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PovilasMatPovilasMat
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Pushing to resolve merge
1 parent 5e7b35a commit eb42883

5 files changed

+22
-24
lines changed

Diff for: ‎bifrost_bridge/_modidx.py

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@@ -5,7 +5,11 @@
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'doc_host': 'https://$GIT_USER_NAME.github.io',
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'git_url': 'https://github.com/$GIT_USER_NAME/bifrost_bridge',
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'lib_path': 'bifrost_bridge'},
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'syms': { 'bifrost_bridge.bifrost': { 'bifrost_bridge.bifrost.process_qc_data': ( 'bifrost.html#process_qc_data',
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'syms': { 'bifrost_bridge.amrfinderplus': { 'bifrost_bridge.amrfinderplus.process_amrfinderplus_data': ( 'amrfinderplus.html#process_amrfinderplus_data',
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'bifrost_bridge/amrfinderplus.py'),
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'bifrost_bridge.amrfinderplus.process_amrfinderplus_data_from_cli': ( 'amrfinderplus.html#process_amrfinderplus_data_from_cli',
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'bifrost_bridge/amrfinderplus.py')},
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'bifrost_bridge.bifrost': { 'bifrost_bridge.bifrost.process_qc_data': ( 'bifrost.html#process_qc_data',
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'bifrost_bridge/bifrost.py')},
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'bifrost_bridge.bracken': { 'bifrost_bridge.bracken.process_bracken_data': ( 'bracken.html#process_bracken_data',
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'bifrost_bridge/bracken.py'),

Diff for: ‎nbs/06_amrfinderplus.ipynb

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},
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{
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"cell_type": "code",
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"execution_count": 1,
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"execution_count": null,
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"metadata": {},
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"outputs": [],
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"source": [
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},
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{
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"cell_type": "code",
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"execution_count": 2,
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"execution_count": null,
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"metadata": {},
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"outputs": [],
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"source": [
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},
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{
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"cell_type": "code",
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"execution_count": 3,
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"execution_count": null,
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"metadata": {},
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"outputs": [],
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"source": [
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},
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{
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"cell_type": "code",
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"execution_count": 4,
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"execution_count": null,
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"metadata": {},
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"outputs": [],
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"source": [
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},
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{
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"cell_type": "code",
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"execution_count": 62,
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"execution_count": null,
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"metadata": {},
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"outputs": [
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{
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"source": [
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"#|hide\n",
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"#Example usage of the function\n",
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"process_amrfinderplus_data(\n",
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" input_path='test_data/amrfinderplus_empty.tsv', \n",
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" output_path='test_data/amrfinderplus_empty_testout.tsv',\n",
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" #filter_columns=\"Query / Template length\"\n",
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")"
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"#process_amrfinderplus_data(\n",
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"# input_path='test_data/amrfinderplus_empty.tsv', \n",
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"# output_path='test_data/amrfinderplus_empty_testout.tsv',\n",
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"# filter_columns=\"Query / Template length\"\n",
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"#)"
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]
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},
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{
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],
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"metadata": {
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"kernelspec": {
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"display_name": "base",
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"display_name": "python3",
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"language": "python",
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"name": "python3"
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},
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"language_info": {
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"codemirror_mode": {
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"name": "ipython",
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"version": 3
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},
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"file_extension": ".py",
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"mimetype": "text/x-python",
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"name": "python",
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"nbconvert_exporter": "python",
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"pygments_lexer": "ipython3",
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"version": "3.11.10"
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}
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},
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"nbformat": 4,

Diff for: ‎test_data/amrfinderplus_empty_testout.tsv

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Protein identifier Contig id Start Stop Strand Gene symbol Sequence name Scope Element type Element subtype Class Subclass Method Target length Reference sequence length % Coverage of reference sequence % Identity to reference sequence Alignment length Accession of closest sequence Name of closest sequence HMM id HMM description
2+

Diff for: ‎test_data/amrfinderplus_long_example_testout.tsv

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Protein id Contig id Start Stop Strand Element symbol Element name Scope Type Subtype Class Subclass Method Target length Reference sequence length % Coverage of reference % Identity to reference Alignment length Closest reference accession Closest reference name HMM accession HMM description
2+
nan,nan,nan,nan,nan,nan,nan,nan,nan,nan,nan,nan,nan,nan,nan,nan,nan,nan,nan,nan,nan,nan,nan,nan,nan,nan,nan,nan,nan,nan,nan,nan,nan,nan,nan,nan,nan,nan,nan,nan,nan,nan,nan,nan,nan,nan 2501M47857_19_417.516,2501M47857_19_417.516,2501M47857_19_417.516,2501M47857_19_417.516,2501M47857_19_417.516,2501M47857_19_417.516,2501M47857_19_417.516,2501M47857_19_417.516,2501M47857_19_417.516,2501M47857_19_417.516,2501M47857_19_417.516,2501M47857_19_417.516,2501M47857_19_417.516,2501M47857_19_417.516,2501M47857_19_417.516,2501M47857_19_417.516,2501M47857_19_417.516,2501M47857_19_417.516,2501M47857_19_417.516,2501M47857_19_417.516,2501M47857_19_417.516,2501M47857_19_417.516,2501M47857_19_417.516,2501M47857_26_361.308,2501M47857_26_361.308,2501M47857_26_361.308,2501M47857_3_660.553,2501M47857_3_660.553,2501M47857_3_660.553,2501M47857_3_660.553,2501M47857_3_660.553,2501M47857_3_660.553,2501M47857_3_660.553,2501M47857_3_660.553,2501M47857_3_660.553,2501M47857_3_660.553,2501M47857_3_660.553,2501M47857_3_660.553,2501M47857_3_660.553,2501M47857_3_660.553,2501M47857_3_660.553,2501M47857_3_660.553,2501M47857_3_660.553,2501M47857_3_660.553,2501M47857_3_660.553,2501M47857_3_660.553 78959,78959,78959,78959,78959,78959,148308,148308,148308,148308,206553,206553,206553,206553,206712,206712,206712,206712,206712,206712,206712,206712,206712,33324,33324,97044,19820,19820,19820,19820,19820,19820,19820,19820,21655,21655,83691,83691,83691,83691,83701,83701,83701,83701,83701,83701 81547,81547,81547,81547,81547,81547,148691,148691,148691,148691,208252,208252,208252,208252,208252,208252,208252,208252,208252,208252,208252,208252,208252,34219,34219,97673,20242,20242,20242,20242,20242,20242,20242,20242,22266,22266,84883,84883,84883,84883,84890,84890,84890,84890,84890,84890 -,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,+,+,-,-,-,-,-,-,-,-,-,-,-,+,+,+,+,+,+,+,+,+,+ gyrA_A70A,gyrA_D85D,gyrA_D90D,gyrA_P104P,gyrA_R285K,gyrA_T86I,rpsL_K43K,rpsL_K88K,rpsL_M1V,rpsL_S122P,23S_A2074A,23S_A2075A,23S_C2627C,23S_T1752C,23S_A1920G,23S_A2074A,23S_A2075A,23S_C1889A,23S_C1894T,23S_C2581T,23S_C2627C,23S_G1918A,23S_T2272C,blaOXA-61_G-57G,blaOXA-61_G727A,cmeR_G86G,rplV_A103V,rplV_A84A,rplV_A88A,rplV_G86G,rplV_H97H,rplV_R85R,rplV_S109A,rplV_V137A,rplD_G74G,rplD_V196A,23S_A412G,23S_G337A,23S_G426T,23S_T428C,23S_A554C,23S_C296G,23S_G298A,23S_G327A,23S_G364C,23S_T571G DNA gyrase subunit A GyrA [WILDTYPE],DNA gyrase subunit A GyrA [WILDTYPE],DNA gyrase subunit A GyrA [WILDTYPE],DNA gyrase subunit A GyrA [WILDTYPE],DNA gyrase subunit A GyrA [UNKNOWN],Campylobacter quinolone resistant GyrA,30S ribosomal protein S12 RpsL [WILDTYPE],30S ribosomal protein S12 RpsL [WILDTYPE],30S ribosomal protein S12 RpsL [UNKNOWN],30S ribosomal protein S12 RpsL [UNKNOWN],Campylobacter 23S ribosomal RNA [WILDTYPE],Campylobacter 23S ribosomal RNA [WILDTYPE],Campylobacter 23S ribosomal RNA [WILDTYPE],Campylobacter 23S ribosomal RNA [UNKNOWN],Campylobacter 23S ribosomal RNA [UNKNOWN],Campylobacter 23S ribosomal RNA [WILDTYPE],Campylobacter 23S ribosomal RNA [WILDTYPE],Campylobacter 23S ribosomal RNA [UNKNOWN],Campylobacter 23S ribosomal RNA [UNKNOWN],Campylobacter 23S ribosomal RNA [UNKNOWN],Campylobacter 23S ribosomal RNA [WILDTYPE],Campylobacter 23S ribosomal RNA [UNKNOWN],Campylobacter 23S ribosomal RNA [UNKNOWN],Campylobacter blaOXA-61 promoter region [WILDTYPE],Campylobacter blaOXA-61 promoter region [UNKNOWN],multidrug efflux system transcriptional regulator CmeR [WILDTYPE],Campylobacter macrolide resistant RplV,50S ribosomal protein L22 [WILDTYPE],50S ribosomal protein L22 [WILDTYPE],50S ribosomal protein L22 [WILDTYPE],50S ribosomal protein L22 [WILDTYPE],50S ribosomal protein L22 [WILDTYPE],50S ribosomal protein L22 [UNKNOWN],50S ribosomal protein L22 [UNKNOWN],50S ribosomal protein L4 [WILDTYPE],50S ribosomal protein L4 [UNKNOWN],Campylobacter 23S ribosomal RNA [UNKNOWN],Campylobacter 23S ribosomal RNA [UNKNOWN],Campylobacter 23S ribosomal RNA [UNKNOWN],Campylobacter 23S ribosomal RNA [UNKNOWN],Campylobacter 23S ribosomal RNA [UNKNOWN],Campylobacter 23S ribosomal RNA [UNKNOWN],Campylobacter 23S ribosomal RNA [UNKNOWN],Campylobacter 23S ribosomal RNA [UNKNOWN],Campylobacter 23S ribosomal RNA [UNKNOWN],Campylobacter 23S ribosomal RNA [UNKNOWN] core,core,core,core,core,core,core,core,core,core,core,core,core,core,core,core,core,core,core,core,core,core,core,core,core,core,core,core,core,core,core,core,core,core,core,core,core,core,core,core,core,core,core,core,core,core AMR,AMR,AMR,AMR,AMR,AMR,AMR,AMR,AMR,AMR,AMR,AMR,AMR,AMR,AMR,AMR,AMR,AMR,AMR,AMR,AMR,AMR,AMR,AMR,AMR,AMR,AMR,AMR,AMR,AMR,AMR,AMR,AMR,AMR,AMR,AMR,AMR,AMR,AMR,AMR,AMR,AMR,AMR,AMR,AMR,AMR POINT,POINT,POINT,POINT,POINT,POINT,POINT,POINT,POINT,POINT,POINT,POINT,POINT,POINT,POINT,POINT,POINT,POINT,POINT,POINT,POINT,POINT,POINT,POINT,POINT,POINT,POINT,POINT,POINT,POINT,POINT,POINT,POINT,POINT,POINT,POINT,POINT,POINT,POINT,POINT,POINT,POINT,POINT,POINT,POINT,POINT QUINOLONE,QUINOLONE,QUINOLONE,QUINOLONE,nan,QUINOLONE,AMINOGLYCOSIDE,AMINOGLYCOSIDE,nan,nan,MACROLIDE,MACROLIDE,MACROLIDE,nan,nan,MACROLIDE,MACROLIDE,nan,nan,nan,MACROLIDE,nan,nan,BETA-LACTAM,nan,MACROLIDE,MACROLIDE,MACROLIDE,MACROLIDE,MACROLIDE,MACROLIDE,MACROLIDE,nan,nan,MACROLIDE,nan,nan,nan,nan,nan,nan,nan,nan,nan,nan,nan QUINOLONE,QUINOLONE,QUINOLONE,QUINOLONE,nan,QUINOLONE,STREPTOMYCIN,STREPTOMYCIN,nan,nan,MACROLIDE,MACROLIDE,MACROLIDE,nan,nan,MACROLIDE,MACROLIDE,nan,nan,nan,MACROLIDE,nan,nan,BETA-LACTAM,nan,MACROLIDE,MACROLIDE,MACROLIDE,MACROLIDE,MACROLIDE,ERYTHROMYCIN/TYLOSIN,ERYTHROMYCIN/TYLOSIN,nan,nan,ERYTHROMYCIN/TYLOSIN,nan,nan,nan,nan,nan,nan,nan,nan,nan,nan,nan POINTX,POINTX,POINTX,POINTX,POINTX,POINTX,POINTX,POINTX,POINTX,POINTX,POINTN,POINTN,POINTN,POINTN,POINTN,POINTN,POINTN,POINTN,POINTN,POINTN,POINTN,POINTN,POINTN,POINTN,POINTN,POINTX,POINTX,POINTX,POINTX,POINTX,POINTX,POINTX,POINTX,POINTX,POINTX,POINTX,POINTN,POINTN,POINTN,POINTN,POINTN,POINTN,POINTN,POINTN,POINTN,POINTN 863,863,863,863,863,863,128,128,128,128,1700,1700,1700,1700,1541,1541,1541,1541,1541,1541,1541,1541,1541,896,896,210,141,141,141,141,141,141,141,141,204,204,1193,1193,1193,1193,1190,1190,1190,1190,1190,1190 863,863,863,863,863,863,128,128,128,128,2912,2912,2912,2912,2912,2912,2912,2912,2912,2912,2912,2912,2912,896,896,210,141,141,141,141,141,141,141,141,204,204,2912,2912,2912,2912,2912,2912,2912,2912,2912,2912 100.0,100.0,100.0,100.0,100.0,100.0,100.0,100.0,100.0,100.0,58.38,58.38,58.38,58.38,52.92,52.92,52.92,52.92,52.92,52.92,52.92,52.92,52.92,100.0,100.0,100.0,100.0,100.0,100.0,100.0,100.0,100.0,100.0,100.0,100.0,100.0,40.97,40.97,40.97,40.97,40.87,40.87,40.87,40.87,40.87,40.87 99.77,99.77,99.77,99.77,99.77,99.77,99.22,99.22,99.22,99.22,99.94,99.94,99.94,99.94,99.61,99.61,99.61,99.61,99.61,99.61,99.61,99.61,99.61,99.89,99.89,100.0,97.87,97.87,97.87,97.87,97.87,97.87,97.87,97.87,99.51,99.51,99.66,99.66,99.66,99.66,99.5,99.5,99.5,99.5,99.5,99.5 863,863,863,863,863,863,128,128,128,128,1700,1700,1700,1700,1541,1541,1541,1541,1541,1541,1541,1541,1541,896,896,210,141,141,141,141,141,141,141,141,204,204,1193,1193,1193,1193,1190,1190,1190,1190,1190,1190 WP_002857904.1,WP_002857904.1,WP_002857904.1,WP_002857904.1,WP_002857904.1,WP_002857904.1,WP_057042458.1,WP_057042458.1,WP_057042458.1,WP_057042458.1,NC_002163.1:396449-399360,NC_002163.1:396449-399360,NC_002163.1:396449-399360,NC_002163.1:396449-399360,NC_022347.1:1040292-1037381,NC_022347.1:1040292-1037381,NC_022347.1:1040292-1037381,NC_022347.1:1040292-1037381,NC_022347.1:1040292-1037381,NC_022347.1:1040292-1037381,NC_022347.1:1040292-1037381,NC_022347.1:1040292-1037381,NC_022347.1:1040292-1037381,NZ_CP022079.1:267177-268072,NZ_CP022079.1:267177-268072,WP_002843095.1,WP_002851214.1,WP_002851214.1,WP_002851214.1,WP_002851214.1,WP_002851214.1,WP_002851214.1,WP_002851214.1,WP_002851214.1,WP_002851146.1,WP_002851146.1,NC_022347.1:1040292-1037381,NC_022347.1:1040292-1037381,NC_022347.1:1040292-1037381,NC_022347.1:1040292-1037381,NC_002163.1:396449-399360,NC_002163.1:396449-399360,NC_002163.1:396449-399360,NC_002163.1:396449-399360,NC_002163.1:396449-399360,NC_002163.1:396449-399360 DNA gyrase subunit A GyrA,DNA gyrase subunit A GyrA,DNA gyrase subunit A GyrA,DNA gyrase subunit A GyrA,DNA gyrase subunit A GyrA,DNA gyrase subunit A GyrA,30S ribosomal protein S12 RpsL,30S ribosomal protein S12 RpsL,30S ribosomal protein S12 RpsL,30S ribosomal protein S12 RpsL,23S ribosomal RNA,23S ribosomal RNA,23S ribosomal RNA,23S ribosomal RNA,23S ribosomal RNA,23S ribosomal RNA,23S ribosomal RNA,23S ribosomal RNA,23S ribosomal RNA,23S ribosomal RNA,23S ribosomal RNA,23S ribosomal RNA,23S ribosomal RNA,blaOXA-61 promoter region,blaOXA-61 promoter region,multidrug efflux system transcriptional regulator CmeR,50S ribosomal protein L22,50S ribosomal protein L22,50S ribosomal protein L22,50S ribosomal protein L22,50S ribosomal protein L22,50S ribosomal protein L22,50S ribosomal protein L22,50S ribosomal protein L22,50S ribosomal protein L4,50S ribosomal protein L4,23S ribosomal RNA,23S ribosomal RNA,23S ribosomal RNA,23S ribosomal RNA,23S ribosomal RNA,23S ribosomal RNA,23S ribosomal RNA,23S ribosomal RNA,23S ribosomal RNA,23S ribosomal RNA nan,nan,nan,nan,nan,nan,nan,nan,nan,nan,nan,nan,nan,nan,nan,nan,nan,nan,nan,nan,nan,nan,nan,nan,nan,nan,nan,nan,nan,nan,nan,nan,nan,nan,nan,nan,nan,nan,nan,nan,nan,nan,nan,nan,nan,nan nan,nan,nan,nan,nan,nan,nan,nan,nan,nan,nan,nan,nan,nan,nan,nan,nan,nan,nan,nan,nan,nan,nan,nan,nan,nan,nan,nan,nan,nan,nan,nan,nan,nan,nan,nan,nan,nan,nan,nan,nan,nan,nan,nan,nan,nan

Diff for: ‎test_data/amrfinderplus_testout.tsv

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Protein identifier Contig id Start Stop Strand Gene symbol Sequence name Scope Element type Element subtype Class Subclass Method Target length Reference sequence length % Coverage of reference sequence % Identity to reference sequence Alignment length Accession of closest sequence Name of closest sequence HMM id HMM description
2+
nan contig00004 33786 34556 + blaOXA-193 OXA-61 family class D beta-lactamase OXA-193 core AMR AMR BETA-LACTAM BETA-LACTAM ALLELEX 257 257 100.0 100.0 257 WP_002783228.1 OXA-61 family class D beta-lactamase OXA-193 nan nan

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