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Refactoring/merge #17

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merged 4 commits into from
May 13, 2024
Merged

Refactoring/merge #17

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a8b726b
adding logging functionality
mattheww95 May 13, 2024
2ac5587
updated locidex merge and unified classes between report and merge
mattheww95 May 13, 2024
56b1d28
updated merge tests
mattheww95 May 13, 2024
b104506
added more merge tests
mattheww95 May 13, 2024
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3 changes: 2 additions & 1 deletion .gitignore
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Original file line number Diff line number Diff line change
Expand Up @@ -2,4 +2,5 @@ __pycache__
*.egg*
.vscode
.pytest_cache
tmp
tmp
.coverage*
36 changes: 36 additions & 0 deletions locidex/example/merge/merge_in/report.json
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{
"db_info": {
"db_name": "Locidex Database",
"db_version": "1.0.0",
"db_date": "2024/30/04",
"db_author": "mw",
"db_desc": "test",
"db_num_seqs": 53,
"is_nucl": true,
"is_prot": true,
"nucleotide_db_name": "nucleotide",
"protein_db_name": "protein"
},
"parameters": {
"mode": "normal",
"min_match_ident": 100,
"min_match_cov": 100,
"max_ambiguous": 0,
"max_internal_stops": 0
},
"data": {
"sample_name": "1",
"profile": {
"1": {
"aroC": "9048803cd72dee3c868cd2dc5dc5650d",
"dnaN": "2772ad8b8e0f7b50f1396c31fbe53f2d",
"hemD": "620f99723c4e190abe096b11ca34b944",
"hisD": "38027ac1ac34817584a176c7e575e97e",
"purE": "9855cbf4009439498bf84cacefce4d8f",
"sucA": "9289fc07cc8e93cfe0716e6f613cefdb",
"thrA": "9e1aa76bb42279ed7ec8fc30f984b65d"
}
},
"seq_data": {}
}
}
36 changes: 36 additions & 0 deletions locidex/example/merge/merge_in/report1.json
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{
"db_info": {
"db_name": "Locidex Database",
"db_version": "1.0.0",
"db_date": "2024/30/04",
"db_author": "mw",
"db_desc": "test",
"db_num_seqs": 53,
"is_nucl": true,
"is_prot": true,
"nucleotide_db_name": "nucleotide",
"protein_db_name": "protein"
},
"parameters": {
"mode": "normal",
"min_match_ident": 100,
"min_match_cov": 100,
"max_ambiguous": 0,
"max_internal_stops": 0
},
"data": {
"sample_name": "2",
"profile": {
"2": {
"aroC": "9048803cd72dee3c868cd2dc5dc5650d",
"dnaN": "2772ad8b8e0f7b50f1396c31fbe53f2d",
"hemD": "620f99723c4e190abe096b11ca34b944",
"hisD": "38027ac1ac34817584a176c7e575e97e",
"purE": "9855cbf4009439498bf84cacefce4d8f",
"sucA": "9289fc07cc8e93cfe0716e6f613cefdb",
"thrA": "9e1aa76bb42279ed7ec8fc30f984b65d"
}
},
"seq_data": {}
}
}
36 changes: 36 additions & 0 deletions locidex/example/merge/merge_in/report2.json
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{
"db_info": {
"db_name": "Locidex Database",
"db_version": "1.0.0",
"db_date": "2024/30/04",
"db_author": "mw",
"db_desc": "test",
"db_num_seqs": 53,
"is_nucl": true,
"is_prot": true,
"nucleotide_db_name": "nucleotide",
"protein_db_name": "protein"
},
"parameters": {
"mode": "normal",
"min_match_ident": 100,
"min_match_cov": 100,
"max_ambiguous": 0,
"max_internal_stops": 0
},
"data": {
"sample_name": "1",
"profile": {
"1": {
"aroC": "9048803cd72dee3c868cd2dc5dc5650d",
"dnaN": "2772ad8b8e0f7b50f1396c31fbe53f2d",
"hemD": "620f99723c4e190abe096b11ca34b944",
"hisD": "38027ac1ac34817584a176c7e575e97e",
"purE": "9855cbf4009439498bf84cacefce4d8f",
"sucA": "9289fc07cc8e93cfe0716e6f613cefdb",
"thrA": "9e1aa76bb42279ed7ec8fc30f984b65d"
}
},
"seq_data": {}
}
}
3 changes: 3 additions & 0 deletions locidex/example/merge/merge_out/profile.tsv
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@@ -0,0 +1,3 @@
sample_id aroC dnaN hemD hisD purE sucA thrA
1 9048803cd72dee3c868cd2dc5dc5650d 2772ad8b8e0f7b50f1396c31fbe53f2d 620f99723c4e190abe096b11ca34b944 38027ac1ac34817584a176c7e575e97e 9855cbf4009439498bf84cacefce4d8f 9289fc07cc8e93cfe0716e6f613cefdb 9e1aa76bb42279ed7ec8fc30f984b65d
2 9048803cd72dee3c868cd2dc5dc5650d 2772ad8b8e0f7b50f1396c31fbe53f2d 620f99723c4e190abe096b11ca34b944 38027ac1ac34817584a176c7e575e97e 9855cbf4009439498bf84cacefce4d8f 9289fc07cc8e93cfe0716e6f613cefdb 9e1aa76bb42279ed7ec8fc30f984b65d
24 changes: 24 additions & 0 deletions locidex/example/merge/merge_out/run.json
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{
"analysis_start_time": "13/05/2024 14:53:14",
"parameters": {
"command": "merge",
"input": [
[
"./locidex/example/merge/merge_in/report.json",
"./locidex/example/merge/merge_in/report1.json"
]
],
"outdir": "./locidex/example/merge/merge_out/",
"n_threads": 1,
"linker": "NNNNNNNNNNNNNNNNNNNN",
"strict": false,
"align": false,
"force": true
},
"result_file": "./locidex/example/merge/merge_out/profile.tsv",
"count_valid_loci": 0,
"count_invalid_loci": 0,
"valid_loci": "",
"invalid_loci": "",
"analysis_end_time": "13/05/2024 14:53:15"
}
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