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Add more sample name options #10

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Add more sample name options #10

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5a741f3
Add more sample name options
troycomi Jul 20, 2021
fb31b2a
Add query-on option
troycomi Sep 7, 2021
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37 changes: 33 additions & 4 deletions archaic_match/__main__.py
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Original file line number Diff line number Diff line change
Expand Up @@ -62,15 +62,27 @@ def main():
"sample, population, and super-population",
metavar="FILE")
population_group.add_argument("--archaic-populations",
required=True,
required=False,
default=[],
nargs='+',
help="List of archaic populations",
metavar="FILE")
population_group.add_argument("--archaic-samples",
required=False,
default=[],
nargs='+',
help="List of archaic samples")
population_group.add_argument("--modern-populations",
required=True,
required=False,
default=[],
nargs='+',
help="List of modern populations",
metavar="FILE")
population_group.add_argument("--modern-superpopulations",
required=False,
default=[],
nargs='+',
help="List of modern superpopulations")
population_group.add_argument("--chrom-sizes",
required=True,
help="Tab delimited file with seqid\tlength "
Expand Down Expand Up @@ -527,14 +539,31 @@ def match_pct(args):
sample_populations = get_sample_populations(args.populations)
logging.debug("Sample populations: {}".format(sample_populations))

archaic_sample_list = get_samplename_list(args.archaic_populations,
sample_populations)
archaic_sample_list = args.archaic_samples
archaic_sample_list += get_samplename_list(args.archaic_populations,
sample_populations)
# remove duplicates
archaic_sample_list = list(set(archaic_sample_list))

logging.debug("Archaic sample list: {}".format(archaic_sample_list))

modern_sample_list = get_samplename_list(args.modern_populations,
sample_populations)
modern_sample_list += get_samplename_list(args.modern_superpopulations,
sample_populations,
match='superpopulation')
modern_sample_list = list(set(modern_sample_list))

logging.debug("Modern sample list: {}".format(modern_sample_list))

if len(archaic_sample_list) == 0:
raise ValueError("Found no archaic samples, be sure to specify "
"`archaic-populations` or `archaic-samples`")

if len(modern_sample_list) == 0:
raise ValueError("Found no modern samples, be sure to specify "
"`modern-populations` or `modern-superpopulations`")

if args.chrom_sizes.isdigit():
chrom_sizes = defaultdict(lambda: int(args.chrom_sizes))
else:
Expand Down
17 changes: 10 additions & 7 deletions archaic_match/funcmodule.py
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Original file line number Diff line number Diff line change
Expand Up @@ -7,13 +7,16 @@
from .classmodule import Window


def get_samplename_list(query_populations, sample_populations):
'''Returns sample names for given population'''
sample_list = list()
for sample in sample_populations.values():
if sample.population in query_populations:
sample_list.append(sample.name)
return sample_list
def get_samplename_list(queries, samples,
match='population'):
'''
Returns sample names for given queries as a list.
Can match to 'population', 'superpopulation' or 'sample'
Default is 'population'
'''
return [sample.name
for sample in samples.values()
if getattr(sample, match) in queries]


def get_chrom_sizes(filename):
Expand Down