def test_alt_chr_pos_to_chromorder():
assert(nc.chr_pos_to_genome_pos('6', 0, 'b37') ==
1062541960)
assert(nc.chr_pos_to_genome_pos('7', 0, 'b37') ==
1233657027)
assert(nc.chr_pos_to_genome_pos('8', 0, 'b37') ==
1392795690)
def test_chr_pos_to_chromorder():
assert(nc.chr_pos_to_genome_pos('chr6', 0) ==
1062541960)
assert(nc.chr_pos_to_genome_pos('chr7', 0) ==
1233657027)
assert(nc.chr_pos_to_genome_pos('chr8', 0) ==
1392795690)
def test_chr_pos_to_genome_pos():
'''
Test the coordinate conversion script.
'''
genome_coord = nc.chr_pos_to_genome_pos('chr1', 10)
assert(genome_coord == 10)
genome_coord = nc.chr_pos_to_genome_pos('chr2', 10)
assert(genome_coord == 249250631)
def line_to_dict(line):
parts = line.split()
d = {}
try:
d['xs'] = [
nc.chr_pos_to_genome_pos(parts[chr1_col],
int(parts[from1_col]), assembly),
nc.chr_pos_to_genome_pos(parts[chr1_col], int(parts[to1_col]),
assembly)
]
d['ys'] = [
nc.chr_pos_to_genome_pos(parts[chr2_col],
int(parts[from2_col]), assembly),
nc.chr_pos_to_genome_pos(parts[chr2_col], int(parts[to2_col]),
assembly)
]
except KeyError:
error_str = (
"ERROR converting chromosome position to genome position. "
"Please make sure you've specified the correct assembly "
"using the --assembly option. "
"Current assembly: {}, chromosomes: {},{}".format(
assembly, parts[chr1_col], parts[chr2_col]))
raise (KeyError(error_str))
d['uid'] = slugid.nice().decode('utf-8')
d['chrOffset'] = d['xs'][0] - int(parts[from1_col])
if importance_column is None:
d['importance'] = max(d['xs'][1] - d['xs'][0],
d['ys'][1] - d['ys'][0])
elif importance_column == 'random':
d['importance'] = random.random()
else:
d['importance'] = float(d[importance_column])
d['fields'] = line
return d
def END_ABS(self, CHROM, END):
chrom_info = nc.get_chrominfo("hg38")
return nc.chr_pos_to_genome_pos("chr" + CHROM, END, chrom_info)
def START_ABS(self, CHROM, START):
chrom_info = nc.get_chrominfo("hg38")
return nc.chr_pos_to_genome_pos("chr" + CHROM, START, chrom_info)
def test_dm3_chr_pos_genome_pos():
assert(nc.chr_pos_to_genome_pos('chr2L', 100, 'dm3') == 100)
assert(nc.chr_pos_to_genome_pos('chr2R', 100, 'dm3') == 23380516)
def test_test3chroms_chr_pos_genome_pos():
assert(nc.chr_pos_to_genome_pos('chr1', 100, 'test3chroms') == 100)
assert(nc.chr_pos_to_genome_pos('chr2', 100, 'test3chroms') == 1100)
def POS_ABS(self, CHROM, POS):
chrom_info = nc.get_chrominfo('hg38')
return nc.chr_pos_to_genome_pos('chr'+CHROM, POS, chrom_info)
def test_test3chroms_chr_pos_genome_pos():
assert (nc.chr_pos_to_genome_pos('chr1', 100, 'test3chroms') == 100)
assert (nc.chr_pos_to_genome_pos('chr2', 100, 'test3chroms') == 1100)
def test_alt_chr_pos_to_chromorder():
assert (nc.chr_pos_to_genome_pos('6', 0, 'b37') == 1062541960)
assert (nc.chr_pos_to_genome_pos('7', 0, 'b37') == 1233657027)
assert (nc.chr_pos_to_genome_pos('8', 0, 'b37') == 1392795690)
def test_chr_pos_to_chromorder():
assert (nc.chr_pos_to_genome_pos('chr6', 0) == 1062541960)
assert (nc.chr_pos_to_genome_pos('chr7', 0) == 1233657027)
assert (nc.chr_pos_to_genome_pos('chr8', 0) == 1392795690)
def test_chr_pos_to_genome_pos():
assert (nc.chr_pos_to_genome_pos('chr1', 100) == 100)
assert (nc.chr_pos_to_genome_pos('chr2', 100) == 249250621 + 100)
assert (nc.chr_pos_to_genome_pos('1', 100, 'grch37') == 100)
def test_dm3_chr_pos_genome_pos():
assert (nc.chr_pos_to_genome_pos('chr2L', 100, 'dm3') == 100)
assert (nc.chr_pos_to_genome_pos('chr2R', 100, 'dm3') == 23380516)
def test_clodius_aggregate_bedgraph1():
input_file = op.join(testdir, 'sample_data', 'dm3_values.tsv')
output_file = '/tmp/dm3_values.hitile'
runner = clt.CliRunner()
result = runner.invoke(
cca.bedgraph,
[input_file, '--output-file', output_file, '--assembly', 'dm3'])
a, b, tb = result.exc_info
"""
print("exc_info:", result.exc_info)
print("result:", result)
print("result.output", result.output)
print("result.error", traceback.print_tb(tb))
print("Exception:", a,b)
"""
# print("result.output", result.output)
f = h5py.File('/tmp/dm3_values.hitile')
# max_zoom = f['meta'].attrs['max-zoom']
# TODO: Make assertions about result
values = f['values_0']
import numpy as np
# print("values:", values[8])
# genome positions are 0 based as stored in hitile files
assert (np.isnan(values[8]))
assert (values[9] == 1)
assert (values[10] == 1)
assert (values[13] == 1)
assert (np.isnan(values[14]))
assert (np.isnan(values[15]))
chrom_info = nc.get_chrominfo('dm3')
chr_2r_pos = nc.chr_pos_to_genome_pos('chr2R', 0, chrom_info)
# print('chr_2r_pos:', chr_2r_pos)
assert (np.isnan(values[chr_2r_pos + 28]))
assert (values[chr_2r_pos + 29] == 77)
assert (values[chr_2r_pos + 38] == 77)
assert (values[chr_2r_pos + 39] == 0)
assert (result.exit_code == 0)
d = cht.get_data(f, 0, 0)
# print("d[:10]", d[:10])
# print("sum(d):", sum([x for x in d if not np.isnan(x)]))
assert (np.nansum(d) > 1.0 and np.nansum(d) < 10.0)
return
input_file = op.join(testdir, 'sample_data', 'test3chroms_values.tsv')
output_file = '/tmp/test3chroms_values.hitile'
runner = clt.CliRunner()
result = runner.invoke(cca.bedgraph, [
input_file, '--output-file', output_file, '--assembly', 'test3chroms'
])
# print('output:', result.output, result)
f = h5py.File('/tmp/test3chroms_values.hitile')
# f['meta'].attrs['max-zoom']
# TODO: Make assertions about result
# print('max_zoom:', max_zoom)
# print("len", len(f['values_0']))
values = f['values_0']
# print('values', values[:100])
# genome positions are 0 based as stored in hitile files
assert (values[8] == 0)
assert (values[9] == 1)
assert (values[10] == 1)
assert (values[13] == 1)
assert (values[14] == 0)
assert (values[15] == 0)
chr2_pos = nc.chr_pos_to_genome_pos('chr2', 0, 'test3chroms')
assert (values[chr2_pos + 28] == 0)
assert (values[chr2_pos + 29] == 77)
assert (values[chr2_pos + 38] == 77)
assert (values[chr2_pos + 39] == 0)
assert (result.exit_code == 0)
d = cht.get_data(f, 0, 0)
assert (sum(d) == 770 + 880 + 5)
def main():
parser = argparse.ArgumentParser(description="""
python chr_pos_to_genome_pos.py -t 1,2:3,4
Convert chromosome,position pairs to genome_positions. Assumes that the
coordinates refer to the hg19 assembly (unless otherwise specified).
Example:
2 NM_000014 chr12 - 9220303 9268825
-> python scripts/chr_pos_to_genome_pos.py -c 3:5,3:6
2 NM_000014 genome - 2115405269 2115453791
--------------------------------
This also works with space-delimited fields:
chr5 56765,56766
->python scripts/chr_pos_to_genome_pos.py -c 1:2
genome 881683465,881683466
""")
parser.add_argument('-a', '--assembly', default='hg19')
parser.add_argument('-s', '--chromsizes-file', default=None)
parser.add_argument('-n', '--new-chrom', default=None)
parser.add_argument(
'-c',
'--columns',
default='1,2',
help="Which columns to translate to genome positions. "
"Column pairs should be 1-based and separated by colons")
#parser.add_argument('-u', '--useless', action='store_true',
# help='Another useless option')
args = parser.parse_args()
if args.chromsizes_file is not None:
chrom_info = nc.get_chrominfo_from_file(args.chromsizes_file)
else:
chrom_info = nc.get_chrominfo(args.assembly)
for line in sys.stdin:
try:
line_output = []
line_parts = line.strip().split()
translated_positions = {}
translated_chroms = {}
for translate_pair in [[int(y) for y in x.split(':')]
for x in args.columns.split(',')]:
# go through the pairs of columns that need to be translated to genome position
# assume that the position column is comma separated list of values (although it doesn't
# actually need to be)
chrom, poss = line_parts[translate_pair[0] - 1], line_parts[
translate_pair[1] - 1].strip(",").split(',')
genome_pos = ",".join(
map(str, [
nc.chr_pos_to_genome_pos(chrom, int(pos), chrom_info)
for pos in poss
]))
#line_output += [genome_pos]
# note that we've translated these columns and shouldn't include them in the output
translated_positions[translate_pair[1] - 1] = genome_pos
translated_chroms[translate_pair[0] - 1] = chrom
for i, part in enumerate(line_parts):
if i in translated_chroms:
# replace chromosome identifiers (e.g. 'chr1') with 'genome' to indicate the positions
if args.new_chrom is None:
line_output += ['genome({})'.format(chrom)]
else:
line_output += [args.new_chrom]
elif i in translated_positions:
# this column used to contain a position so we need to replace it with a translated
# position
line_output += [translated_positions[i]]
else:
# if this column didn't contain a translated position output it as is
line_output += [part]
try:
print("\t".join(map(str, line_output)))
except BrokenPipeError:
# Output is probably being run through "head" or something similar
break
except KeyError as ke:
print("KeyError:", ke, line.strip(), file=sys.stderr)
def test_chr_pos_to_genome_pos():
assert(nc.chr_pos_to_genome_pos('chr1', 100) == 100)
assert(nc.chr_pos_to_genome_pos('chr2', 100) == 249250621 + 100)
assert(nc.chr_pos_to_genome_pos('1', 100, 'grch37') == 100)
def main():
parser = argparse.ArgumentParser(description="""
python chr_pos_to_genome_pos.py -t 1,2:3,4
Convert chromosome,position pairs to genome_positions. Assumes that the
coordinates refer to the hg19 assembly (unless otherwise specified).
Example:
2 NM_000014 chr12 - 9220303 9268825
-> python scripts/chr_pos_to_genome_pos.py -c 3:5,3:6
2 NM_000014 genome - 2115405269 2115453791
--------------------------------
This also works with space-delimited fields:
chr5 56765,56766
->python scripts/chr_pos_to_genome_pos.py -c 1:2
genome 881683465,881683466
""")
parser.add_argument('-a', '--assembly', default='hg19')
parser.add_argument('-s', '--chromsizes-file', default=None)
parser.add_argument('-n', '--new-chrom', default=None)
parser.add_argument('-c', '--columns', default='1,2',
help="Which columns to translate to genome positions. "
"Column pairs should be 1-based and separated by colons")
#parser.add_argument('-u', '--useless', action='store_true',
# help='Another useless option')
args = parser.parse_args()
if args.chromsizes_file is not None:
chrom_info = nc.get_chrominfo_from_file(args.chromsizes_file)
else:
chrom_info = nc.get_chrominfo(args.assembly)
for line in sys.stdin:
try:
line_output = []
line_parts = line.strip().split()
translated_positions = {}
translated_chroms = {}
for translate_pair in [[int (y) for y in x.split(':')] for x in args.columns.split(',')]:
# go through the pairs of columns that need to be translated to genome position
# assume that the position column is comma separated list of values (although it doesn't
# actually need to be)
chrom,poss = line_parts[translate_pair[0]-1], line_parts[translate_pair[1]-1].strip(",").split(',')
genome_pos = ",".join(map(str,[nc.chr_pos_to_genome_pos( chrom, int(pos), chrom_info) for pos in poss]))
#line_output += [genome_pos]
# note that we've translated these columns and shouldn't include them in the output
translated_positions[translate_pair[1]-1] = genome_pos
translated_chroms[translate_pair[0]-1] = chrom
for i,part in enumerate(line_parts):
if i in translated_chroms:
# replace chromosome identifiers (e.g. 'chr1') with 'genome' to indicate the positions
if args.new_chrom is None:
line_output += ['genome({})'.format(chrom)]
else:
line_output += [args.new_chrom]
elif i in translated_positions:
# this column used to contain a position so we need to replace it with a translated
# position
line_output += [translated_positions[i]]
else:
# if this column didn't contain a translated position output it as is
line_output += [part]
try:
print("\t".join(map(str, line_output)))
except BrokenPipeError:
# Output is probably being run through "head" or something similar
break
except KeyError as ke:
print("KeyError:", ke, line.strip(), file=sys.stderr)
