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add tb tests #64

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merged 11 commits into from
Oct 11, 2021
Merged

add tb tests #64

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c9c5f8c
add tests
jodyphelan Oct 11, 2021
beb06f5
fix typo
jodyphelan Oct 11, 2021
66aa365
add tbprofiler to init
jodyphelan Oct 11, 2021
987be51
set required metadata
jodyphelan Oct 11, 2021
51ce299
add in new fields
jodyphelan Oct 11, 2021
58ab313
add in new fields
jodyphelan Oct 11, 2021
6950fce
fix tests
jodyphelan Oct 11, 2021
0390963
fix tests
jodyphelan Oct 11, 2021
48bd902
add metadata back in
jodyphelan Oct 11, 2021
776c899
fix typo
jodyphelan Oct 11, 2021
58512a2
fix typo
jodyphelan Oct 11, 2021
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18 changes: 10 additions & 8 deletions hAMRonization/TBProfilerIO.py
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Original file line number Diff line number Diff line change
Expand Up @@ -3,8 +3,7 @@
import json
from .Interfaces import hAMRonizedResultIterator

required_metadata = ['analysis_software_version',
'reference_database_version']
required_metadata = []


class TBProfilerIterator(hAMRonizedResultIterator):
Expand All @@ -15,15 +14,16 @@ def __init__(self, source, metadata):

self.field_mapping = {
'filename': 'input_file_name',
'gene': 'gene_symbol',
'gene': 'gene_name',
'gene_symbol': 'gene_symbol',
'gene_name': 'gene_name',
'drug': 'drug_class',
'type': 'genetic_variation_type',
'frequency': 'variant_frequency',
'db_name': 'reference_database_id',
'db_version': 'reference_database_version',
'tbprofiler_version': 'analysis_software_version'

'software_name': 'analysis_software_version',
'tbprofiler_version': 'analysis_software_version',
'reference_accession': 'reference_accession'
}

super().__init__(source, self.field_mapping, self.metadata)
Expand All @@ -38,14 +38,16 @@ def parse(self, handle):
for drug in variant["drugs"]:
result = {
'filename': handle.name,
'gene': variant['gene'],
'gene_symbol': variant['gene'],
'gene_name': variant['gene'],
'drug': drug['drug'],
'type': 'protein_variant' if variant['change'][0]=="p" else "nucleotide_variant",
'frequency': variant['freq'],
'db_name': json_obj['db_version']['name'],
'db_version': json_obj['db_version']['commit'],
'tbprofiler_version': json_obj['tbprofiler_version']
'tbprofiler_version': json_obj['tbprofiler_version'],
'software_name': 'tb-profiler',
'reference_accession': variant['feature_id']
}
yield self.hAMRonize(result, self.metadata)

9 changes: 6 additions & 3 deletions hAMRonization/__init__.py
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Original file line number Diff line number Diff line change
Expand Up @@ -17,7 +17,7 @@
from hAMRonization import CSStarIO
from hAMRonization import AmrPlusPlusIO
from hAMRonization import ResFamsIO

from hAMRonization import TBProfilerIO

_FormatToIterator = {
"abricate": AbricateIO.AbricateIterator,
Expand All @@ -34,7 +34,8 @@
"staramr": StarAmrIO.StarAmrIterator,
"csstar": CSStarIO.CSStarIterator,
"amrplusplus": AmrPlusPlusIO.AmrPlusPlusIterator,
"resfams": ResFamsIO.ResFamsIterator
"resfams": ResFamsIO.ResFamsIterator,
"tbprofiler": TBProfilerIO.TBProfilerIterator
}

_ReportFileToUse = {
Expand All @@ -52,7 +53,8 @@
"staramr": "resfinder.tsv",
"csstar": "OUTPUT.tsv",
"amrplusplus": "gene.tsv",
"resfams": "resfams.tblout"
"resfams": "resfams.tblout",
"tbprofiler": "OUTPUT.results.json"
}


Expand All @@ -72,6 +74,7 @@
"amrplusplus": AmrPlusPlusIO.required_metadata,
"resfams": ResFamsIO.required_metadata,
"groot": GrootIO.required_metadata,
"tbprofiler": TBProfilerIO.required_metadata,
}


Expand Down
4 changes: 4 additions & 0 deletions hAMRonization/hAMRonizedResult.py
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Expand Up @@ -19,6 +19,10 @@ class hAMRonizedResult():
reference_accession: str
analysis_software_name: str
analysis_software_version: str

# variant specific optional fields
variant_frequency: float = None
genetic_variation_type: str = None
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At the moment I've made this non mandatory but potentially in the final spec it should be?

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This will be lost when I approve and merge. Can you open an issue? ❤️

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Sure!


# optional fields
sequence_identity: float = None
Expand Down
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