SYMBOL INDEX (107 symbols across 25 files)

FILE: hAMRonization/AbricateIO.py
  class AbricateIterator (line 10) | class AbricateIterator(hAMRonizedResultIterator):
    method __init__ (line 11) | def __init__(self, source, metadata):
    method parse (line 36) | def parse(self, handle):

FILE: hAMRonization/AmrFinderPlusIO.py
  class AmrFinderPlusIterator (line 20) | class AmrFinderPlusIterator(hAMRonizedResultIterator):
    method __init__ (line 61) | def __init__(self, source, metadata):
    method parse (line 72) | def parse(self, handle):

FILE: hAMRonization/AmrPlusPlusIO.py
  class AmrPlusPlusIterator (line 14) | class AmrPlusPlusIterator(hAMRonizedResultIterator):
    method __init__ (line 15) | def __init__(self, source, metadata):
    method parse (line 35) | def parse(self, handle):

FILE: hAMRonization/AribaIO.py
  class AribaIterator (line 20) | class AribaIterator(hAMRonizedResultIterator):
    method __init__ (line 21) | def __init__(self, source, metadata):
    method parse (line 63) | def parse(self, handle):

FILE: hAMRonization/CSStarIO.py
  class CSStarIterator (line 16) | class CSStarIterator(hAMRonizedResultIterator):
    method __init__ (line 17) | def __init__(self, source, metadata):
    method parse (line 34) | def parse(self, handle):

FILE: hAMRonization/DeepArgIO.py
  class DeepArgIterator (line 14) | class DeepArgIterator(hAMRonizedResultIterator):
    method __init__ (line 15) | def __init__(self, source, metadata):
    method parse (line 41) | def parse(self, handle):

FILE: hAMRonization/FARGeneIO.py
  class FARGeneIOIterator (line 15) | class FARGeneIOIterator(hAMRonizedResultIterator):
    method __init__ (line 16) | def __init__(self, source, metadata):
    method parse (line 56) | def parse(self, handle):

FILE: hAMRonization/GrootIO.py
  class GrootIterator (line 16) | class GrootIterator(hAMRonizedResultIterator):
    method __init__ (line 17) | def __init__(self, source, metadata):
    method parse (line 36) | def parse(self, handle):

FILE: hAMRonization/Interfaces.py
  class hAMRonizedResultIterator (line 15) | class hAMRonizedResultIterator(ABC):
    method __init__ (line 23) | def __init__(self, source, field_map, metadata):
    method hAMRonize (line 59) | def hAMRonize(self, report_data, metadata, field_map_override=None):
    method __next__ (line 78) | def __next__(self):
    method __iter__ (line 85) | def __iter__(self):
    method parse (line 94) | def parse(self, handle):
    method write (line 99) | def write(
  function generate_tool_subparser (line 190) | def generate_tool_subparser(subparser, analysis_tool):
  function generic_cli_interface (line 224) | def generic_cli_interface():

FILE: hAMRonization/KmerResistanceIO.py
  class KmerResistanceIterator (line 14) | class KmerResistanceIterator(hAMRonizedResultIterator):
    method __init__ (line 15) | def __init__(self, source, metadata):
    method parse (line 42) | def parse(self, handle):

FILE: hAMRonization/MykrobeIO.py
  class MykrobeIterator (line 11) | class MykrobeIterator(hAMRonizedResultIterator):
    method __init__ (line 42) | def __init__(self, source, metadata):
    method parse (line 67) | def parse(self, handle):

FILE: hAMRonization/ResFamsIO.py
  class ResFamsIterator (line 14) | class ResFamsIterator(hAMRonizedResultIterator):
    method __init__ (line 15) | def __init__(self, source, metadata):
    method parse (line 51) | def parse(self, handle):

FILE: hAMRonization/ResFinderIO.py
  class ResFinderIterator (line 20) | class ResFinderIterator(hAMRonizedResultIterator):
    method __init__ (line 26) | def __init__(self, source, metadata):
    method parse (line 32) | def parse(self, handle):
  function _get_start_pos (line 201) | def _get_start_pos(p0, p1):
  function _get_end_pos (line 205) | def _get_end_pos(p0, p1):
  function _get_strand (line 209) | def _get_strand(p0, p1):
  function _get_length (line 213) | def _get_length(p0, p1):
  function _safe_round (line 217) | def _safe_round(n, d):
  function _empty_to_none (line 221) | def _empty_to_none(s):
  function _condense_notes (line 225) | def _condense_notes(notes, pmids):
  function fold (line 235) | def fold(fun, acc, lst):  # Python's missing function (why have map but ...

FILE: hAMRonization/RgiIO.py
  class RgiIterator (line 20) | class RgiIterator(hAMRonizedResultIterator):
    method __init__ (line 21) | def __init__(self, source, metadata):
    method parse (line 110) | def parse(self, handle):

FILE: hAMRonization/SraxIO.py
  class SraxIterator (line 15) | class SraxIterator(hAMRonizedResultIterator):
    method __init__ (line 16) | def __init__(self, source, metadata):
    method parse (line 35) | def parse(self, handle):

FILE: hAMRonization/Srst2IO.py
  class Srst2Iterator (line 14) | class Srst2Iterator(hAMRonizedResultIterator):
    method __init__ (line 15) | def __init__(self, source, metadata):
    method parse (line 40) | def parse(self, handle):

FILE: hAMRonization/StarAmrIO.py
  class StarAmrIterator (line 14) | class StarAmrIterator(hAMRonizedResultIterator):
    method __init__ (line 15) | def __init__(self, source, metadata):
    method parse (line 41) | def parse(self, handle):

FILE: hAMRonization/TBProfilerIO.py
  class TBProfilerIterator (line 10) | class TBProfilerIterator(hAMRonizedResultIterator):
    method __init__ (line 11) | def __init__(self, source, metadata):
    method parse (line 33) | def parse(self, handle):

FILE: hAMRonization/__init__.py
  function parse (line 85) | def parse(handle, metadata, tool):

FILE: hAMRonization/hAMRonizedResult.py
  class hAMRonizedResult (line 8) | class hAMRonizedResult:
    method __post_init__ (line 54) | def __post_init__(self):

FILE: hAMRonization/hamronize.py
  function main (line 6) | def main():

FILE: hAMRonization/summarize.py
  function format_interactive_json (line 13) | def format_interactive_json(combined_records):
  function generate_interactive_report (line 75) | def generate_interactive_report(combined_report_data):
  function check_report_type (line 676) | def check_report_type(file_path):
  function summarize_reports (line 694) | def summarize_reports(report_paths, summary_type, output_path=None):

FILE: schema/csv2json.py
  function string_list_to_list (line 15) | def string_list_to_list(string):
  function interface_label_to_property_key (line 21) | def interface_label_to_property_key(interface_label):
  function parse_properties_table (line 28) | def parse_properties_table(path_to_properties_table):
  function get_required_fields (line 129) | def get_required_fields(path_to_properties_table):
  function main (line 141) | def main(args):

FILE: test/test_interfaces.py
  function not_raises (line 11) | def not_raises(exception, msg):
  function test_empty_input_report (line 18) | def test_empty_input_report():
  function test_summarize_empty_reports (line 51) | def test_summarize_empty_reports():

FILE: test/test_parsing_validity.py
  function not_raises (line 7) | def not_raises(exception, msg):
  function test_abricate (line 14) | def test_abricate():
  function test_amrfinderplus (line 65) | def test_amrfinderplus():
  function test_amrplusplus (line 116) | def test_amrplusplus():
  function test_ariba (line 164) | def test_ariba():
  function test_ariba_var (line 213) | def test_ariba_var():
  function test_kmerresistance (line 247) | def test_kmerresistance():
  function test_resfinder (line 295) | def test_resfinder():
  function test_rgi_variants (line 418) | def test_rgi_variants():
  function test_rgi_orf_mode (line 448) | def test_rgi_orf_mode():
  function test_rgi (line 482) | def test_rgi():
  function test_srax (line 533) | def test_srax():
  function test_groot (line 585) | def test_groot():
  function test_deeparg (line 636) | def test_deeparg():
  function test_srst2 (line 684) | def test_srst2():
  function test_csstar (line 732) | def test_csstar():
  function test_tbprofiler (line 781) | def test_tbprofiler():
  function test_mykrobe_empty (line 831) | def test_mykrobe_empty():
  function test_mykrobe (line 838) | def test_mykrobe():
  function test_staramr_resfinder (line 889) | def test_staramr_resfinder():
  function test_staramr_pointfinder (line 916) | def test_staramr_pointfinder():
  function test_resfams (line 945) | def test_resfams():
  function test_fargene (line 965) | def test_fargene():