_args,required_args,'vcf_to_ima')
+    #parser = createParser()
+    #if len(sys_args) == 0:
+    #    parser.print_help()
+    #    sys.exit(1)
+
+    #required_args = ['vcfname','popname']
+    #args = getArgsWithConfig(parser,sys_args,required_args,'vcf_to_ima')
+    if __name__ != "__main__":
+        kwargs = argprase_kwargs(kwargs,parseArguments)
+    args = argparse.Namespace(**kwargs)
     checkArgs(args)
     logArgs(args)
     #validateFiles(args)
@@ -674,5 +681,5 @@ def vcf_to_ima(sys_args):
     output_file.close()
 
 if __name__ == "__main__":
-    initLogger()
-    vcf_to_ima(sys.argv[1:])
+    #initLogger()
+    vcf_to_ima(**parseArguments())