def check_bowtie_mapping(mapping,offset_or_nibble):
"""Generator function to test import of bowtie files under many read mapping rules
Parameters
----------
mapping : str
String specifying mapping rule. "fiveprime",
"threeprime", "center", or "fiveprime_variable"
offset_or_nibble : int or str
Integer specifying offset or nibble (only for center mapping)
or str specifying filename of variable offset dict text file
"""
# assure correct mapping function was applied
# by comparing counts loaded from a bowtie file
# under those map rules to a vector corresponding
# to known answers for those rules
argstr = "--countfile_format bowtie --count_files %s --%s " % (bowtiefilename, mapping)
if mapping == "center":
argstr += ("--nibble %s" % offset_or_nibble)
else:
argstr += ("--offset %s" % offset_or_nibble)
args = alignment_file_parser.parse_args(shlex.split(argstr))
ga = get_genome_array_from_args(args)
assert_greater(ga.sum(),0)
check_genome_array_against_vector(ga,mapping,offset_or_nibble)
def test_alignment_parser_open_bam_makes_bamgenomearray():
argstr = "--countfile_format BAM --count_files %s --fiveprime" % bamfilename
args = alignment_file_parser.parse_args(shlex.split(argstr))
assert_equal(bamfilename,args.count_files[0])
ga = get_genome_array_from_args(args)
assert_true(isinstance(ga,BAMGenomeArray))
def check_bam_mapping(mapping,offset_or_nibble):
"""Generator function to test import of BAM files under many read mapping rules
Parameters
----------
mapping : str
String specifying mapping rule. "fiveprime",
"threeprime", "center", or "fiveprime_variable"
offset_or_nibble : int or str
Integer specifying offset or nibble (only for center mapping)
or str specifying filename of variable offset dict text file
"""
argstr = "--countfile_format BAM --count_files %s --%s " % (bamfilename, mapping)
if mapping == "center":
argstr += ("--nibble %s" % offset_or_nibble)
else:
argstr += ("--offset %s" % offset_or_nibble)
mapdict = {
"fiveprime" : FivePrimeMapFactory,
"threeprime" : ThreePrimeMapFactory,
"center" : CenterMapFactory,
"fiveprime_variable" : VariableFivePrimeMapFactory,
}
args = alignment_file_parser.parse_args(shlex.split(argstr))
ga = get_genome_array_from_args(args)
#assert_equal(mapping,ga.map_fn.__mapping__)a
assert_true(isinstance(ga.map_fn,mapdict[mapping]))
# assure correct mapping function was applied
# by comparing counts loaded from a bowtie file
# under those map rules to a vector corresponding
# to known answers for those rules
assert_greater(ga.sum(),0)
check_genome_array_against_vector(ga,mapping,offset_or_nibble)
def alignment_parser_check_set_sum(fmt,filename):
my_sum = 5
argstr = "--countfile_format %s --count_files %s --fiveprime --sum %s" % (fmt,filename,my_sum)
args = alignment_file_parser.parse_args(shlex.split(argstr))
ga = get_genome_array_from_args(args)
assert_equal(my_sum,ga.sum())
def alignment_parser_check_normalize(fmt,filename):
argstr = "--countfile_format %s --count_files %s --fiveprime --normalize" % (fmt,filename)
args = alignment_file_parser.parse_args(shlex.split(argstr))
ga = get_genome_array_from_args(args)
assert_true(ga._normalize)
def test_alignment_parser_wiggle_with_sparsegenomearray():
argstr = "--countfile_format wiggle --count_files %s --big_genome" % wigglefilename
args = alignment_file_parser.parse_args(shlex.split(argstr))
ga = get_genome_array_from_args(args)
assert_true(isinstance(ga,SparseGenomeArray))
def test_alignment_parser_open_wiggle_makes_genomearray():
argstr = "--countfile_format wiggle --count_files %s" % wigglefilename
args = alignment_file_parser.parse_args(shlex.split(argstr))
ga = get_genome_array_from_args(args)
assert_true(isinstance(ga,GenomeArray))
def test_alignment_parser_open_bigwig_makes_bigwiggenomearray():
argstr = "--countfile_format bigwig --count_files %s" % bigwigfilename
args = alignment_file_parser.parse_args(shlex.split(argstr))
ga = get_genome_array_from_args(args)
assert_true(isinstance(ga,BigWigGenomeArray))
