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Add LTR regions to HIV, as part of #589.
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@donkirkby
donkirkby committed Jul 2, 2021
1 parent 6f6f098 commit 30749b0
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2 changes: 1 addition & 1 deletion micall/core/coverage_plots.py
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Original file line number Diff line number Diff line change
Expand Up @@ -43,9 +43,9 @@ def coverage_plot(amino_csv,
@param excluded_projects: a list of project names to exclude
@return: a list of full paths to the image files.
"""
# imports project information from JSON
if coverage_maps_path is None:
coverage_maps_path, _ = os.path.split(amino_csv.name)
# imports project information from JSON
projects = project_config.ProjectConfig.loadScoring()
reader = DictReader(amino_csv)
writer = DictWriter(coverage_scores_csv,
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4 changes: 2 additions & 2 deletions micall/data/landmark_references.yaml
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Original file line number Diff line number Diff line change
Expand Up @@ -3,7 +3,7 @@
coordinates: HIV1-B-FR-K03455-seed
landmarks:
# 1-based, inclusive positions in HXB2, including stop codons.
- {name: "5' LTR", start: 1, end: 634, frame: 0, colour: darkgrey}
- {name: "5' LTR", full_name: "HIV1B-5' LTR", start: 1, end: 634, frame: 0, colour: darkgrey, stop: N}
- {name: gag, full_name: HIV1B-gag, start: 790, end: 2292, frame: 0, colour: lightblue}
- {name: vif, full_name: HIV1B-vif, start: 5041, end: 5619, frame: 0, colour: steelblue}

Expand All @@ -17,7 +17,7 @@
# Actually starts at 8379, spliced to the end of rev in the middle of a codon.
- {name: rev, full_name: rev2, start: 8378, end: 8653, frame: 1, colour: yellowgreen}

- {name: "3' LTR", start: 9086, end: 9719, frame: 1, colour: darkgrey}
- {name: "3' LTR", full_name: "HIV1B-3' LTR", start: 9086, end: 9719, frame: 1, colour: darkgrey, stop: N}
- {name: pol, start: 2085, end: 5096, frame: 2, colour: orange}
- {name: vpr, full_name: HIV1B-vpr, start: 5559, end: 5850, frame: 2, colour: turquoise}
- {name: rev, start: 5970, end: 6048, frame: 2, colour: yellowgreen, stop: N}
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266 changes: 266 additions & 0 deletions micall/projects.json
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Original file line number Diff line number Diff line change
Expand Up @@ -1314,6 +1314,240 @@
"HIV1-P-FR-GU111555-seed"
]
},
{
"coordinate_region": "HIV1B-3' LTR",
"seed_region_names": [
"HIV1-A1-CD-AM000053-seed",
"HIV1-A1-CM-KP718928-seed",
"HIV1-A1-CY-JF683783-seed",
"HIV1-A1-IN-KT152839-seed",
"HIV1-A1-KE-KF716474-seed",
"HIV1-A1-RU-JX500694-seed",
"HIV1-A1-RW-KF716472-seed",
"HIV1-A1-SN-AY521629-seed",
"HIV1-A1-UG-KF716486-seed",
"HIV1-A1-ZA-KT183312-seed",
"HIV1-A2-CD-AF286238-seed",
"HIV1-A2-CM-GU201516-seed",
"HIV1-A2-CY-AF286237-seed",
"HIV1-B-BR-KJ849801-seed",
"HIV1-B-CA-JF320424-seed",
"HIV1-B-CH-KC797225-seed",
"HIV1-B-CN-KP109511-seed",
"HIV1-B-CU-KR914676-seed",
"HIV1-B-ES-KT276255-seed",
"HIV1-B-FR-K03455-seed",
"HIV1-B-FR-KF716496-seed",
"HIV1-B-HT-EU839602-seed",
"HIV1-B-JP-KF716498-seed",
"HIV1-B-KR-KJ140263-seed",
"HIV1-B-RU-JX500708-seed",
"HIV1-B-SE-KP411828-seed",
"HIV1-B-TH-KP109514-seed",
"HIV1-B-US-KT284371-seed",
"HIV1-B-ZA-KP109515-seed",
"HIV1-C-BR-JX140663-seed",
"HIV1-C-BW-AF443115-seed",
"HIV1-C-CN-KC870038-seed",
"HIV1-C-CY-JF683803-seed",
"HIV1-C-ES-KT276258-seed",
"HIV1-C-ET-AY713417-seed",
"HIV1-C-IN-KC156210-seed",
"HIV1-C-KE-KT022371-seed",
"HIV1-C-MW-KC156214-seed",
"HIV1-C-SE-KP411835-seed",
"HIV1-C-TZ-KC156220-seed",
"HIV1-C-US-KF526226-seed",
"HIV1-C-YE-AY795906-seed",
"HIV1-C-ZA-KP109517-seed",
"HIV1-C-ZM-KF716467-seed",
"HIV1-CON-XX-Consensus-seed",
"HIV1-CPZ-CD-U42720-seed",
"HIV1-CPZ-CM-DQ373064-seed",
"HIV1-CPZ-CM-FR686511-seed",
"HIV1-CPZ-TZ-JN091691-seed",
"HIV1-CPZ-US-AF103818-seed",
"HIV1-D-CM-JX140670-seed",
"HIV1-D-CY-FJ388945-seed",
"HIV1-D-KE-KF716476-seed",
"HIV1-D-KR-DQ054367-seed",
"HIV1-D-SN-AB485648-seed",
"HIV1-D-TZ-AY253311-seed",
"HIV1-D-UG-KF716479-seed",
"HIV1-D-UG-KF716480-seed",
"HIV1-D-YE-AY795907-seed",
"HIV1-D-ZA-EF633445-seed",
"HIV1-F1-AO-FJ900266-seed",
"HIV1-F1-AR-DQ189088-seed",
"HIV1-F1-BR-FJ771010-seed",
"HIV1-F1-BR-KJ849782-seed",
"HIV1-F1-BR-KJ849791-seed",
"HIV1-F1-CY-JF683771-seed",
"HIV1-F1-ES-FJ670516-seed",
"HIV1-F1-ES-KJ883138-seed",
"HIV1-F1-RO-AB485658-seed",
"HIV1-F1-RU-GQ290462-seed",
"HIV1-F2-CM-AY371158-seed",
"HIV1-F2-CM-JX140672-seed",
"HIV1-F2-CM-JX140673-seed",
"HIV1-G-CM-JX140676-seed",
"HIV1-G-CM-KP109502-seed",
"HIV1-G-CM-KP718923-seed",
"HIV1-G-CN-JN106043-seed",
"HIV1-G-ES-GU362882-seed",
"HIV1-G-ES-KT276261-seed",
"HIV1-G-GH-AB287004-seed",
"HIV1-G-KE-KF716477-seed",
"HIV1-G-NG-JN248593-seed",
"HIV1-G-PT-FR846409-seed",
"HIV1-GOR-CM-FJ424866-seed",
"HIV1-GOR-CM-KP004990-seed",
"HIV1-GOR-CM-KP004991-seed",
"HIV1-H-BE-AF190127-seed",
"HIV1-H-BE-AF190128-seed",
"HIV1-H-CF-AF005496-seed",
"HIV1-H-GB-FJ711703-seed",
"HIV1-J-CD-EF614151-seed",
"HIV1-J-SE-AF082394-seed",
"HIV1-J-SE-AF082395-seed",
"HIV1-K-CD-AJ249235-seed",
"HIV1-K-CM-AJ249239-seed",
"HIV1-N-CM-AY532635-seed",
"HIV1-N-CM-DQ017382-seed",
"HIV1-N-CM-GQ324959-seed",
"HIV1-N-CM-GQ324962-seed",
"HIV1-N-FR-JN572926-seed",
"HIV1-O-BE-L20587-seed",
"HIV1-O-CM-AY169802-seed",
"HIV1-O-CM-AY169804-seed",
"HIV1-O-CM-AY169807-seed",
"HIV1-O-CM-AY169808-seed",
"HIV1-O-CM-AY169815-seed",
"HIV1-O-FR-AF407418-seed",
"HIV1-O-GA-JX245015-seed",
"HIV1-O-SN-AJ302646-seed",
"HIV1-O-US-JN571034-seed",
"HIV1-P-CM-HQ179987-seed",
"HIV1-P-FR-GU111555-seed"
]
},
{
"coordinate_region": "HIV1B-5' LTR",
"seed_region_names": [
"HIV1-A1-CD-AM000053-seed",
"HIV1-A1-CM-KP718928-seed",
"HIV1-A1-CY-JF683783-seed",
"HIV1-A1-IN-KT152839-seed",
"HIV1-A1-KE-KF716474-seed",
"HIV1-A1-RU-JX500694-seed",
"HIV1-A1-RW-KF716472-seed",
"HIV1-A1-SN-AY521629-seed",
"HIV1-A1-UG-KF716486-seed",
"HIV1-A1-ZA-KT183312-seed",
"HIV1-A2-CD-AF286238-seed",
"HIV1-A2-CM-GU201516-seed",
"HIV1-A2-CY-AF286237-seed",
"HIV1-B-BR-KJ849801-seed",
"HIV1-B-CA-JF320424-seed",
"HIV1-B-CH-KC797225-seed",
"HIV1-B-CN-KP109511-seed",
"HIV1-B-CU-KR914676-seed",
"HIV1-B-ES-KT276255-seed",
"HIV1-B-FR-K03455-seed",
"HIV1-B-FR-KF716496-seed",
"HIV1-B-HT-EU839602-seed",
"HIV1-B-JP-KF716498-seed",
"HIV1-B-KR-KJ140263-seed",
"HIV1-B-RU-JX500708-seed",
"HIV1-B-SE-KP411828-seed",
"HIV1-B-TH-KP109514-seed",
"HIV1-B-US-KT284371-seed",
"HIV1-B-ZA-KP109515-seed",
"HIV1-C-BR-JX140663-seed",
"HIV1-C-BW-AF443115-seed",
"HIV1-C-CN-KC870038-seed",
"HIV1-C-CY-JF683803-seed",
"HIV1-C-ES-KT276258-seed",
"HIV1-C-ET-AY713417-seed",
"HIV1-C-IN-KC156210-seed",
"HIV1-C-KE-KT022371-seed",
"HIV1-C-MW-KC156214-seed",
"HIV1-C-SE-KP411835-seed",
"HIV1-C-TZ-KC156220-seed",
"HIV1-C-US-KF526226-seed",
"HIV1-C-YE-AY795906-seed",
"HIV1-C-ZA-KP109517-seed",
"HIV1-C-ZM-KF716467-seed",
"HIV1-CON-XX-Consensus-seed",
"HIV1-CPZ-CD-U42720-seed",
"HIV1-CPZ-CM-DQ373064-seed",
"HIV1-CPZ-CM-FR686511-seed",
"HIV1-CPZ-TZ-JN091691-seed",
"HIV1-CPZ-US-AF103818-seed",
"HIV1-D-CM-JX140670-seed",
"HIV1-D-CY-FJ388945-seed",
"HIV1-D-KE-KF716476-seed",
"HIV1-D-KR-DQ054367-seed",
"HIV1-D-SN-AB485648-seed",
"HIV1-D-TZ-AY253311-seed",
"HIV1-D-UG-KF716479-seed",
"HIV1-D-UG-KF716480-seed",
"HIV1-D-YE-AY795907-seed",
"HIV1-D-ZA-EF633445-seed",
"HIV1-F1-AO-FJ900266-seed",
"HIV1-F1-AR-DQ189088-seed",
"HIV1-F1-BR-FJ771010-seed",
"HIV1-F1-BR-KJ849782-seed",
"HIV1-F1-BR-KJ849791-seed",
"HIV1-F1-CY-JF683771-seed",
"HIV1-F1-ES-FJ670516-seed",
"HIV1-F1-ES-KJ883138-seed",
"HIV1-F1-RO-AB485658-seed",
"HIV1-F1-RU-GQ290462-seed",
"HIV1-F2-CM-AY371158-seed",
"HIV1-F2-CM-JX140672-seed",
"HIV1-F2-CM-JX140673-seed",
"HIV1-G-CM-JX140676-seed",
"HIV1-G-CM-KP109502-seed",
"HIV1-G-CM-KP718923-seed",
"HIV1-G-CN-JN106043-seed",
"HIV1-G-ES-GU362882-seed",
"HIV1-G-ES-KT276261-seed",
"HIV1-G-GH-AB287004-seed",
"HIV1-G-KE-KF716477-seed",
"HIV1-G-NG-JN248593-seed",
"HIV1-G-PT-FR846409-seed",
"HIV1-GOR-CM-FJ424866-seed",
"HIV1-GOR-CM-KP004990-seed",
"HIV1-GOR-CM-KP004991-seed",
"HIV1-H-BE-AF190127-seed",
"HIV1-H-BE-AF190128-seed",
"HIV1-H-CF-AF005496-seed",
"HIV1-H-GB-FJ711703-seed",
"HIV1-J-CD-EF614151-seed",
"HIV1-J-SE-AF082394-seed",
"HIV1-J-SE-AF082395-seed",
"HIV1-K-CD-AJ249235-seed",
"HIV1-K-CM-AJ249239-seed",
"HIV1-N-CM-AY532635-seed",
"HIV1-N-CM-DQ017382-seed",
"HIV1-N-CM-GQ324959-seed",
"HIV1-N-CM-GQ324962-seed",
"HIV1-N-FR-JN572926-seed",
"HIV1-O-BE-L20587-seed",
"HIV1-O-CM-AY169802-seed",
"HIV1-O-CM-AY169804-seed",
"HIV1-O-CM-AY169807-seed",
"HIV1-O-CM-AY169808-seed",
"HIV1-O-CM-AY169815-seed",
"HIV1-O-FR-AF407418-seed",
"HIV1-O-GA-JX245015-seed",
"HIV1-O-SN-AJ302646-seed",
"HIV1-O-US-JN571034-seed",
"HIV1-P-CM-HQ179987-seed",
"HIV1-P-FR-GU111555-seed"
]
},
{
"coordinate_region": "HIV1B-gag",
"seed_region_names": [
Expand Down Expand Up @@ -32054,6 +32288,38 @@
],
"seed_group": "HIV1-seed"
},
"HIV1B-3' LTR": {
"is_nucleotide": true,
"reference": [
"TGGAAGGGCTAATTCACTCCCAAAGAAGACAAGATATCCTTGATCTGTGGATCTACCACACACAA",
"GGCTACTTCCCTGATTAGCAGAACTACACACCAGGGCCAGGGGTCAGATATCCACTGACCTTTGG",
"ATGGTGCTACAAGCTAGTACCAGTTGAGCCAGATAAGATAGAAGAGGCCAATAAAGGAGAGAACA",
"CCAGCTTGTTACACCCTGTGAGCCTGCATGGGATGGATGACCCGGAGAGAGAAGTGTTAGAGTGG",
"AGGTTTGACAGCCGCCTAGCATTTCATCACGTGGCCCGAGAGCTGCATCCGGAGTACTTCAAGAA",
"CTGCTGACATCGAGCTTGCTACAAGGGACTTTCCGCTGGGGACTTTCCAGGGAGGCGTGGCCTGG",
"GCGGGACTGGGGAGTGGCGAGCCCTCAGATCCTGCATATAAGCAGCTGCTTTTTGCCTGTACTGG",
"GTCTCTCTGGTTAGACCAGATCTGAGCCTGGGAGCTCTCTGGCTAACTAGGGAACCCACTGCTTA",
"AGCCTCAATAAAGCTTGCCTTGAGTGCTTCAAGTAGTGTGTGCCCGTCTGTTGTGTGACTCTGGT",
"AACTAGAGATCCCTCAGACCCTTTTAGTCAGTGTGGAAAATCTCTAGCA"
],
"seed_group": null
},
"HIV1B-5' LTR": {
"is_nucleotide": true,
"reference": [
"TGGAAGGGCTAATTCACTCCCAACGAAGACAAGATATCCTTGATCTGTGGATCTACCACACACAA",
"GGCTACTTCCCTGATTAGCAGAACTACACACCAGGGCCAGGGATCAGATATCCACTGACCTTTGG",
"ATGGTGCTACAAGCTAGTACCAGTTGAGCCAGAGAAGTTAGAAGAAGCCAACAAAGGAGAGAACA",
"CCAGCTTGTTACACCCTGTGAGCCTGCATGGAATGGATGACCCGGAGAGAGAAGTGTTAGAGTGG",
"AGGTTTGACAGCCGCCTAGCATTTCATCACATGGCCCGAGAGCTGCATCCGGAGTACTTCAAGAA",
"CTGCTGACATCGAGCTTGCTACAAGGGACTTTCCGCTGGGGACTTTCCAGGGAGGCGTGGCCTGG",
"GCGGGACTGGGGAGTGGCGAGCCCTCAGATCCTGCATATAAGCAGCTGCTTTTTGCCTGTACTGG",
"GTCTCTCTGGTTAGACCAGATCTGAGCCTGGGAGCTCTCTGGCTAACTAGGGAACCCACTGCTTA",
"AGCCTCAATAAAGCTTGCCTTGAGTGCTTCAAGTAGTGTGTGCCCGTCTGTTGTGTGACTCTGGT",
"AACTAGAGATCCCTCAGACCCTTTTAGTCAGTGTGGAAAATCTCTAGCA"
],
"seed_group": null
},
"HIV1B-gag": {
"is_nucleotide": false,
"reference": [
Expand Down
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