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import argparse
from goby.SequenceSegmentInformation import SequenceSegmentInformationGenerator
def print_segment_info(ssi, bases_to_print, print_all_bases, samples_to_print, print_all_samples):
print("Start position: reference index {}, reference id {}, location {}".format(ssi.start_position.reference_index,
ssi.start_position.reference_id,
ssi.start_position.location))
print("End position: reference index {}, reference id {}, location {}".format(ssi.end_position.reference_index,
ssi.end_position.reference_id,
ssi.end_position.location))
print("Length: {}".format(ssi.length))
print("\n")
samples_printed = 0
for sample_idx, sample in enumerate(ssi.sample, 1):
if samples_printed < samples_to_print or print_all_samples:
print("Sample number: {}".format(sample_idx))
bases_printed = 0
for base_idx, base in enumerate(sample.base, 1):
if bases_printed < bases_to_print or print_all_bases:
print("Base number: {}".format(base_idx))
print("Features: {}".format(", ".join(map(str, base.features))))
print("Labels: {}".format(", ".join(map(str, base.labels))))
print("Color: {}".format(", ".join(map(str, base.color))))
print("TrueLabel: {}".format(", ".join(map(str, base.trueLabel))))
print("HasCandidateIndel: {}".format(base.hasCandidateIndel))
print("HasTrueIndel: {}".format(base.hasTrueIndel))
print("IsVariant: {}".format(base.isVariant))
print("\n")
bases_printed += 1
else:
break
samples_printed += 1
else:
break
print("\n\n")
def main(args):
ssi_generator = SequenceSegmentInformationGenerator(args.input)
segments_printed = 0
for segment_idx, segment_info in enumerate(ssi_generator, 1):
if segments_printed < args.segments_to_print or args.print_all_segments:
print("Segment number: {}".format(segment_idx))
print_segment_info(segment_info, args.bases_to_print, args.print_all_bases, args.samples_to_print,
args.print_all_samples)
segments_printed += 1
else:
break
if __name__ == "__main__":
parser = argparse.ArgumentParser()
parser.add_argument("-i", "--input", type=str, required=True, help="SSI input file.")
parser.add_argument("-b", "--bases-to-print", type=int, default=1, help="Number of bases to print for each sample.")
parser.add_argument("--print-all-bases", dest="print_all_bases", help="If set, prints all bases.",
action="store_true")
parser.add_argument("-s", "--segments-to-print", type=int, default=1, help="Number of segments to print.")
parser.add_argument("--print-all-segments", dest="print_all_segments", help="If set, prints all segments.",
action="store_true")
parser.add_argument("-a", "--samples-to-print", type=int, default=1, help="Number of samples to print for each SSI.")
parser.add_argument("--print-all-samples", dest="print_all_samples", help="If set, print all samples.",
action="store_true")
parser_args = parser.parse_args()
main(parser_args)
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