From 38b7b520ec5e773a870c6f9b3f7f6a07d30f0a57 Mon Sep 17 00:00:00 2001 From: Nicholas Hathaway Date: Wed, 19 Nov 2025 12:19:56 -0500 Subject: [PATCH 1/3] was still using old fields; --- src/pmotools/pmo_engine/pmo_reader.py | 8 +++----- 1 file changed, 3 insertions(+), 5 deletions(-) diff --git a/src/pmotools/pmo_engine/pmo_reader.py b/src/pmotools/pmo_engine/pmo_reader.py index 742d4b4..b65abff 100644 --- a/src/pmotools/pmo_engine/pmo_reader.py +++ b/src/pmotools/pmo_engine/pmo_reader.py @@ -158,13 +158,11 @@ def combine_multiple_pmos(pmos: list[dict]): new_index = len(pmo_out["panel_info"]) # update target indexes to make sure reaction points to the right target indexes for reaction in panel_copy["reactions"]: - for target_id_reaction in range( - len(reaction["target_id_reactions"]) - ): - reaction["target_id_reactions"][ + for target_id_reaction in range(len(reaction["panel_targets"])): + reaction["panel_targets"][ target_id_reaction ] = target_info_old_index_key[pmo_index][ - reaction["target_id_reactions"][target_id_reaction] + reaction["panel_targets"][target_id_reaction] ] pmo_out["panel_info"].append(panel_copy) panel_info_out_index_key[panel_copy["panel_name"]] = new_index From 8d3943cf59fa668219fef67876724bffacd4a947 Mon Sep 17 00:00:00 2001 From: Nicholas Hathaway Date: Wed, 19 Nov 2025 13:00:03 -0500 Subject: [PATCH 2/3] fix for having the same specimen in different files when combining; --- src/pmotools/pmo_engine/pmo_reader.py | 44 +++++++++++++++++++++------ 1 file changed, 34 insertions(+), 10 deletions(-) diff --git a/src/pmotools/pmo_engine/pmo_reader.py b/src/pmotools/pmo_engine/pmo_reader.py index b65abff..0d2d7eb 100644 --- a/src/pmotools/pmo_engine/pmo_reader.py +++ b/src/pmotools/pmo_engine/pmo_reader.py @@ -225,10 +225,12 @@ def combine_multiple_pmos(pmos: list[dict]): # update project_id pmo_out["specimen_info"] = copy.deepcopy(pmos[0]["specimen_info"]) specimen_names = [] + specimen_index_key = {} duplicate_specimen_names = [] for specimen in pmo_out["specimen_info"]: if specimen["specimen_name"] in specimen_names: duplicate_specimen_names.append(specimen["specimen_name"]) + specimen_index_key[specimen["specimen_name"]] = len(specimen_names) specimen_names.append(specimen["specimen_name"]) # key1 pmo_index, key2 old_index, val new_index @@ -237,16 +239,38 @@ def combine_multiple_pmos(pmos: list[dict]): for specimen_info_index, specimen_info in enumerate(pmo["specimen_info"]): # checkin for duplicates if specimen_info["specimen_name"] in specimen_names: - duplicate_specimen_names.append(specimen_info["specimen_name"]) - specimen_names.append(specimen_info["specimen_name"]) - new_index = len(pmo_out["specimen_info"]) - # update project_id - specimen_info_copy = copy.deepcopy(specimen_info) - specimen_info_copy["project_id"] = project_info_old_index_key[ - pmo_index - ][specimen_info_copy["project_id"]] - pmo_out["specimen_info"].append(specimen_info_copy) - specimen_info_old_index_key[pmo_index][specimen_info_index] = new_index + # if specimen is exactly the same, then no issues + # @todo allow merging of info and as long as the meta present in both are the same then it should be fine + if ( + specimen_info + != pmo_out["specimen_info"][ + specimen_index_key[specimen_info["specimen_name"]] + ] + ): + duplicate_specimen_names.append(specimen_info["specimen_name"]) + specimen_info_old_index_key[pmo_index][ + specimen_info_index + ] = specimen_index_key[specimen_info["specimen_name"]] + else: + # update key for the already present id + specimen_info_old_index_key[pmo_index][ + specimen_info_index + ] = specimen_index_key[specimen_info["specimen_name"]] + else: + specimen_index_key[specimen_info["specimen_name"]] = len( + specimen_names + ) + specimen_names.append(specimen_info["specimen_name"]) + new_index = len(pmo_out["specimen_info"]) + # update project_id + specimen_info_copy = copy.deepcopy(specimen_info) + specimen_info_copy["project_id"] = project_info_old_index_key[ + pmo_index + ][specimen_info_copy["project_id"]] + pmo_out["specimen_info"].append(specimen_info_copy) + specimen_info_old_index_key[pmo_index][ + specimen_info_index + ] = new_index ## library_sample_info pmo_out["library_sample_info"] = copy.deepcopy(pmos[0]["library_sample_info"]) From 040633eda941a05a740a61b3c1cafbd4a14321fe Mon Sep 17 00:00:00 2001 From: Nicholas Hathaway Date: Fri, 21 Nov 2025 15:48:04 -0800 Subject: [PATCH 3/3] added more tests for properly throwing dup library_sample_names and specimen_names; --- src/pmotools/pmo_engine/pmo_reader.py | 7 + ...mple_2_for_library_sample_dup_testing.json | 8495 +++++++++++++++++ ...um_pmo_example_2_for_spec_dup_testing.json | 8495 +++++++++++++++++ tests/test_pmo_engine/test_pmo_reader.py | 42 + 4 files changed, 17039 insertions(+) create mode 100644 tests/data/minimum_pmo_example_2_for_library_sample_dup_testing.json create mode 100644 tests/data/minimum_pmo_example_2_for_spec_dup_testing.json diff --git a/src/pmotools/pmo_engine/pmo_reader.py b/src/pmotools/pmo_engine/pmo_reader.py index 0d2d7eb..f31e9e0 100644 --- a/src/pmotools/pmo_engine/pmo_reader.py +++ b/src/pmotools/pmo_engine/pmo_reader.py @@ -278,6 +278,13 @@ def combine_multiple_pmos(pmos: list[dict]): library_sample_info_old_index_key = defaultdict(dict) duplicate_library_sample_names = [] library_sample_names = [] + # have to add the library_sample_names already added in the first PMO + for library_sample in pmo_out["library_sample_info"]: + if library_sample["library_sample_name"] in library_sample_names: + duplicate_library_sample_names.append( + library_sample["library_sample_name"] + ) + library_sample_names.append(library_sample["library_sample_name"]) for pmo_index, pmo in enumerate(pmos[1:], start=1): for library_sample_info_index, library_sample_info in enumerate( pmo["library_sample_info"] diff --git a/tests/data/minimum_pmo_example_2_for_library_sample_dup_testing.json b/tests/data/minimum_pmo_example_2_for_library_sample_dup_testing.json new file mode 100644 index 0000000..50673cd --- /dev/null +++ b/tests/data/minimum_pmo_example_2_for_library_sample_dup_testing.json @@ -0,0 +1,8495 @@ +{ + "bioinformatics_methods_info" : + [ + { + "methods" : + [ + { + "additional_argument" : + [ + "--bamExtractTrimToRegion", + "--bed /tank/data/plasmodium/falciparum/beds/targeted_panels/heome1/heome1_Pf3D7_withPrimers.bed", + "--genomeDir /tank/data/genomes/plasmodium/genomes/pf/genomes/", + "--primaryGenome Pf3D7", + "--bam bams/{SAMPLE}.sorted.bam" + ], + "program" : "PathWeaver BamExtractPathwaysFromRegion", + "program_description" : "Extract reads from a bam file for a specific genomic locatioon and then assembles local haplotypes for that region", + "program_version" : "1.0.0-dev" + }, + { + "additional_argument" : + [ + "--overWriteDir", + "--fracCutOff 0.005", + "--dout popClusteringTrimmedParagon", + "--replicateMinTotalReadCutOff 10", + "--clusterCutOff 5", + "--pat _heome1", + "--numThreads 10", + "--groupingsFile /tank/data/plasmodium/falciparum/pfdata/metadata/meta.tab.txt", + "--genome2bit /tank/data/genomes/plasmodium/genomes/pf/genomes/Pf3D7.2bit", + "--trimBedFnp /tank/data/plasmodium/falciparum/beds/targeted_panels/heome1/heome1_Pf3D7_inserts_trimmed1.bed" + ], + "program" : "PathWeaver runProcessClustersOnRecon", + "program_description" : "Compare across samples for each target to create population level identifiers and do post artifact cleanup", + "program_version" : "1.0.0-dev" + } + ] + } + ], + "bioinformatics_run_info" : + [ + { + "bioinformatics_methods_id" : 0, + "bioinformatics_run_name" : "PathWeaver-Heome1", + "run_date" : "2024-09-03" + } + ], + "detected_microhaplotypes" : + [ + { + "bioinformatics_run_id" : 0, + "library_samples" : + [ + { + "library_sample_id" : 1, + "target_results" : + [ + { + "mhaps" : + [ + { + "mhap_id" : 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"Pf3D7_03_v3", + "end" : 142180, + "genome_id" : 0, + "start" : 141962, + "strand" : "+" + }, + "microhaplotypes" : + [ + { + "seq" : "GCATTTATAACAAAATATCAGAAGATGGAAAAACCAAAAATAGCCTACTTAGCGATATATCAAAATTATTTAAAATTGTAAAAGAAAGCAAATTAATATTTGTAACTGGATTTTTATTAACAACCTTGTCAGCAATTGTAGATTCATACATTCCAATTTTTCTATCCAAAACGGTATCTTTTGTAATGGAAAGAAAAAAATTTACATTTCTTAAAA" + }, + { + "seq" : "GCATTTATAACAAAATATCAGAAGATGGAAAAACCAAAAATAGCCTACTTAGCGATATATCAAAATTATTTAAAATTGTAAAAGAAAGCAAATTAATATTTGTAACTGGATTTTTATTAACAACCTTGTCAGCAATTGTCGATTCATACATTCCAATTTTTTTATCCAAAACGGTATCTTTTGTAATGGAAAGAAAAAGTTTTACATTTCTTAAAA" + } + ], + "target_id" : 37 + }, + { + "mhap_location" : + { + "chrom" : "Pf3D7_03_v3", + "end" : 221494, + "genome_id" : 0, + "start" : 221362, + "strand" : "+" + }, + "microhaplotypes" : + [ + { + "seq" : "TGAACTATTTACGACATTAAACACACTGGAACATTTTTCCATTTTACAAATTTTTTTTTCAATATCATTTTCATAATCTAATTCGTCTTTAGGTTTATTAGCAGAGCCAGGCTTTATTCTAACTTGAATA" + }, + { + "seq" : "TGAACTATTTACGACATTAAACACACTGGAACATTTTTCCATTTTACAAATTTTTTTTTCAATATCATTTTCATAATCTAATTGGTCTTTAGGTTTATCAGCAGAGCCAGGCTTTATTCTAACTTGAATA" + } + ], + "target_id" : 57 + }, + { + "mhap_location" : + { + "chrom" : "Pf3D7_03_v3", + "end" : 618580, + "genome_id" : 0, + "start" : 618395, + "strand" : "+" + }, + "microhaplotypes" : + [ + { + "seq" : "AAAAGAGATTATAGAAGTGGAAAGAAGACATATATAATACAAGCTCTACGATATGCATTAACATATTATAGCAAACTTTCAAATAGAAAGGAAGCACCTAAAGTAACCATGTTATTTACAGATGGAAATGATCCCTATGAATCAGAAAAGGGATTACAGGATATTGCATTATTATATAGAAAA" + }, + { + "seq" : "AAAAGAGATTATAGAAGTGGAAAGAAGACATATATAATACAAGCTCTACGATATGCATTAACATATTATAGCAAACTTTCAAATAGAAAGGAAGCACCTAAAGTAACCATGTTATTTACAGATGGAAATGATTCCTATGAATCAGAAAAGGGATTACAGGATATTGCATTATTATATAGAAAA" + } + ], + "target_id" : 94 + }, + { + "mhap_location" : + { + "chrom" : "Pf3D7_03_v3", + "end" : 654174, + "genome_id" : 0, + "start" : 654001, + "strand" : "+" + }, + "microhaplotypes" : + [ + { + "seq" : "TATTTTTATAATTTCCTTTCATCTTATTTTTTTCTTTATATTTTTTTTTTTCATATGTAAGATTTATATAATCACTTTCGCTTTTTCTAACGCTTTTGAACTTTTTAAATGTACTTCCTTCATTATTTCTAATTCTCGTAAACACAAGAATAAATATTTTGATATATCTTA" + }, + { + "seq" : "TATTTTTATAATTTCCTTTCATCTTATTTTTTTCTTTATATTTTTTTTTTTCATATGTAAGATTTATATAATCACTTTCGCTTTTTCTAACGCTTTTGAACTTTTTAAATGTACTTCGTTCATTATTTCTAATTCTCGTAAACACAAGAATAAATATTTTGATATATCTTA" + } + ], + "target_id" : 90 + }, + { + "mhap_location" : + { + "chrom" : "Pf3D7_03_v3", + "end" : 850988, + "genome_id" : 0, + "start" : 850815, + "strand" : "+" + }, + "microhaplotypes" : + [ + { + "seq" : "CATATTCGTTTCAGCGTTTATAGAGCGAATATTATCGATTATGTCTATATTCCCTAAAATATGTACATAATAATCTCCATTTAATAATGTTACTTTCTTAAGAATATTTTTGTATATGACATCAAAGATATTACGAGTTAACAATACATCTACATTTCGGTCTATTATATA" + }, + { + "seq" : "CATATTCGTTTCAGCGTTTATAGAGCGAAAATTATCGATTATGTCTATATTCCCTAAAATATGTACATAATAATCTCCATTTAATAATGTTACTTTCTTAAGAATATTTTTGTATATGACATCAAAGATATTACGAGTTAACAATACATCTACATTTCGGTCTATTATATA" + } + ], + "target_id" : 48 + }, + { + "mhap_location" : + { + "chrom" : "Pf3D7_01_v3", + "end" : 180114, + "genome_id" : 0, + "start" : 179902, + "strand" : "+" + }, + "microhaplotypes" : + [ + { + "seq" : "TTTCGATATAGGACATATAGATCATAATATAAACGAATATGAAAAACGTTTTACAATTTTAAAAGAATCTTTTTTTCATAAGTCATTAAAATTTATGGATTATATATGGATTGTTATAATGAAACGAGAAAATAATACATTTTTAAATAGATTAAGAAATGAACAAGTGAGGGCATCGTTATTAATAACAGGTATTATAAACGAAAATAT" + }, + { + "seq" : "TTTCGATACAGGACATATAGATCATAATATAAACGAATATGAAAAACATTTTACAATTTTAAAAAAATCTTTTTTTCATAAGTCATTAAAATTTATGGATTATATATGGATTGTTATAATGAAACGAGATAATAATACATTTTTAAATAGATTAAGAAATGAACAAGTGAGGGCATCGTTATTAATAACAGGTATTATAAACGAAAATAT" + } + ], + "target_id" : 82 + }, + { + "mhap_location" : + { + "chrom" : "Pf3D7_04_v3", + "end" : 110086, + "genome_id" : 0, + "start" : 109911, + "strand" : "+" + }, + "microhaplotypes" : + [ + { + "seq" : "ATATTTGTATATATTCTAGTAAACACTTTAGGTACACCTGCAAGTACCTCAACATCTGAATTATATAAATCTTTAGAAAAACAACTAATATCCTTACTCCATATATTTATTTTTATACCAAGAATAACAGCCATATAAACCAAAACTCTCTCAAATGCATGTGATACAGGTAA" + }, + { + "seq" : "ATATTTGTATATATTCTAGTAAACACTTTAGGTACACCTGCAAGTACCTCAACATCTGAATTATATAAATCTTTAGAAAAACAACTAATATCCTTACTCCATATATTTATTTTTATACCAAGAATAACAGCCATATAAACCAAAACTCTCTCAAATACATGTGATACAGGTAA" + } + ], + "target_id" : 74 + }, + { + "mhap_location" : + { + "chrom" : "Pf3D7_04_v3", + "end" : 133700, + "genome_id" : 0, + "start" : 133490, + "strand" : "+" + }, + "microhaplotypes" : + [ + { + "seq" : "TAGATTTTTTCCCTCCAACAGATGCACTCACTTTAGGTGTTTTAAACTTAGTTGTATGTTGACCCCCCTCATTATTTAGTTTACCTTTATTTAATCTTTTACCAGCAGTAGAAACTACATTCTCTCGATTATCATTACCTACTTCAGTCTTTACAATTGTAGGAGGTGTTTTAACATGATCATCCCCTCCATGAGGAGTAACCCTTAA" + }, + { + "seq" : "TAGATTTTTTCCCTTCAGCAGGTGCCCTCACTTTAGGTGTTTTAAACTTAGTTGTATGTGGAACCCCATCTTTATTTGCTTTACCTCTATTTAATCTTTTACCAGCAGTAGAAACTACATTCTCTCGATTATCATTACCTACTTCAGTCTTTACAATTGTAGGAGGTGTTTTAACATGATTATCCCCTCCATGAGGAGTAACCCTTAA" + } + ], + "target_id" : 43 + }, + { + "mhap_location" : + { + "chrom" : "Pf3D7_04_v3", + "end" : 141944, + "genome_id" : 0, + "start" : 141777, + "strand" : "+" + }, + "microhaplotypes" : + [ + { + "seq" : "TTTCAAATTATATAAAGACAGAACTAAGAAATATAAACCTGCAAGAAATAAAAAACAATATAATAAAAATATTTAAAGAATTCAAATCTGCACACAAAGAAATTAAAAAAGAATCAAAACAAATTAATAAAGAATTTACCAAAATGGATGTCGTCATAAATCAAT" + }, + { + "seq" : "TTTCAAATTATATAAAGACAGAACTAAGAAATATAAACCTGCAAGAAATAAAAAACAATATAATAAAAATATTTAAAGAATTCGAATCTGCACACAAAGAAATTAAAAAAGAATCAAAACAAATTAATAAAGAATTTACCAAAATGGATGTCGTCATAAATCAAT" + }, + { + "seq" : "TTTCAAATTATATAAAGACAGAACTAAGAAATATAAACCTGCAAGAAATAAAAAACAATATAATAAAAATATTTAAAGAATTCGAATCTGCACACAAAGAAATTAAAAAAGAATCAGAACAAATTAATAAAGAATTTACCAAAATGGATGTCGTCATAAATCAAT" + } + ], + "target_id" : 70 + }, + { + "mhap_location" : + { + "chrom" : "Pf3D7_04_v3", + "end" : 415825, + "genome_id" : 0, + "start" : 415652, + "strand" : "+" + }, + "microhaplotypes" : + [ + { + "seq" : "TGCTAGTTTTGCTGCTCATGAAAATAAAAGCTACTCATATGAAGGTCGTACATATAAAATGTATCCACCTGAATTTAATACATTAATGTTAAAAGCAGATTATTTTATAAGAGATATAAATACACGAGGATTTAGAGAAGTAAATATGGATTCATGTAAATCATATACAAA" + } + ], + "target_id" : 15 + }, + { + "mhap_location" : + { + "chrom" : "Pf3D7_04_v3", + "end" : 544860, + "genome_id" : 0, + "start" : 544717, + "strand" : "+" + }, + "microhaplotypes" : + [ + { + "seq" : "TATATTTTACATAATAACAATCTTTCATGTAATGATTATAATTTAAATAATCTTTCATTTAATATAAATAAATATATAAATGAAGAAAAAGGCAAAAATAAAAAAACAAATCAACATATATCAGAACAATTTTTATTTCCT" + }, + { + "seq" : "TATATTTTACATAATAACAATCCTTCATGTAATGATTATAATTTAAATAATCTTTCATTTAATATAAATAAATATATAAATGAAGAAAAAGGCAAAAATAAAAAAACAAATCAACATATATCAGAACAATTTTTATTTCCT" + } + ], + "target_id" : 96 + }, + { + "mhap_location" : + { + "chrom" : "Pf3D7_04_v3", + "end" : 748435, + "genome_id" : 0, + "start" : 748229, + "strand" : "+" + }, + "microhaplotypes" : + [ + { + "seq" : "AAATGTAATTCCCTAGATATGAAATATTTTCGTGCAGTTACAACATATGTGAATGAATCAAAATATGAAAAATTGAAATATAAGAGATGTAAATATTTAAACAAAGAAACTGTGGATAATGTAAATGATATGCCTAATTCTAAAAAATTACAAAATGTTGTAGTTATGGGAAGAACAAACTGGGAAAGCATTCCAAAAAAATTT" + } + ], + "target_id" : 72 + }, + { + "mhap_location" : + { + "chrom" : "Pf3D7_04_v3", + "end" : 748695, + "genome_id" : 0, + "start" : 748532, + "strand" : "+" + }, + "microhaplotypes" : + [ + { + "seq" : "ATAGTTTTACTTGGGAAATTAAATTACTATAAATGTTTTATTATAGGAGGTTCCGTTGTTTATCAAGAATTTTTAGAAAAGAAATTAATAAAAAAAATATATTTTACTAGAATAAATAGTACATATGAATGTGATGTATTTTTTCCAGAAATAAATGAAAA" + } + ], + "target_id" : 58 + }, + { + "mhap_location" : + { + "chrom" : "Pf3D7_04_v3", + "end" : 802712, + "genome_id" : 0, + "start" : 802524, + "strand" : "+" + }, + "microhaplotypes" : + [ + { + "seq" : "AAATTATTATAGAAAGATAGAAGTTATTTTATATGAATGGTTATATTTTCATTATAATAATGTATATAACACCAAAGTAAAAAAACAAAAATTTATATTTACCCAACAAAAAAAAGACATATCAAAACATAACAAGTTATATCTTCAGTATGATCAAAATAAAAGAAATTCTGAAATAGAACATAC" + }, + { + "seq" : "AAATTATTATAGAAAGATAGAAGTTATTTTATATGAATGGTTATATTTTCATTATAATAATGTATATAACACCAAAGTAAAAAAACAAAAATTTATATTTACCCAACAAAAAAAAGACATATCAAAACATAACAAGTTATATCTTCAGTATGATCAAAATAAAAGAAATTCTGAAATAGAACGTAC" + } + ], + "target_id" : 92 + }, + { + "mhap_location" : + { + "chrom" : "Pf3D7_04_v3", + "end" : 1037843, + "genome_id" : 0, + "start" : 1037633, + "strand" : "+" + }, + "microhaplotypes" : + [ + { + "seq" : "TCTTATAAAGTTAATGAAATTGCTCAACTTAATTTAACCATAGAAAGAGATTTAACAGATGATGCTGTGATTTTTGCACACTCACTTTATTTACCATTTGAAAAAGAAGAAATGTGGTGGATCGTTATCGGAATTAAAAAAATGAACTTACTTTTATCTATCAAAAAATTATCTTTATTGAAAAGTATCAATAATATAAAAATTAATT" + }, + { + "seq" : "TCTTATAAAGTTAATGAAATAGCTCAACTTAATTTAACCATAGAAAGAGATTTAACAGATGATGCTGTGATTTTTGCACACTCACTTTATTTACCATTTGAAAAAGAAGAAATGTGGTGGATCGTTATCGGAATTAAAAAAATGAACTTACTTTTATCTATCAAAAAATTATCTTTATTGAAAAGTGTCAATAATATAAAAATTAATT" + } + ], + "target_id" : 52 + }, + { + "mhap_location" : + { + "chrom" : "Pf3D7_04_v3", + "end" : 1100830, + "genome_id" : 0, + "start" : 1100655, + "strand" : "+" + }, + "microhaplotypes" : + [ + { + "seq" : "ATGTTCTAAGATCTGATGGAAAAATATCTGATCAAGGTTCTCAGAAAAGTCCTCCTAAGGAACTTTCTAATAAACAAATGACTCCTGCTCAACGTAAGAATGTGCCACATTTTGTTGAAAGAAGAGGCTATGGAAATAGTCATGTTAGGGGTAACGCACTTAAAAAAATTAGT" + }, + { + "seq" : "ATGTTCTAAGATCTGGTGGAAAAATATCTGATCAAGGTTCTCAGAAAAGTCCTCCTAAGGAACTTTCTAATAAACAAATGACTCCTGCTCAACGTAAGAATGTGCCACATTTTGTTGAAAGAAGAGGCTATGGAAATAGTCATGTTAGGGGTAACTCACTTAAAAAAATTAGT" + } + ], + "target_id" : 81 + }, + { + "mhap_location" : + { + "chrom" : "Pf3D7_01_v3", + "end" : 181672, + "genome_id" : 0, + "start" : 181556, + "strand" : "+" + }, + "microhaplotypes" : + [ + { + "seq" : "TCATTCTTTTTTTAACTAAAACTATTCATCTCAAAAATATAAGATATTTTATATGACGAATGCCATTGTATTTTTTGTTACGTAAAACCTGACTTCTTCAAGGAAAACACATGC" + }, + { + "seq" : "TCATTCTTTTTTTAACGAAAACTATTCATCTCAAAAATATAAGATATTTTATATGACGAATGCCATTGTATTTTTTGTTACGTAAAACCTGACTTCTTCAAGGAAAACACATGC" + } + ], + "target_id" : 64 + }, + { + "mhap_location" : + { + "chrom" : "Pf3D7_04_v3", + "end" : 1102577, + "genome_id" : 0, + "start" : 1102388, + "strand" : "+" + }, + "microhaplotypes" : + [ + { + "seq" : "AAGAAATAAATAAAATAATTTATACAAACGAATTTAATAATTATGAAGATAAAATATATGAAGATGTCAAATATATTAAAGAACAGGAAAATGAAATATACTTGAGAGATGGAATTGAAGAGTTACATATGGATGAACCAAGTCGGGATGTATATGTTGATGATGAAAATGATTATATATTTTTAGA" + }, + { + "seq" : "AAGAAATAAATAAAATAATTTATACAAACGAATTTAATAATTATGAAGATAAAATATATGAAGATGTCAAATATATTAAAGAACAGGAAAATGAAATGTACTTGAGAGATGGAATTGAAGAGTTACATATGGATGAACCAAGTGGGGATGTATATTTTGATGATCAAGATGATTATATATTTTTAGA" + } + ], + "target_id" : 67 + }, + { + "mhap_location" : + { + "chrom" : "Pf3D7_04_v3", + "end" : 1113603, + "genome_id" : 0, + "start" : 1113449, + "strand" : "+" + }, + "microhaplotypes" : + [ + { + "seq" : "AATCATCTAAGAATAAACTTTTTTGTTTAAACCATTTATTGAACATTTCACTTAAATGTGATTCAATTTTTTTTTCTGAGCTTTCCATAATTTGATTACATCTATTCAATTTGTTTGTATAAGTATTAGGTCTTATTATTCTTTTACGTTTT" + }, + { + "seq" : "AATCATCTAAGAATAAACTTTTTTGTTTAAACCATTTATTGAACATTTCACTTAAATGTGATTCAATTTTTTTTTCTGAGATTTCCATAATTTGATTACATCTATTCAATTTGTTTGTATAATTATTAGGTCTTATTATTCTTTTACGTTTT" + }, + { + "seq" : "AATCATCTAAGAATAAACTTTTTTGTTTAAACCATTTATTGAACATTTCACTTAAATGTGATTCAATTTTTTTTTCTGAGCTTTCCATAATTTGATTACATCTATTCAATTTGTTTGTATAATTATTAGGTCTTATTATTCTTTTACGTTTT" + } + ], + "target_id" : 61 + }, + { + "mhap_location" : + { + "chrom" : "Pf3D7_04_v3", + "end" : 1128672, + "genome_id" : 0, + "start" : 1128488, + "strand" : "+" + }, + "microhaplotypes" : + [ + { + "seq" : "TTGAAAGAGTTAAAGGGAAAAATACAAAATTATTTAGATAATGATATTCAATTGAGTAATGGAAAACTCCTATATAAGGATACATGGGATAGAATTGATTTGAAGTTTTGTAGAACGGTAGCAATAGAAGAGGCAGAATACACTAGAAAATTTTATAGCTTAATTAATGATAAACATACAAT" + }, + { + "seq" : "TTGAAAGAATTAAAGGGAAAAATACAAAATTATTTAGATAATGATATTCAATTGAGTAATGGAAAACTCCTATATAAGGATACATGGGATAGAATTGATTTGAAGTTTTGTAGAACGATAGCAATAGAAGAGGCAGAATACACTAGAAAATTTTATAGCTTAATTAATGATAAACATACAAT" + } + ], + "target_id" : 54 + }, + { + "mhap_location" : + { + "chrom" : "Pf3D7_05_v3", + "end" : 329549, + "genome_id" : 0, + "start" : 329377, + "strand" : "+" + }, + "microhaplotypes" : + [ + { + "seq" : "TTGTGATGTATATAAATTCCCTTCTTCTTTATGTACCACATTATAAGAACCACGAACATATTCTTTTAAAAATGTTAACTTACTTCCAACAAATATATAATCAAAACAAAATTTTTTATTGTCGAAATGTTCTCGTTCAACCCCATTCATATTTCGGATATCATTATTTA" + } + ], + "target_id" : 33 + }, + { + "mhap_location" : + { + "chrom" : "Pf3D7_05_v3", + "end" : 958220, + "genome_id" : 0, + "start" : 958058, + "strand" : "+" + }, + "microhaplotypes" : + [ + { + "seq" : "TTTATATCATTTGTATGTGCTGTATTATCAGGAGGAACATTACCTTTTTTTATATCTGTGTTTGGTGTAATATTAAAGAACATGAATTTAGGTGATGATATTAATCCTATAATATTATCATTAGTATCTATAGGTTTAGTACAATTTATATTATCAATGA" + }, + { + "seq" : "TTTATATCATTTGTATGTGCTGTATTATCAGGAGGAACATTACCTTTTTTTATATCTGTGTTTGGTGTAATATTAAAGAACATGTATTTAGGTGATGATATTAATCCTATAATATTATCATTAGTATCTATAGGTTTAGTACAATTTATATTATCAATGA" + } + ], + "target_id" : 49 + }, + { + "mhap_location" : + { + "chrom" : "Pf3D7_05_v3", + "end" : 958505, + "genome_id" : 0, + "start" : 958388, + "strand" : "+" + }, + "microhaplotypes" : + [ + { + "seq" : "ACGAAATTTATAACAATTTTTACATATGCCAGTTCCTTTTTAGGGTTATTTATTTGGTCATTAATAAAAAATGCACGTTTGACTTTATGTATTACTTGCGTTTTTCCGTTAATTT" + }, + { + "seq" : "ACGAAATTTATAACAATTTTTACATATGCCAGTTCCTTTTTAGGTTTATATATTTGGTCATTAATAAAAAATGCACGTTTGACTTTATGTATTACTTGCGTTTTTCCGTTAATTT" + } + ], + "target_id" : 46 + }, + { + "mhap_location" : + { + "chrom" : "Pf3D7_05_v3", + "end" : 1042280, + "genome_id" : 0, + "start" : 1042161, + "strand" : "+" + }, + "microhaplotypes" : + [ + { + "seq" : "TATTATTACGGTACCATTATATGATTCTTTAGGTCCTCAATCAAGTAGATTTATATTAGATCAAACACAGATGGAAACTATTGTATGTAACAAGACATGTGCTCGTAATTTATTTAA" + } + ], + "target_id" : 4 + }, + { + "mhap_location" : + { + "chrom" : "Pf3D7_05_v3", + "end" : 1309743, + "genome_id" : 0, + "start" : 1309608, + "strand" : "+" + }, + "microhaplotypes" : + [ + { + "seq" : "AATGAAGAAAATATGTCTGACAGACCAAACAGTTTATCTCATGATAAGGATCAACACCACGATGAAACACATAATGAACAATATGGATTATACGTAAAAGAAATGGAATCTAAAGTTGAAAAATTAGCTGAAA" + } + ], + "target_id" : 27 + }, + { + "mhap_location" : + { + "chrom" : "Pf3D7_06_v3", + "end" : 145500, + "genome_id" : 0, + "start" : 145342, + "strand" : "+" + }, + "microhaplotypes" : + [ + { + "seq" : "ATTTGAATAAAATTTATCATTCACAATATTATATTTTTGTTTCTTCTTTTTTCCCATAATATTATTATTTTGTTCACAATATATGTTCATGTGTCCCCTCTTTTTCTGTAAAATATTAAAATGTTTCTTACTATGCTTTTCTTCATTTTTAATAAC" + } + ], + "target_id" : 44 + }, + { + "mhap_location" : + { + "chrom" : "Pf3D7_06_v3", + "end" : 532377, + "genome_id" : 0, + "start" : 532194, + "strand" : "+" + }, + "microhaplotypes" : + [ + { + "seq" : "GAACAATTGTTAAACACCAAATTGGGTGAAACAAAAAACCACCTGAACAGAACCCCATTTATACCTGAATCGGTCATACGAGAAAGGAAATTACGCCAAGAAAAAGCGCAATCCACAAACAACATGTTCGATTCAACAAACGCAGATAGTATTACTTCCCCATGTGATCCAACGAATGCCA" + }, + { + "seq" : "GAACAATTGCTAAACACCAAATTGGGTGAAACAAAAAACCACCTGAACAGAACCCCATTTATACCTGAATCGGTCATACGAGAAAGGAAATTACGCCAAGAAAAAGCGCAATCCACAAACAACATGTTCGATTCAACAAACGCAGATAGTATTACTTCCCCATGTGATCCAACGAATGCCA" + } + ], + "target_id" : 39 + }, + { + "mhap_location" : + { + "chrom" : "Pf3D7_01_v3", + "end" : 496142, + "genome_id" : 0, + "start" : 495970, + "strand" : "+" + }, + "microhaplotypes" : + [ + { + "seq" : "GAAAGTAGCGAATACCCTGTAGAAATTGTTAGTAAACCTCTGGAATGGTTATTGTTTCATGATTTTACTACGCCTGGTGTTACTGCACTACCTGAAGAATTACCATTAACGAGCTATAAAGTAACACCTACTTCTATTAATGTATTGCATAAAGAGGGCCCCACTTTAAA" + }, + { + "seq" : "GAAAGTAGCGAATACCCTGTAGAAATTGTTAGTAAACCTCTGGAATGGTTATTGTTTCATGATTTTACTACGCCTGATGTTACTGCACTACCTGAAGAATTACCATTAACGAGCTATAAAGTAACACCTACTTCTATTAATGTATTGCATAAAGAGGGCCCCACTTTAAA" + } + ], + "target_id" : 62 + }, + { + "mhap_location" : + { + "chrom" : "Pf3D7_07_v3", + "end" : 165421, + "genome_id" : 0, + "start" : 165234, + "strand" : "+" + }, + "microhaplotypes" : + [ + { + "seq" : "TAATTATCATTATTATTATAATTATCATTGTTATTATTATTGTTGTTGTTGTTATTATTATTTCCTTTATTATTTAATATGCATTTTTTAATATCCATTTTATTATTTATCATATCAGTACTTTTATTTTTCTCCTTTTCGTTTATAGCTTTTTCCCTATGCACCCTGAATTTCCCATTTTTTTT" + }, + { + "seq" : "TCATTATTATTATTATTATAATTATCATTTTTATTATTATTGTTGTTATTATTATTTCCTTTATTATTTAATATGCATTTTTTAATATCCATTTTATTATTTATCATATCAGTACTTTTATTTTTCTCCTTTTCGTTTATAGCTTTTTCCCTATGCACCCTGAATTTCCCATTTTTTTT" + } + ], + "target_id" : 29 + }, + { + "mhap_location" : + { + "chrom" : "Pf3D7_07_v3", + "end" : 166166, + "genome_id" : 0, + "start" : 166034, + "strand" : "+" + }, + "microhaplotypes" : + [ + { + "seq" : "TTTTATTTGAACTTTTTTATTTTCTTCATTATCAATATAAAAACAACAATCTTTAAATTTATGAAATAACACCCAACTTAATGTATAAAATATAATTTCTATAAAATCAAAATTAATGTAATAACCTAAT" + } + ], + "target_id" : 59 + }, + { + "mhap_location" : + { + "chrom" : "Pf3D7_07_v3", + "end" : 299004, + "genome_id" : 0, + "start" : 298885, + "strand" : "+" + }, + "microhaplotypes" : + [ + { + "seq" : "CATTCAATATGGTTCTGAGCTTAAAGATGTTATCCTTATACATGTTTCTATTCTCATTCGTTATAACATCAATGACATATAAAACATATCTCTCAAATATTTTGTGAACAATATTAT" + } + ], + "target_id" : 41 + }, + { + "mhap_location" : + { + "chrom" : "Pf3D7_07_v3", + "end" : 730087, + "genome_id" : 0, + "start" : 729974, + "strand" : "+" + }, + "microhaplotypes" : + [ + { + "seq" : "TTTATGTGAAATTTTAAATAAAGAGAAATTGTTTGTGCACACATCTATTTTGGGATATATATCTAATCGTTTATGTTACGATATAAAAAAATATAGATGTTCATTATTGAA" + }, + { + "seq" : "TTTATGTGAAATTTTAAATAAAGAGAAATTGTTTGTGCACACATCTATTTTGGGATATATATCTAATCGTTTATGTTACGATATAGAAAAATATAGATGTTCATTATTGAA" + } + ], + "target_id" : 75 + }, + { + "mhap_location" : + { + "chrom" : "Pf3D7_07_v3", + "end" : 1149584, + "genome_id" : 0, + "start" : 1149414, + "strand" : "+" + }, + "microhaplotypes" : + [ + { + "seq" : "AATATTTAATATTTTTGTTTAGGAAGTTTTCAAAATTGATGACATTGATAACCGTTTTTATTAAATCGCTTGGGTTGTTTGTGTGTTCCATTGTAGAAGACATAATTTTAAGAATGTGTTTTTGTGTTATTAAACAAAACTTTGTTACTATATGGAATCGTATGTTAT" + }, + { + "seq" : "AATATTTAATATTTTTGTTTAGGAAGTTTTCAAAATTGATGACATTGATAACCGTTTTTATTAAATCGCTTGGGTTGTTTGTGTGTTCTATAGTAGAAGACATAATTTTAAGAATGTGTTTTTGTGTTATTAAACAAAACTTTGTTACTATATGGAATCGTATGTTAT" + }, + { + "seq" : "AATATTTAATATTTTTGTTTAGGAAGTTTTCAAAATTGATGACATTGATAACCGTTTTTATTAAATCGCTTGGGTTGTTTGTGTGTTCTATTGTAGAAGACATAATTTTAAGAATGTGTTTTTGTGTTATTAAACAAAACTTTGTTACTATATGGAATCGTATGTTAT" + } + ], + "target_id" : 45 + }, + { + "mhap_location" : + { + "chrom" : "Pf3D7_07_v3", + "end" : 1358910, + "genome_id" : 0, + "start" : 1358693, + "strand" : "+" + }, + "microhaplotypes" : + [ + { + "seq" : "AGAATCTCAACTTTTGCTTAAAAAAAATGATAACAAATATAATTCTAAATTTTGTAATGATTTGAAGAATAGTTTTTTAGATTATGGACATCTTGCTATGGGAAATGATATGGATTTTGGAGGTTATTCAACTAAGGCAGAAAACAAAATTCAAGAAGTTTTTAAAGGGGCTCATGGGAAAATAAGTGAACATGAAATTAAAAATTTTAGAAAAG" + } + ], + "target_id" : 35 + }, + { + "mhap_location" : + { + "chrom" : "Pf3D7_08_v3", + "end" : 102499, + "genome_id" : 0, + "start" : 102325, + "strand" : "+" + }, + "microhaplotypes" : + [ + { + "seq" : "TAATTTTCTCAAGTAACATATTTTTGTCTTGACTACTTTCATCTGTAAATGGAACGAATACTCTTTGCTTACCTGCAAAAAGGACAACTGACATATGAGCCTTATCCTTACTTACATTCGAATTAAGGACCATAGATTCTAAAAATGGTATAGTTCCTTTTAACCAATAATC" + } + ], + "target_id" : 86 + }, + { + "mhap_location" : + { + "chrom" : "Pf3D7_08_v3", + "end" : 336646, + "genome_id" : 0, + "start" : 336467, + "strand" : "+" + }, + "microhaplotypes" : + [ + { + "seq" : "AAATTTACAGAAAAATTTAGATTTAATCATATGGCTAAAAAAGAATATAAAAGAAGGAGAAGCTTTAATTTCTGATATACCCACATCAAGTTTTTTAAGGTGTACTACAAATTATAAATTTGTATTGCATCCACAATATGAAGATAGTAACTTGAGAAAGAGGGTTCAAGATTATTA" + }, + { + "seq" : "AAATTTACAGAAAAATTTAGATTTAATCATATGGCTAAAAAAGAATATAAAAGAAGGAGAAGCTTTAATTTCTGATATACCTACATCAAGTTTTTTAAGGTGTACTACAAATTATAAATTTGTATTGCATCCCCAATATGAAGATAGTAACTTGAGAAAGAGGGTTCAAGATTATTA" + } + ], + "target_id" : 85 + }, + { + "mhap_location" : + { + "chrom" : "Pf3D7_08_v3", + "end" : 339356, + "genome_id" : 0, + "start" : 339167, + "strand" : "+" + }, + "microhaplotypes" : + [ + { + "seq" : "TCATTACTATTCTTTATCCATATATATGTTGTTATATCAGTTGCACCTGAGGGTGGATTCAAACCTCTTGCTTGTATAATATATGCACGTACTACTAAATTACGTGTTAATCTATATTCTCTTACTAAATCATCACATTTCTTTATCATTTCTTTTTTTAAATACATTGTCTTTTCATCATACACAT" + }, + { + "seq" : "TCATTACTATTCTTTATCCATATATATGTTGTTATATCAGTTGCACCGGATGGTGGATTCAAACCTCTTGCTTGTATAATATATGCACGTACTACTAAATTACGTGTTAATCTATATTCTCTTACTAAATCACCACATTTCTTTATCATTTCTTTTTTTAAATACATTGTCTTTTCATCATACACAT" + } + ], + "target_id" : 80 + }, + { + "mhap_location" : + { + "chrom" : "Pf3D7_08_v3", + "end" : 550217, + "genome_id" : 0, + "start" : 549992, + "strand" : "+" + }, + "microhaplotypes" : + [ + { + "seq" : "ACTAACAAATTATGATAATCTAGTTTATGATATAAAAAATTATTTAGAACAAAGATTAAATTTTCTTGTATTAAATGGAATACCTCGTTATAGGATACTATTTGATATTGGATTAGGATTTGCGAAGAAACATGATCAATCTATTAAACTCTTACAAAATATACATGTATATGATGAGTATCCACTTTTTATTGGATATTCAAGAAAAAGATTTATTGCCCAT" + } + ], + "target_id" : 93 + }, + { + "mhap_location" : + { + "chrom" : "Pf3D7_01_v3", + "end" : 512387, + "genome_id" : 0, + "start" : 512198, + "strand" : "+" + }, + "microhaplotypes" : + [ + { + "seq" : "TAAAGAAATTAAGTGAAGATGATTATGAAAAAAATTGTAGACATTTAAATTATTTAATAGATAATATAAGAGAATTATTTTTTAGTTCTAAAAATATTAGAATTCCTGATTTAGCTCGTAAATATTTGTGGGATAATCAAATTGAAGGAAATCTCAAAAAATTAATATCTTCAGCAACAAAATATAA" + }, + { + "seq" : "TAAAGAAATTAAGTGAAGATGATTATGAAAAAAATTGTAGACATTTAAATTATTTAATAGATAATATAAGAGAATTATTTTTTAGTTCTAAAAATATTAGAATTCTTGATGTAGCTCGTAAATATTTGTGGGATAATCAAATTGAAGGAAATCTCAAAAAATTAATATCTTCAGAAACAAAAAATAA" + } + ], + "target_id" : 38 + }, + { + "mhap_location" : + { + "chrom" : "Pf3D7_08_v3", + "end" : 933142, + "genome_id" : 0, + "start" : 933022, + "strand" : "+" + }, + "microhaplotypes" : + [ + { + "seq" : "TGGTTTTAATGAGGATGATTTAGATAAAGAGTTTTTTTTTGATTTGCCGTCGATTAGTGGTTTTTCAAGTAATGGTATGAAAAAATGTAATTTAAGAAATTTATTAAAAAGATTAGAA" + } + ], + "target_id" : 3 + }, + { + "mhap_location" : + { + "chrom" : "Pf3D7_08_v3", + "end" : 1269455, + "genome_id" : 0, + "start" : 1269319, + "strand" : "+" + }, + "microhaplotypes" : + [ + { + "seq" : "CCTTAGCATTAATAACACTTATAGGAGGTATTTATATGACTAAAGGAAGAAAAAGTTCCATATGGCATAATTCAGAAATAAATGATACACTTTATGATGTTGTTCTTGAAACAGTGAATCAAGGAAATACAGAT" + }, + { + "seq" : "CCTTAGCATTAATAACACTTATAGGAGGTATTTATATGACTAAAGGAAGAAAAAGTTCCATATGGCATAATTCAGAAATAAATGATACACTTTATGATATTGTTCTTGAAACAGTGAATCAAGGAAATACAGAT" + } + ], + "target_id" : 32 + }, + { + "mhap_location" : + { + "chrom" : "Pf3D7_08_v3", + "end" : 1344818, + "genome_id" : 0, + "start" : 1344685, + "strand" : "+" + }, + "microhaplotypes" : + [ + { + "seq" : "AATATATCTTTTACTTTATCTGTAAGTTTCATGGAATCTATTATTTCATCTGCATATTTTATTTTTGCCTCGTTTATATATTTACCTGCTTTTAATTTACATAAACATTTTTCTATTAAGTTTTGATCATT" + } + ], + "target_id" : 30 + }, + { + "mhap_location" : + { + "chrom" : "Pf3D7_08_v3", + "end" : 1363086, + "genome_id" : 0, + "start" : 1362890, + "strand" : "+" + }, + "microhaplotypes" : + [ + { + "seq" : "GTAAAAAAAAAGGGTTTTCCTAAAAAACCATCGGTTCATGGTTTTACACAGATGGTGTTTTTGCAGCTTACTAATATAGTCATGTATGCCCTTTGTTTTATGAGCCTTTCACAAATATATGCTTATTTCGAAAACGTGAATTTTTATATTATAAGCAATTTTCGTTTCCTTGAGAGATATTTTAATATATTCAA" + }, + { + "seq" : "GTAAAAAAAAAGGGTTTTCCTAAAAAACCATCGGTTCATGGTTTTACACAGATGGTGTTTTTGAAGATTACTAATATAGTCATGTATGCCCTTTGTTTTATGAGCCTTTCACAAATATATGCTTATTTCGAAAACGTGAATTTTTATATTATAAGCAATTTTCGTTTCCTTGAGAGATATTTTAATATATTCAA" + }, + { + "seq" : "GTAAACAAAAAGGGTTTTCCTAAAAAACCATTGGTTCATGGTTTTACACAGATGGTGTTTTTGCAGCTTACTAATATAGTCATGTATGCCCTTTGTTTTATGGACCTTTCACAAATATATGCTTATTTCGAAAACGTGAATTTTTATATTATAAGCAATTTTCGTTTCCTTGAGAGATATTTTAATATATTCAA" + } + ], + "target_id" : 28 + }, + { + "mhap_location" : + { + "chrom" : "Pf3D7_09_v3", + "end" : 517091, + "genome_id" : 0, + "start" : 516927, + "strand" : "+" + }, + "microhaplotypes" : + [ + { + "seq" : "TGTTTGTGTAATAAAGGATATTTCTATAATGTCAAGAAACAACAATGTGAAGAATGTCCCATAGGTTTTTATTGTCCAGAAATAAGCTCAAAAAATAATATAAAAAAACCTATCAAATGTCCTAAAAATTCCTCAAGTATAAAAAAAGGTATGTATATATCA" + }, + { + "seq" : "TGTTTGTGTAATAAAGGATATTTCTATAATGTCAAGAAACAACAATGTAAAGAATGTCCCATAGGTTTTTATTGTCCAGAAATAAGCTCAAAAAATAATATAAAAAAACCTATCAAATGTCCTAAAAATTCCTCAAGTATAAAAAAAGGTATGTATATATCA" + }, + { + "seq" : "TGTTTGTGTAATAAAGGATATTTCTATAATGTCAAGAAACAACAATGTAAAGAATGTCCCATAGGTTTTTATTGTCCAAAAATAAGCTCAAAAAATAATATAAAAAAACCTATCAAATGTCCTAAAAATTCCTCAAGTATAAAAAAAGGTATGTATATATCA" + } + ], + "target_id" : 26 + }, + { + "mhap_location" : + { + "chrom" : "Pf3D7_09_v3", + "end" : 596333, + "genome_id" : 0, + "start" : 596132, + "strand" : "+" + }, + "microhaplotypes" : + [ + { + "seq" : "TTATTTTCGTTTTTTTTTATATTATCATTATAATTATATGTATTTACAAAGAATTTATTATTATTTGTTTCTTTATAATTATATTCATTTTCTTTATTACTTAAGGAATTTATATTTGATAAAACTTGTTGTACTCTTTCTTCTTTGTTGATGTGAATATTTGAGAAAATAATAATAAATGTAATGACTAGGGCTATGT" + } + ], + "target_id" : 25 + }, + { + "mhap_location" : + { + "chrom" : "Pf3D7_09_v3", + "end" : 685791, + "genome_id" : 0, + "start" : 685600, + "strand" : "+" + }, + "microhaplotypes" : + [ + { + "seq" : "CAAAGGAACAAGATAATTTTTTCAATTTTTATAAAAGTAATATATATGATATGGAAAATAGAACATGTAATAATAATATATTACAATATTGTGTTATGAATAATAAATCATATTTATTTCATAATATATCATCCAAAAAAAATATATATATAAAAAAAAAGAATCATCAGTTTTCTTTATTCATATATT" + } + ], + "target_id" : 77 + }, + { + "mhap_location" : + { + "chrom" : "Pf3D7_09_v3", + "end" : 1179077, + "genome_id" : 0, + "start" : 1178893, + "strand" : "+" + }, + "microhaplotypes" : + [ + { + "seq" : "CAAATTACCCTTAGCCCCAGATATGGTAAAGACATATCACTGTTATAAATTAGGAAAGCAAGCAGCTAAATTATTAGAATCTATCATTTTAAAGAAAAAGTTCGTAAGATTTAGAGTTACTGATGCTATTGATGTATATGATTTCTTTTATATAAAGAAAGTTTTATCCAGTCGTATTAAGA" + }, + { + "seq" : "CAAATTATCCTTAGCCCCAGATATGGTAAAGACATATCACTGTTATAAATTAGGAAAGCAAGCAGCTGAATTATTAGAATCTATCATTTTAAAGAAAAAGTTCGTAAGATTTAGAGTTACTGATGCTATTGATGTATATGATTTCTTTTATATAAAGAAAGTTTTATCCAGTCGTATTAAGA" + } + ], + "target_id" : 89 + }, + { + "mhap_location" : + { + "chrom" : "Pf3D7_09_v3", + "end" : 1406540, + "genome_id" : 0, + "start" : 1406404, + "strand" : "+" + }, + "microhaplotypes" : + [ + { + "seq" : "AATTAATTTTAATGATGATGTTACTTTAGAAACACAATCCATGATAGCACACGGAGGGTCTTTGTCAGAAATAGAAGAAACTGGAGATTTATCTTCAGATGTTGATAGATTACTTTCATCAATCGAAACTACTC" + } + ], + "target_id" : 51 + }, + { + "mhap_location" : + { + "chrom" : "Pf3D7_09_v3", + "end" : 1437302, + "genome_id" : 0, + "start" : 1437113, + "strand" : "+" + }, + "microhaplotypes" : + [ + { + "seq" : "TAAAACCTGACAGCTTTGTACAGTTATATTTACCCAATTAGAATGTTCAAACATATTTAAGTGTTGCCATTCTTCAAATAATTTTTTTTCATATTCAGTTTTTGGTTGGTTTTTAAATTCTTTTGATAATGTACCTTCTGCGGATGGTATAGGGAAGTTAAAAATTTTATTACTTACTTTGTTTGAT" + } + ], + "target_id" : 87 + }, + { + "mhap_location" : + { + "chrom" : "Pf3D7_01_v3", + "end" : 531899, + "genome_id" : 0, + "start" : 531681, + "strand" : "+" + }, + "microhaplotypes" : + [ + { + "seq" : "AAAGAAAGATGTTAAGAAAAAAAAGATCGATATGATAAATATATTACACATTCCTACAAATAATTATAGCATGCCAAATGAAAAAGATATAAACAGTTATGAATTTTTTGGATCTGAACCTATTGAATTATATGATGGAAAATCTAATAAGAATTGTGTTATAACTAGCCAATCTTATATTTGTATTGAAAACCCGCATGCTGCCATATTATCCGA" + }, + { + "seq" : "AAAGAAAGATGTTAAGAAAAAAAAGATCGATATGATAAATATATTACACATACCTACAAATAATTATAACATGCCAAATGAAAAAGATATAAACAGTTATGAATTTTTTGGATCTGAACCTATTGAATTATATGATGTAAAATCTAATAAGAATTGTGTTATAACTAGCCAATCTTATATTTGTATTGAAAACCCGCATGCTGCCATATTATCCGA" + }, + { + "seq" : "AAAGAAAGATGTTAAGAAAAAAAAGATCGATATGATAAATATATTACACATACCTACAAATAATTATAACATGCCAAATAAAAAAGATATAAACAGTTATGAATTTTTTGGATCTGAACCTATTGAATTATATGATGTAAAATCTAATAAGAATTGTGTTATAACTAGCCAATCTTATATTTGTATTGAAAACCCGCATGCTGCCATATTATCCGA" + } + ], + "target_id" : 24 + }, + { + "mhap_location" : + { + "chrom" : "Pf3D7_10_v3", + "end" : 377208, + "genome_id" : 0, + "start" : 377094, + "strand" : "+" + }, + "microhaplotypes" : + [ + { + "seq" : "ACCAAAAAATGATACCTGTACGTTTTTCTCCAGGAGAAACAAAAAAATTAGAAAGGATTCTCAAAAAAGTAGACGACTTTTTCTGTGCCAATATTAAAGCGCAATATACCTG" + } + ], + "target_id" : 63 + }, + { + "mhap_location" : + { + "chrom" : "Pf3D7_10_v3", + "end" : 992543, + "genome_id" : 0, + "start" : 992370, + "strand" : "+" + }, + "microhaplotypes" : + [ + { + "seq" : "TTTTAAAAAAAAAAATTATGATATAAAATCTTCAATTAATAAAAGATCTATCCAGTTCTTTACAGACACTAATATAGATCATTATATAGCATATGAATATTATAAGGAGGACCGTACAGAATTTATATTAACTATTATGAATGAAAAAAATATTACTCATCAAGAAACTCA" + } + ], + "target_id" : 65 + }, + { + "mhap_location" : + { + "chrom" : "Pf3D7_10_v3", + "end" : 1386868, + "genome_id" : 0, + "start" : 1386699, + "strand" : "+" + }, + "microhaplotypes" : + [ + { + "seq" : "GAGAACAGGTTAAATATATTGAAGACGTGGTTTGATAATCAGGTATTTCTTTAATTAAATATTCATGATATTGTTCGTTAGATACATAAATTAATTCGTCCTCCACATTTTGCTGTTCTGTTATAATTTGTGAAGAAGCTTGGTTTGTCTTATTTGGTAATTGCTCT" + }, + { + "seq" : "GGGAACAGGTTAAATATATTGAAGACGTGGTTTGATAATCAGGTATTTCTTTAATTAAATATTCATGATATTGTTCGTTAGATACATAAATTAATTCGTCCTCCACATTTTGCTGTTCTGTTATAATTTGTGAAGAAGCTTGGTTTGTCTTATTTGGTAATTGCTCT" + } + ], + "target_id" : 34 + }, + { + "mhap_location" : + { + "chrom" : "Pf3D7_10_v3", + "end" : 1399710, + "genome_id" : 0, + "start" : 1399543, + "strand" : "+" + }, + "microhaplotypes" : + [ + { + "seq" : "ACATCAGAACATAGTAAAGATTTAAATAATAATGATTCAAAAAATGAATCTAGTGATATTATTTCAGAAAATAATAAATCAAATAAAGTAGAAAATCATTTTGAATCATTATCAGATTTAGAATTACTTGAAAATTCCTCACAAGATAATTTAGACAAAGATACA" + }, + { + "seq" : "ACATCAGAACATAGTAAAGATTTAAATAATAATGATTCAAAAAATGAATCTAGTGATATTATTTCAGAAAATAATAAATCAAATAAAGTACAAAATCATTTTGAATCATTATCAGATTTAGAATTACTTGAAAATTCCTCACAAGATAATTTAGACAAAGATACA" + } + ], + "target_id" : 71 + }, + { + "mhap_location" : + { + "chrom" : "Pf3D7_10_v3", + "end" : 1436681, + "genome_id" : 0, + "start" : 1436478, + "strand" : "+" + }, + "microhaplotypes" : + [ + { + "seq" : "GAGGAGAAACACGTTTTATCTCATAATTCATATGAGAAAACTAAAAATAATGAAAATAATAAATTTTTCGATAAGGATAAAGAGTTATCGATGTCTAATGTAAAAAATGTGTCACAAACAAATTTCAAAAGTCTTTTAAGAAATCTTGGTGTTTCAGAGAATATATTCCTTAAAGAAAATAAATTAAATAAGGAAGGGAAA" + }, + { + "seq" : "GAGAAGAAACACGTTTTATCTCATAATTCATATGAGAAAACTAAAAATAATGAAAATAATAAATTTTTCGATAAGGATAAAGAGTTAACGATGTCTAATGTAAAAAATGTGTCACAAACAAATTTCAAAAGTCTTTTAAGAAATCTTGGTGTTTCAGAGAATATATTCCTTAAAGAAAATAAATTAAATAAGGAAGGGAAA" + } + ], 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"seq" : "TCTCATTCCTTTGAAAATATGAACTATTCAACTCATCAAGGTTTTCATATGTTATTTCATAACTGCCATCATCTGAATCCTCTTCATCACTACTACTTAAAGAATGCTCTTCTACAGTTATATCTTCATAATGATTATTTTTAGGAAAATATTCTTCAGATCTTTCTATAAATTCTGTTCCATTA" + } + ], + "target_id" : 60 + }, + { + "mhap_location" : + { + "chrom" : "Pf3D7_11_v3", + "end" : 1552639, + "genome_id" : 0, + "start" : 1552429, + "strand" : "+" + }, + "microhaplotypes" : + [ + { + "seq" : "ATATCGACAATTATAAAGAAAAAATAGAAAATTTTAATGAAAGATATTATGAAGATGATTTAAGTTTCTTAAACTTTCCAGGAACCATAACAAGTTATGATAAAAACCATCAAAGAGATAAAAGAAAAAACTGTTTTGAAGAATATCTAGACAATAATAATTATTTTATTGATAGTAATCTAAAGGAAGTTATAGAAAATAATATATA" + } + ], + "target_id" : 19 + }, + { + "mhap_location" : + { + "chrom" : "Pf3D7_01_v3", + "end" : 532843, + "genome_id" : 0, + "start" : 532689, + "strand" : "+" + }, + "microhaplotypes" : + [ + { + "seq" : "CTTTCTTAATTCTATGAATGAAGAATATACGCATATTAATTTAAATAACTTTATACATAATGATAACAATGATAAAGACGAAAATTATACATTAGATCAGGTGGAAGAATATCCTATGACTAGTTATCAAAATAATATATACAAGGATTTTT" + }, + { + "seq" : "CTTTCTTAATTCTATGAATGAAGAATATACGCATATTAATTTAAATAACTTTATACATAATAATAACCATGATAATGACGAAAATTATACATTAGATCAGGTGGAAGGATATCCTATGACTAGTTATCAAAATAATATATACAAGGATTTTT" + } + ], + "target_id" : 40 + }, + { + "mhap_location" : + { + "chrom" : "Pf3D7_11_v3", + "end" : 1751054, + "genome_id" : 0, + "start" : 1750864, + "strand" : "+" + }, + "microhaplotypes" : + [ + { + "seq" : "TATTAAAAACAACAAATAAATTACCAAGGTCATGGAAAAAACTCTTGTTAAATCTATCCATTAGATTTCAAACAATACCTATAGGTGGTTCTATCGAAATCATATCAAAGGATGAGAAAAATATTTCTGTGACACGATCCAGTGAATATAATGCAACAACATATGAGCATTACACATTTCCCAAATGG" + }, + { + "seq" : "TATTAAAAACAACAGATAAATTACCAAGGTCATGGAAAAAACTCTTGTTAAATCTATCCATTAGATTTCAAACAATACCTATAGGTGGTTCTATCGAAATCATATCAAAGGATGAGAAAAATATTTCTATGACACGATCCAGTGAATATAATGCAACAACATATGAGCATTACACATTTCCCAAATGG" + } + ], + "target_id" : 21 + }, + { + "mhap_location" : + { + "chrom" : "Pf3D7_11_v3", + "end" : 1816424, + "genome_id" : 0, + "start" : 1816210, + "strand" : "+" + }, + "microhaplotypes" : + [ + { + "seq" : "TTGACTTCTCCGGGTTTGTTACATTATCATTACAACCAATATTATTAAGGTTAATATTATTTTTATCATTATTATTGTTGTTTTCATTTGTGTGGTTATATAATAACAATGATGTGTCGTCTATTGGATCATTTTGCACAAGGTCAATATCATTAGAATTATGTTTCATATTATTTGTATACATTTTTTTGTAATTATCATTTTTTCTTACT" + }, + { + "seq" : "TTGACTTCTCCGGGTTTGTTACATTATCATTACAACCAATATTATTAAGGTTAATATTATTTTTATCATTATTATTGTTGTTTTCATTTGTGTGGTTATATAATAACAATGATGTGTCGTCTATTGGATCATTTTGCACAAGGTCAATATCATTAGAATTATGTTTCCTATTATTTGTATACATTTTTTTGTAATTATCATTTTTTCTTACT" + } + ], + "target_id" : 18 + }, + { + "mhap_location" : + { + "chrom" : "Pf3D7_12_v3", + "end" : 63279, + "genome_id" : 0, + "start" : 63165, + "strand" : "+" + }, + "microhaplotypes" : + [ + { + "seq" : "ATAATTTCACCTTTTGAATTACATATGTCTGTATTCAAAAATTTTATATCTCTACTCCATATATTTATCTTTACACCCAAAAACAAAGCAATGAAAAAAACAACCCTTTCAT" + }, + { + "seq" : "ATAATTTCACCTTTTGAATTACATATGTCTGTATTCAAAAATTTTATATCTCTACTCCATATATTTATCTTTACACCCAAAAACAAAGTAATGAAAAAAATAACCCTTTCAT" + } + ], + "target_id" : 69 + }, + { + "mhap_location" : + { + "chrom" : "Pf3D7_12_v3", + "end" : 660009, + "genome_id" : 0, + "start" : 659890, + "strand" : "+" + }, + "microhaplotypes" : + [ + { + "seq" : "GGTCGACTTTTGGTGGTTTAACATTTTCAGCTATGAGTTTTTCGACTGATGGCAATCCTACTTTGATTAATTCCTTTAACATAAGTTTTGCGTGTTTTTTTACTTCTGATTTGATAT" + }, + { + "seq" : "GGTCGACTTTTGGTGGTTTAACATTTTCAGCTACGAGTTTTTCGACTGATGGCAATCCTACTTTGATTAATTCCTTTAACATAAGTTTTGCGTGTCTTTTTACTTCTGATTTGATAT" + } + ], + "target_id" : 16 + }, + { + "mhap_location" : + { + "chrom" : "Pf3D7_12_v3", + "end" : 684260, + "genome_id" : 0, + "start" : 684087, + "strand" : "+" + }, + "microhaplotypes" : + [ + { + "seq" : "ATATCAAGATGGTAGTATTGTTTTAGATGTTAGTAGTACGAGAGATAAACTTTATGGAGAAGTTGAGTGGGAAGGATATAAATTTGAACTTGTGGATACAGGAGGTTTAGTTTTTGAACAAGAAAAGTTTTCAAAAGAAATAAAGGATCAAATTCTTATGGCTCTAAAAGA" + }, + { + "seq" : "ATATCAAGATGGTAGTATTGTTTTAGATGTTAGTAGTACGAGAGATAAACTTTATGGAGAAGTTGAGTGGGAAGGATATAAATTTGAACTTGTGGATACAGGAGGTTTAGTTTTTGAACAAGAAAAGTTTTCAAAAGAAATAAAGGATCAAATTTTTATGGCTCTAAAAGA" + } + ], + "target_id" : 14 + }, + { + "mhap_location" : + 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"genome_id" : 0, + "start" : 2050129, + "strand" : "+" + }, + "microhaplotypes" : + [ + { + "seq" : "TTTAAACTTTGAATCTGTTCAATTAATAACACTTCATCATTGTCTTCGCCTTTTATAATATCTCCATGATTATGTGCTCCTCTAATTAAGGTATCACTAACCTGTTGTTCATCTGTCGCATGAGAACTAGTAGATATATCTGGTTTATTTTTTTTCTTTCTTTTTGTTATTTCTAATTTTTT" + }, + { + "seq" : "TTTAAACTTTGAATCTGTTCAATTAATAACACTTCATCATTGTCTTCTCCTTTTATAATATCCCCATGATTATGTGCTCCTCTAATTAAGGTATCACTAACCTGTTGTTCATCTGTCGCATGAGAACTAGTAGATATATCTGGTTTATTTTTTTTCTTTCTTTTTGTTATTTCTAATTTTTT" + } + ], + "target_id" : 36 + }, + { + "mhap_location" : + { + "chrom" : "Pf3D7_13_v3", + "end" : 103878, + "genome_id" : 0, + "start" : 103658, + "strand" : "+" + }, + "microhaplotypes" : + [ + { + "seq" : "ACTGATGTTAATGAAGGCCAAAATGGAAAAAGTTTAACACAAGAAAAAACCCTAAAACAAATTCCTTCGACATCACCAAATAATTTAGAACAAAAATTACAACAAACACATATTTCTTCTTCCCAACAAAAACATTTAATAAAAACTACTCCTACTTCAGATTCAACTACAACTTCATCAAGCTCTTCTGTTCCTCTTACAAAACAATCCCTTCATTC" + }, + { + "seq" : "ACTGATGTTAATGAAGGCCAAAATGGAAAACGTTTAACACAAGAAAAAACCCTAAAACAAATTCCTTCGACATCACCAAATAATTTAGAACAAAAATTACAACAAACACATATTTCTTCTTCCCAACAAAAACATTTAATAAAAACTACTCCTACTTCAGATTCAACTACAACTTCATCAAGCTCTTCTGTTCCTCTTACAAAACAATCCCTTCATTC" + } + ], + "target_id" : 13 + }, + { + "mhap_location" : + { + "chrom" : "Pf3D7_13_v3", + "end" : 156721, + "genome_id" : 0, + "start" : 156565, + "strand" : "+" + }, + "microhaplotypes" : + [ + { + "seq" : "ATAGAGTTATTATGTTCGAATTAATGACCAGATTGTTTCGATTTTATACAAAACCAATAGACCTTATTATTACTATGAATACACACAGATATGACACACCTATATTGTTAAAACATTCAAACAGCTTACAACTTATCTTATCAAATCAACAAAA" + } + ], + "target_id" : 17 + }, + { + "mhap_location" : + { + "chrom" : "Pf3D7_01_v3", + "end" : 534367, + "genome_id" : 0, + "start" : 534214, + "strand" : "+" + }, + "microhaplotypes" : + [ + { + "seq" : "GATAAAAAAAGAAAATGTAACAATCTACCTTGTGATTGTATCTTATGTAAAAAAAAGCACAATGTTTGTTATTGTAATATGTGTAAAAAGAAAGAAAAAAATATGAGAGAAGATTTATCGGTTGTAAAATATAATGAATATCCGATTAGTG" + }, + { + "seq" : "GATAAAAAAAGAAAATGTAATAATCTACTTTGTGATTGTATCTTATGTAAAAAAAAGCACAATGTTTGTTATTGTAATATGTGTAAAAAGAAAGAGAAAAATATGAGAGAAGATTTATCGGTTGTAAAATATAATGAATATCCGATTAGTG" + }, + { + "seq" : "GATAAAAAAAGAAAATGTAATAATCTACCTTGTGATTGTATCTTATGTAAAAAAAAGCACAATGTTTGTTATTGTAATATGTGTAAAAAGAAAGAAAAAAATATGAGAGAAGATTTATCGGTTGTAAAATATAATGAATATCCGATTAGTG" + } + ], + "target_id" : 84 + }, + { + "mhap_location" : + { + "chrom" : "Pf3D7_13_v3", + "end" : 1150492, + "genome_id" : 0, + "start" : 1150302, + "strand" : "+" + }, + "microhaplotypes" : + [ + { + "seq" : "TAAAAAAAGCAAACAAAAAGAAAAGAGAATGGAAGATTTAAGTATTGAGGAAAATTTGAAAGAGAAATTAATAAACCTAAATATTCAGAAACAGTATAGTGGTTTCCATATGAAAGAAATGGAGGAACAAAATATTCCTGAATTAAATATTCCACAACTTTCAGCTATTCATAATAGAGAAGATATGA" + }, + { + "seq" : "TAAAAAAAGCAAACAAAAAGAAAAGAGAATGGAAGATTTAAGTATTGAGGAAAATTTGAAAGAGAAATTAATAAACCTAAATATTCAGAAACAGTATAGTGGTTTCCATATGAAAGAAATGGAGGAACAAAATATTCCTGAATTAAATATTCCACAACTTTCAGCTACTCATAATAGAGAAGATATGA" + } + ], + "target_id" : 9 + }, + { + "mhap_location" : + { + "chrom" : "Pf3D7_13_v3", + "end" : 1419669, + "genome_id" : 0, + "start" : 1419542, + "strand" : "+" + }, + "microhaplotypes" : + [ + { + "seq" : "TGGTTTTTGTACTTTTTGTCCTTGTGTTGATATCTCTTGTTCATTTTTAGATTGAGTATCTGTTTCACTTTGTGCCTTTACCTTTGATAATACGTTTTTACCGAATAATCCTAAATTTTGGAATA" + }, + { + "seq" : "TGGTTTTTGTACTTCTTTTCCTTGTGTTGATATCTCTTGTTCATTTTTAGATTGAGTATCTGTTTCACTTTGTGCCTTTACCTTTGATAATACGTTTTTACCGAATAATCCTAAATTTTGGAATA" + } + ], + "target_id" : 8 + }, + { + "mhap_location" : + { + "chrom" : "Pf3D7_13_v3", + "end" : 1725569, + "genome_id" : 0, + "start" : 1725364, + "strand" : "+" + }, + "microhaplotypes" : + [ + { + "seq" : "CCAATACAATAAATTCTACCATTTGACGTAACACCACAATTATTTCTTCTAGGTATATTTAAATTACTTGAAACATACCATACATCTCTTAAACGATCATACACCTCAGTTTCAAATAAAGCCTTATAATCATAGTTATTACCACCAAAAACGTATAAGAAATTATTCAATACAGCACTTCCAAAATAAGCTTTTTTGGTAGA" + } + ], + "target_id" : 10 + }, + { + "mhap_location" : + { + "chrom" : "Pf3D7_13_v3", + "end" : 1876533, + "genome_id" : 0, + "start" : 1876351, + "strand" : "+" + 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"AACATTTTTTTAACATCTTTACCTTTTTGACTTGGTTCTTCATCATAATTCTGTTGTTCTGCAGAATCAGCATTTACTTCAGTTTCTTCTTTATTTTGAAAAGTGTTTGATTCTACATGAGAATTGGAAGATGAACGTCTATGTTTTACTTCTGTATAACTAGTACGTTCTCCAGTATGATGAGCCTTAAGGTTTACATCTTCAGTTTCTT" + } + ], + "target_id" : 7 + }, + { + "mhap_location" : + { + "chrom" : "Pf3D7_13_v3", + "end" : 2479245, + "genome_id" : 0, + "start" : 2479085, + "strand" : "+" + }, + "microhaplotypes" : + [ + { + "seq" : "CCATGCTTTATCAAAACAAAGTAATGAAAATGTAATACATTATTCTTGTCGATCTATATGTGCTTTTACAAAAAACCCTAAGGGTTTAGAAGCGGTAAAGGATATCAAGGACTTTGCGAATATTATAAGTAAATCTGTTGGTGATTTGAGTAAAGAGA" + } + ], + "target_id" : 6 + }, + { + "mhap_location" : + { + "chrom" : "Pf3D7_13_v3", + "end" : 2481287, + "genome_id" : 0, + "start" : 2481105, + "strand" : "+" + }, + "microhaplotypes" : + [ + { + "seq" : "GAACTTACTTTAGAAGCCATGAATTCGGCCGATGATCCATTGGAAGCATTTAAAAATACTTTATTAATATTTGATTTTAATTTATCTGAATTTGATAAGGATCCATATGTAAATGGTGTGCATGATTTAGCATCTAATATAAAGGATTGTTTAAGAAAAGGAGGTCACAGTAAAATATAT" + } + ], + "target_id" : 47 + }, + { + "mhap_location" : + { + "chrom" : "Pf3D7_13_v3", + "end" : 2669306, + "genome_id" : 0, + "start" : 2669134, + "strand" : "+" + }, + "microhaplotypes" : + [ + { + "seq" : "AAAAAAATACATTTAAATCTATAATATTTGTAATAAATGATAAGAATATTAGTAATAATAGGGTACTACTATTTGTAAATACTTTTCTACATAATTTATCAATAGTAGGAAATATGATATTCTTTTTGTTTGGCTTTATTTTATCTGGGATTTTCCAATCATAAAGTTCG" + } + ], + "target_id" : 5 + }, + { + "mhap_location" : + { + "chrom" : "Pf3D7_14_v3", + "end" : 40136, + "genome_id" : 0, + "start" : 39952, + "strand" : "+" + }, + "microhaplotypes" : + [ + { + "seq" : "CATAGAAATATGTGCGAAAATTGGGAAAAAAATAAATAACAGGAATTGTTATATAAATTGAATCAAGAATGGCACAAAGAAAATAATACTGGTGACTTTCACACTAGTGATATCACACACAATAGTGGTATTACATACACTAGTGGTAACATACCTAGTGAAAGTAATAGTAGTTATATCCA" + }, + { + "seq" : "CATAGAAATATGTGCGAAAATTGGGAAAAAAATAAATAACAGGAATTGTTATATAAATTGAATCAAGAATGGCACAAAGAAAATAATACTGGTGACTTTCACACTAGTGATATCACACACAATAGTGGTATTACATACAGTAGTGGTAACATACCTAGTGAAAGTAATAGTAGTTATATCCA" + } + ], + "target_id" : 55 + }, + { + "mhap_location" : + { + "chrom" : "Pf3D7_01_v3", + "end" : 535109, + "genome_id" : 0, + "start" : 534940, + "strand" : "+" + }, + "microhaplotypes" : + [ + { + "seq" : "ATACTCCGTCAGATATTCAAAATGAATGTATTTGTTCAAAAATAAATGAAGATAGAAATAATGATATGATAAACATATCTGAAATATATTATCGTTTCATTAAATTTATAACAATGATTGAAATATATTTGTGTGTAATAGAGGAAATTAAAAGGGAAGAATGGGAA" + } + ], + "target_id" : 76 + }, + { + "mhap_location" : + { + "chrom" : "Pf3D7_14_v3", + "end" : 120350, + "genome_id" : 0, + "start" : 120214, + "strand" : "+" + }, + "microhaplotypes" : + [ + { + "seq" : "TTACAATGTTCTTCGCATTCGAAATTTTTTTCAGGATTACTTGAAAAGCCTTCTGGACAATTACAATATTCATATCCATGAGCATTGTTACAAACACCTTTTCCACAATTTAAAAAACATTTTTCTTCATTTAA" + }, + { + "seq" : "TTACAATGTTCTTCGCATTCGAAATTTTTTTCAGGATTACTTGAAAAGCCTTGTGGACAATTACAATATTCATATCCATGAGCATTCTTACAAACACCTTTTCCACAATTTAAAAAACATTTTTCTTCATTTAA" + }, + { + "seq" : "TTACAATGTTCTTCGCATTCGAAATTTTTTTCAGGATTACTTGAAAAGCCTTCTGGACAATTACAATATTCATATCCATGAGCATTCTTACAAACACCTTTTCCACAATTTAAAAAACATTTTTCTTCATTTAA" + } + ], + "target_id" : 83 + }, + { + "mhap_location" : + { + "chrom" : "Pf3D7_14_v3", + "end" : 150293, + "genome_id" : 0, + "start" : 150104, + "strand" : "+" + }, + "microhaplotypes" : + [ + { + "seq" : "TAATAATAGTAATATAAAGAATTATTCAGCTGTAGATATATTCTCACCCAAAAAAACTGGAAAGGAATGTATTAAATGTCTCCCAGATAATTTTTGTGAATGCGAATGTAGTTGTAAAAATAAAACAGGTTTTTCAATGAAATATAGACATGCCAGTAAGGGATCTAAAAGATATCGTAAAAAAATG" + }, + { + "seq" : "TAATAATAGTAATATAAAGAATTATTCAGCTGTAGATATATTCTCACCCAAAAAAACTGGAAAGGAATGTATTAAATGTCTCCCAGATAATTTTTGTGAATGCGAATGTAGTTGTAAAAATAAAACAGGTTTTTCAATGAAATATAGACATGCCAGTAAGGGATCTAAAAGATATAGTAAAAAAATG" + } + ], + "target_id" : 97 + }, + { + "mhap_location" : + { + "chrom" : "Pf3D7_14_v3", + "end" : 279785, + "genome_id" : 0, + "start" : 279662, + "strand" : "+" + }, + "microhaplotypes" : + [ + { + "seq" : "AGTTATAGTGATTCATATAAGGTAAATTGTATTAATTTCTCTGAAGGATTTTGTTGCTGTCATCCAATAAATAATTTAGCACTATTATATGGAGAGTATCAACAAAATCAAGAATCAAAAA" + } + ], + "target_id" : 88 + }, + { + "mhap_location" : + { + 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"genome_version" : "2020-09-01", + "gff_url" : "https://plasmodb.org/common/downloads/release-65/Pfalciparum3D7/gff/data/PlasmoDB-65_Pfalciparum3D7.gff", + "name" : "3D7", + "taxon_id" : + [ + 5833 + ], + "url" : "https://plasmodb.org/common/downloads/release-65/Pfalciparum3D7/fasta/data/PlasmoDB-65_Pfalciparum3D7_Genome.fasta" + } + ] +} diff --git a/tests/data/minimum_pmo_example_2_for_spec_dup_testing.json b/tests/data/minimum_pmo_example_2_for_spec_dup_testing.json new file mode 100644 index 0000000..090cdbd --- /dev/null +++ b/tests/data/minimum_pmo_example_2_for_spec_dup_testing.json @@ -0,0 +1,8495 @@ +{ + "bioinformatics_methods_info" : + [ + { + "methods" : + [ + { + "additional_argument" : + [ + "--bamExtractTrimToRegion", + "--bed /tank/data/plasmodium/falciparum/beds/targeted_panels/heome1/heome1_Pf3D7_withPrimers.bed", + "--genomeDir /tank/data/genomes/plasmodium/genomes/pf/genomes/", + "--primaryGenome Pf3D7", + "--bam bams/{SAMPLE}.sorted.bam" + ], + "program" : "PathWeaver BamExtractPathwaysFromRegion", + "program_description" : "Extract reads from a bam file for a specific genomic locatioon and then assembles local haplotypes for that region", + "program_version" : "1.0.0-dev" + }, + { + "additional_argument" : + [ + "--overWriteDir", + "--fracCutOff 0.005", + "--dout popClusteringTrimmedParagon", + "--replicateMinTotalReadCutOff 10", + "--clusterCutOff 5", + "--pat _heome1", + "--numThreads 10", + "--groupingsFile /tank/data/plasmodium/falciparum/pfdata/metadata/meta.tab.txt", + "--genome2bit /tank/data/genomes/plasmodium/genomes/pf/genomes/Pf3D7.2bit", + "--trimBedFnp /tank/data/plasmodium/falciparum/beds/targeted_panels/heome1/heome1_Pf3D7_inserts_trimmed1.bed" + ], + "program" : "PathWeaver runProcessClustersOnRecon", + "program_description" : "Compare across samples for each target to create population level identifiers and do post artifact cleanup", + "program_version" : "1.0.0-dev" + } + ] + } + ], + "bioinformatics_run_info" : + [ + 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"TCTTATAAAGTTAATGAAATAGCTCAACTTAATTTAACCATAGAAAGAGATTTAACAGATGATGCTGTGATTTTTGCACACTCACTTTATTTACCATTTGAAAAAGAAGAAATGTGGTGGATCGTTATCGGAATTAAAAAAATGAACTTACTTTTATCTATCAAAAAATTATCTTTATTGAAAAGTGTCAATAATATAAAAATTAATT" + } + ], + "target_id" : 52 + }, + { + "mhap_location" : + { + "chrom" : "Pf3D7_04_v3", + "end" : 1100830, + "genome_id" : 0, + "start" : 1100655, + "strand" : "+" + }, + "microhaplotypes" : + [ + { + "seq" : "ATGTTCTAAGATCTGATGGAAAAATATCTGATCAAGGTTCTCAGAAAAGTCCTCCTAAGGAACTTTCTAATAAACAAATGACTCCTGCTCAACGTAAGAATGTGCCACATTTTGTTGAAAGAAGAGGCTATGGAAATAGTCATGTTAGGGGTAACGCACTTAAAAAAATTAGT" + }, + { + "seq" : "ATGTTCTAAGATCTGGTGGAAAAATATCTGATCAAGGTTCTCAGAAAAGTCCTCCTAAGGAACTTTCTAATAAACAAATGACTCCTGCTCAACGTAAGAATGTGCCACATTTTGTTGAAAGAAGAGGCTATGGAAATAGTCATGTTAGGGGTAACTCACTTAAAAAAATTAGT" + } + ], + "target_id" : 81 + }, + { + "mhap_location" : + { + "chrom" : "Pf3D7_01_v3", + "end" : 181672, + "genome_id" : 0, + "start" : 181556, + "strand" : "+" + }, + "microhaplotypes" : + [ + { + "seq" : "TCATTCTTTTTTTAACTAAAACTATTCATCTCAAAAATATAAGATATTTTATATGACGAATGCCATTGTATTTTTTGTTACGTAAAACCTGACTTCTTCAAGGAAAACACATGC" + }, + { + "seq" : "TCATTCTTTTTTTAACGAAAACTATTCATCTCAAAAATATAAGATATTTTATATGACGAATGCCATTGTATTTTTTGTTACGTAAAACCTGACTTCTTCAAGGAAAACACATGC" + } + ], + "target_id" : 64 + }, + { + "mhap_location" : + { + "chrom" : "Pf3D7_04_v3", + "end" : 1102577, + "genome_id" : 0, + "start" : 1102388, + "strand" : "+" + }, + "microhaplotypes" : + [ + { + "seq" : "AAGAAATAAATAAAATAATTTATACAAACGAATTTAATAATTATGAAGATAAAATATATGAAGATGTCAAATATATTAAAGAACAGGAAAATGAAATATACTTGAGAGATGGAATTGAAGAGTTACATATGGATGAACCAAGTCGGGATGTATATGTTGATGATGAAAATGATTATATATTTTTAGA" + }, + { + "seq" : "AAGAAATAAATAAAATAATTTATACAAACGAATTTAATAATTATGAAGATAAAATATATGAAGATGTCAAATATATTAAAGAACAGGAAAATGAAATGTACTTGAGAGATGGAATTGAAGAGTTACATATGGATGAACCAAGTGGGGATGTATATTTTGATGATCAAGATGATTATATATTTTTAGA" + } + ], + "target_id" : 67 + }, + { + "mhap_location" : + { + "chrom" : "Pf3D7_04_v3", + "end" : 1113603, + "genome_id" : 0, + "start" : 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"TTGAAAGAATTAAAGGGAAAAATACAAAATTATTTAGATAATGATATTCAATTGAGTAATGGAAAACTCCTATATAAGGATACATGGGATAGAATTGATTTGAAGTTTTGTAGAACGATAGCAATAGAAGAGGCAGAATACACTAGAAAATTTTATAGCTTAATTAATGATAAACATACAAT" + } + ], + "target_id" : 54 + }, + { + "mhap_location" : + { + "chrom" : "Pf3D7_05_v3", + "end" : 329549, + "genome_id" : 0, + "start" : 329377, + "strand" : "+" + }, + "microhaplotypes" : + [ + { + "seq" : "TTGTGATGTATATAAATTCCCTTCTTCTTTATGTACCACATTATAAGAACCACGAACATATTCTTTTAAAAATGTTAACTTACTTCCAACAAATATATAATCAAAACAAAATTTTTTATTGTCGAAATGTTCTCGTTCAACCCCATTCATATTTCGGATATCATTATTTA" + } + ], + "target_id" : 33 + }, + { + "mhap_location" : + { + "chrom" : "Pf3D7_05_v3", + "end" : 958220, + "genome_id" : 0, + "start" : 958058, + "strand" : "+" + }, + "microhaplotypes" : + [ + { + "seq" : "TTTATATCATTTGTATGTGCTGTATTATCAGGAGGAACATTACCTTTTTTTATATCTGTGTTTGGTGTAATATTAAAGAACATGAATTTAGGTGATGATATTAATCCTATAATATTATCATTAGTATCTATAGGTTTAGTACAATTTATATTATCAATGA" + }, + { + "seq" : "TTTATATCATTTGTATGTGCTGTATTATCAGGAGGAACATTACCTTTTTTTATATCTGTGTTTGGTGTAATATTAAAGAACATGTATTTAGGTGATGATATTAATCCTATAATATTATCATTAGTATCTATAGGTTTAGTACAATTTATATTATCAATGA" + } + ], + "target_id" : 49 + }, + { + "mhap_location" : + { + "chrom" : "Pf3D7_05_v3", + "end" : 958505, + "genome_id" : 0, + "start" : 958388, + "strand" : "+" + }, + "microhaplotypes" : + [ + { + "seq" : "ACGAAATTTATAACAATTTTTACATATGCCAGTTCCTTTTTAGGGTTATTTATTTGGTCATTAATAAAAAATGCACGTTTGACTTTATGTATTACTTGCGTTTTTCCGTTAATTT" + }, + { + "seq" : "ACGAAATTTATAACAATTTTTACATATGCCAGTTCCTTTTTAGGTTTATATATTTGGTCATTAATAAAAAATGCACGTTTGACTTTATGTATTACTTGCGTTTTTCCGTTAATTT" + } + ], + "target_id" : 46 + }, + { + "mhap_location" : + { + "chrom" : "Pf3D7_05_v3", + "end" : 1042280, + "genome_id" : 0, + "start" : 1042161, + "strand" : "+" + }, + "microhaplotypes" : + [ + { + "seq" : "TATTATTACGGTACCATTATATGATTCTTTAGGTCCTCAATCAAGTAGATTTATATTAGATCAAACACAGATGGAAACTATTGTATGTAACAAGACATGTGCTCGTAATTTATTTAA" + } + ], + "target_id" : 4 + }, + { + "mhap_location" : + { + "chrom" : "Pf3D7_05_v3", + "end" : 1309743, + "genome_id" : 0, + "start" : 1309608, + "strand" : "+" + }, + "microhaplotypes" : + [ + { + "seq" : "AATGAAGAAAATATGTCTGACAGACCAAACAGTTTATCTCATGATAAGGATCAACACCACGATGAAACACATAATGAACAATATGGATTATACGTAAAAGAAATGGAATCTAAAGTTGAAAAATTAGCTGAAA" + } + ], + "target_id" : 27 + }, + { + "mhap_location" : + { + "chrom" : "Pf3D7_06_v3", + "end" : 145500, + "genome_id" : 0, + "start" : 145342, + "strand" : "+" + }, + "microhaplotypes" : + [ + { + "seq" : "ATTTGAATAAAATTTATCATTCACAATATTATATTTTTGTTTCTTCTTTTTTCCCATAATATTATTATTTTGTTCACAATATATGTTCATGTGTCCCCTCTTTTTCTGTAAAATATTAAAATGTTTCTTACTATGCTTTTCTTCATTTTTAATAAC" + } + ], + "target_id" : 44 + }, + { + "mhap_location" : + { + "chrom" : "Pf3D7_06_v3", + "end" : 532377, + "genome_id" : 0, + "start" : 532194, + "strand" : "+" + }, + "microhaplotypes" : + [ + { + "seq" : "GAACAATTGTTAAACACCAAATTGGGTGAAACAAAAAACCACCTGAACAGAACCCCATTTATACCTGAATCGGTCATACGAGAAAGGAAATTACGCCAAGAAAAAGCGCAATCCACAAACAACATGTTCGATTCAACAAACGCAGATAGTATTACTTCCCCATGTGATCCAACGAATGCCA" + }, + { + "seq" : "GAACAATTGCTAAACACCAAATTGGGTGAAACAAAAAACCACCTGAACAGAACCCCATTTATACCTGAATCGGTCATACGAGAAAGGAAATTACGCCAAGAAAAAGCGCAATCCACAAACAACATGTTCGATTCAACAAACGCAGATAGTATTACTTCCCCATGTGATCCAACGAATGCCA" + } + ], + "target_id" : 39 + }, + { + "mhap_location" : + { + "chrom" : "Pf3D7_01_v3", + "end" : 496142, + "genome_id" : 0, + "start" : 495970, + "strand" : "+" + }, + "microhaplotypes" : + [ + { + "seq" : "GAAAGTAGCGAATACCCTGTAGAAATTGTTAGTAAACCTCTGGAATGGTTATTGTTTCATGATTTTACTACGCCTGGTGTTACTGCACTACCTGAAGAATTACCATTAACGAGCTATAAAGTAACACCTACTTCTATTAATGTATTGCATAAAGAGGGCCCCACTTTAAA" + }, + { + "seq" : "GAAAGTAGCGAATACCCTGTAGAAATTGTTAGTAAACCTCTGGAATGGTTATTGTTTCATGATTTTACTACGCCTGATGTTACTGCACTACCTGAAGAATTACCATTAACGAGCTATAAAGTAACACCTACTTCTATTAATGTATTGCATAAAGAGGGCCCCACTTTAAA" + } + ], + "target_id" : 62 + }, + { + "mhap_location" : + { + "chrom" : "Pf3D7_07_v3", + "end" : 165421, + "genome_id" : 0, + "start" : 165234, + "strand" : "+" + }, + "microhaplotypes" : + [ + { + "seq" : "TAATTATCATTATTATTATAATTATCATTGTTATTATTATTGTTGTTGTTGTTATTATTATTTCCTTTATTATTTAATATGCATTTTTTAATATCCATTTTATTATTTATCATATCAGTACTTTTATTTTTCTCCTTTTCGTTTATAGCTTTTTCCCTATGCACCCTGAATTTCCCATTTTTTTT" + }, + { + "seq" : "TCATTATTATTATTATTATAATTATCATTTTTATTATTATTGTTGTTATTATTATTTCCTTTATTATTTAATATGCATTTTTTAATATCCATTTTATTATTTATCATATCAGTACTTTTATTTTTCTCCTTTTCGTTTATAGCTTTTTCCCTATGCACCCTGAATTTCCCATTTTTTTT" + } + ], + "target_id" : 29 + }, + { + "mhap_location" : + { + "chrom" : "Pf3D7_07_v3", + "end" : 166166, + "genome_id" : 0, + "start" : 166034, + "strand" : "+" + }, + "microhaplotypes" : + [ + { + "seq" : "TTTTATTTGAACTTTTTTATTTTCTTCATTATCAATATAAAAACAACAATCTTTAAATTTATGAAATAACACCCAACTTAATGTATAAAATATAATTTCTATAAAATCAAAATTAATGTAATAACCTAAT" + } + ], + "target_id" : 59 + }, + { + "mhap_location" : + { + "chrom" : "Pf3D7_07_v3", + "end" : 299004, + "genome_id" : 0, + "start" : 298885, + "strand" : "+" + }, + "microhaplotypes" : + [ + { + "seq" : "CATTCAATATGGTTCTGAGCTTAAAGATGTTATCCTTATACATGTTTCTATTCTCATTCGTTATAACATCAATGACATATAAAACATATCTCTCAAATATTTTGTGAACAATATTAT" + } + ], + "target_id" : 41 + }, + { + "mhap_location" : + { + "chrom" : "Pf3D7_07_v3", + "end" : 730087, + "genome_id" : 0, + "start" : 729974, + "strand" : "+" + }, + "microhaplotypes" : + [ + { + "seq" : "TTTATGTGAAATTTTAAATAAAGAGAAATTGTTTGTGCACACATCTATTTTGGGATATATATCTAATCGTTTATGTTACGATATAAAAAAATATAGATGTTCATTATTGAA" + }, + { + "seq" : "TTTATGTGAAATTTTAAATAAAGAGAAATTGTTTGTGCACACATCTATTTTGGGATATATATCTAATCGTTTATGTTACGATATAGAAAAATATAGATGTTCATTATTGAA" + } + ], + "target_id" : 75 + }, + { + "mhap_location" : + { + "chrom" : "Pf3D7_07_v3", + "end" : 1149584, + "genome_id" : 0, + "start" : 1149414, + "strand" : "+" + }, + "microhaplotypes" : + [ + { + "seq" : "AATATTTAATATTTTTGTTTAGGAAGTTTTCAAAATTGATGACATTGATAACCGTTTTTATTAAATCGCTTGGGTTGTTTGTGTGTTCCATTGTAGAAGACATAATTTTAAGAATGTGTTTTTGTGTTATTAAACAAAACTTTGTTACTATATGGAATCGTATGTTAT" + }, + { + "seq" : "AATATTTAATATTTTTGTTTAGGAAGTTTTCAAAATTGATGACATTGATAACCGTTTTTATTAAATCGCTTGGGTTGTTTGTGTGTTCTATAGTAGAAGACATAATTTTAAGAATGTGTTTTTGTGTTATTAAACAAAACTTTGTTACTATATGGAATCGTATGTTAT" + }, + { + "seq" : "AATATTTAATATTTTTGTTTAGGAAGTTTTCAAAATTGATGACATTGATAACCGTTTTTATTAAATCGCTTGGGTTGTTTGTGTGTTCTATTGTAGAAGACATAATTTTAAGAATGTGTTTTTGTGTTATTAAACAAAACTTTGTTACTATATGGAATCGTATGTTAT" + } + ], + "target_id" : 45 + }, + { + "mhap_location" : + { + "chrom" : "Pf3D7_07_v3", + "end" : 1358910, + "genome_id" : 0, + "start" : 1358693, + "strand" : "+" + }, + "microhaplotypes" : + [ + { + "seq" : "AGAATCTCAACTTTTGCTTAAAAAAAATGATAACAAATATAATTCTAAATTTTGTAATGATTTGAAGAATAGTTTTTTAGATTATGGACATCTTGCTATGGGAAATGATATGGATTTTGGAGGTTATTCAACTAAGGCAGAAAACAAAATTCAAGAAGTTTTTAAAGGGGCTCATGGGAAAATAAGTGAACATGAAATTAAAAATTTTAGAAAAG" + } + ], + "target_id" 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"target_id" : 93 + }, + { + "mhap_location" : + { + "chrom" : "Pf3D7_01_v3", + "end" : 512387, + "genome_id" : 0, + "start" : 512198, + "strand" : "+" + }, + "microhaplotypes" : + [ + { + "seq" : "TAAAGAAATTAAGTGAAGATGATTATGAAAAAAATTGTAGACATTTAAATTATTTAATAGATAATATAAGAGAATTATTTTTTAGTTCTAAAAATATTAGAATTCCTGATTTAGCTCGTAAATATTTGTGGGATAATCAAATTGAAGGAAATCTCAAAAAATTAATATCTTCAGCAACAAAATATAA" + }, + { + "seq" : "TAAAGAAATTAAGTGAAGATGATTATGAAAAAAATTGTAGACATTTAAATTATTTAATAGATAATATAAGAGAATTATTTTTTAGTTCTAAAAATATTAGAATTCTTGATGTAGCTCGTAAATATTTGTGGGATAATCAAATTGAAGGAAATCTCAAAAAATTAATATCTTCAGAAACAAAAAATAA" + } + ], + "target_id" : 38 + }, + { + "mhap_location" : + { + "chrom" : "Pf3D7_08_v3", + "end" : 933142, + "genome_id" : 0, + "start" : 933022, + "strand" : "+" + }, + "microhaplotypes" : + [ + { + "seq" : "TGGTTTTAATGAGGATGATTTAGATAAAGAGTTTTTTTTTGATTTGCCGTCGATTAGTGGTTTTTCAAGTAATGGTATGAAAAAATGTAATTTAAGAAATTTATTAAAAAGATTAGAA" + } + ], + "target_id" : 3 + }, + { + "mhap_location" : + { + "chrom" : "Pf3D7_08_v3", + "end" : 1269455, + "genome_id" : 0, + "start" : 1269319, + "strand" : "+" + }, + "microhaplotypes" : + [ + { + "seq" : "CCTTAGCATTAATAACACTTATAGGAGGTATTTATATGACTAAAGGAAGAAAAAGTTCCATATGGCATAATTCAGAAATAAATGATACACTTTATGATGTTGTTCTTGAAACAGTGAATCAAGGAAATACAGAT" + }, + { + "seq" : "CCTTAGCATTAATAACACTTATAGGAGGTATTTATATGACTAAAGGAAGAAAAAGTTCCATATGGCATAATTCAGAAATAAATGATACACTTTATGATATTGTTCTTGAAACAGTGAATCAAGGAAATACAGAT" + } + ], + "target_id" : 32 + }, + { + "mhap_location" : + { + "chrom" : "Pf3D7_08_v3", + "end" : 1344818, + "genome_id" : 0, + "start" : 1344685, + "strand" : "+" + }, + "microhaplotypes" : + [ + { + "seq" : "AATATATCTTTTACTTTATCTGTAAGTTTCATGGAATCTATTATTTCATCTGCATATTTTATTTTTGCCTCGTTTATATATTTACCTGCTTTTAATTTACATAAACATTTTTCTATTAAGTTTTGATCATT" + } + ], + "target_id" : 30 + }, + { + "mhap_location" : + { + "chrom" : "Pf3D7_08_v3", + "end" : 1363086, + "genome_id" : 0, + "start" : 1362890, + "strand" : "+" + }, + "microhaplotypes" : + [ + { + "seq" : "GTAAAAAAAAAGGGTTTTCCTAAAAAACCATCGGTTCATGGTTTTACACAGATGGTGTTTTTGCAGCTTACTAATATAGTCATGTATGCCCTTTGTTTTATGAGCCTTTCACAAATATATGCTTATTTCGAAAACGTGAATTTTTATATTATAAGCAATTTTCGTTTCCTTGAGAGATATTTTAATATATTCAA" + }, + { + "seq" : "GTAAAAAAAAAGGGTTTTCCTAAAAAACCATCGGTTCATGGTTTTACACAGATGGTGTTTTTGAAGATTACTAATATAGTCATGTATGCCCTTTGTTTTATGAGCCTTTCACAAATATATGCTTATTTCGAAAACGTGAATTTTTATATTATAAGCAATTTTCGTTTCCTTGAGAGATATTTTAATATATTCAA" + }, + { + "seq" : "GTAAACAAAAAGGGTTTTCCTAAAAAACCATTGGTTCATGGTTTTACACAGATGGTGTTTTTGCAGCTTACTAATATAGTCATGTATGCCCTTTGTTTTATGGACCTTTCACAAATATATGCTTATTTCGAAAACGTGAATTTTTATATTATAAGCAATTTTCGTTTCCTTGAGAGATATTTTAATATATTCAA" + } + ], + "target_id" : 28 + }, + { + "mhap_location" : + { + "chrom" : "Pf3D7_09_v3", + "end" : 517091, + "genome_id" : 0, + "start" : 516927, + "strand" : "+" + }, + "microhaplotypes" : + [ + { + "seq" : "TGTTTGTGTAATAAAGGATATTTCTATAATGTCAAGAAACAACAATGTGAAGAATGTCCCATAGGTTTTTATTGTCCAGAAATAAGCTCAAAAAATAATATAAAAAAACCTATCAAATGTCCTAAAAATTCCTCAAGTATAAAAAAAGGTATGTATATATCA" + }, + { + "seq" : "TGTTTGTGTAATAAAGGATATTTCTATAATGTCAAGAAACAACAATGTAAAGAATGTCCCATAGGTTTTTATTGTCCAGAAATAAGCTCAAAAAATAATATAAAAAAACCTATCAAATGTCCTAAAAATTCCTCAAGTATAAAAAAAGGTATGTATATATCA" + }, + { + "seq" : "TGTTTGTGTAATAAAGGATATTTCTATAATGTCAAGAAACAACAATGTAAAGAATGTCCCATAGGTTTTTATTGTCCAAAAATAAGCTCAAAAAATAATATAAAAAAACCTATCAAATGTCCTAAAAATTCCTCAAGTATAAAAAAAGGTATGTATATATCA" + } + ], + "target_id" : 26 + }, + { + "mhap_location" : + { + "chrom" : "Pf3D7_09_v3", + "end" : 596333, + "genome_id" : 0, + "start" : 596132, + "strand" : "+" + }, + "microhaplotypes" : + [ + { + "seq" : "TTATTTTCGTTTTTTTTTATATTATCATTATAATTATATGTATTTACAAAGAATTTATTATTATTTGTTTCTTTATAATTATATTCATTTTCTTTATTACTTAAGGAATTTATATTTGATAAAACTTGTTGTACTCTTTCTTCTTTGTTGATGTGAATATTTGAGAAAATAATAATAAATGTAATGACTAGGGCTATGT" + } + ], + "target_id" : 25 + }, + { + "mhap_location" : + { + "chrom" : "Pf3D7_09_v3", + "end" : 685791, + "genome_id" : 0, + "start" : 685600, + "strand" : "+" + }, + "microhaplotypes" : + [ + { + "seq" : "CAAAGGAACAAGATAATTTTTTCAATTTTTATAAAAGTAATATATATGATATGGAAAATAGAACATGTAATAATAATATATTACAATATTGTGTTATGAATAATAAATCATATTTATTTCATAATATATCATCCAAAAAAAATATATATATAAAAAAAAAGAATCATCAGTTTTCTTTATTCATATATT" + } + ], + "target_id" : 77 + }, + { + "mhap_location" : + { + "chrom" : "Pf3D7_09_v3", + "end" : 1179077, + "genome_id" : 0, + "start" : 1178893, + "strand" : "+" + }, + "microhaplotypes" : + [ + { + "seq" : "CAAATTACCCTTAGCCCCAGATATGGTAAAGACATATCACTGTTATAAATTAGGAAAGCAAGCAGCTAAATTATTAGAATCTATCATTTTAAAGAAAAAGTTCGTAAGATTTAGAGTTACTGATGCTATTGATGTATATGATTTCTTTTATATAAAGAAAGTTTTATCCAGTCGTATTAAGA" + }, + { + "seq" : "CAAATTATCCTTAGCCCCAGATATGGTAAAGACATATCACTGTTATAAATTAGGAAAGCAAGCAGCTGAATTATTAGAATCTATCATTTTAAAGAAAAAGTTCGTAAGATTTAGAGTTACTGATGCTATTGATGTATATGATTTCTTTTATATAAAGAAAGTTTTATCCAGTCGTATTAAGA" + } + ], + "target_id" : 89 + }, + { + "mhap_location" : + { + "chrom" : "Pf3D7_09_v3", + "end" : 1406540, + "genome_id" : 0, + "start" : 1406404, + "strand" : "+" + }, + "microhaplotypes" : + [ + { + "seq" : "AATTAATTTTAATGATGATGTTACTTTAGAAACACAATCCATGATAGCACACGGAGGGTCTTTGTCAGAAATAGAAGAAACTGGAGATTTATCTTCAGATGTTGATAGATTACTTTCATCAATCGAAACTACTC" + } + ], + "target_id" : 51 + }, + { + "mhap_location" : + { + "chrom" : "Pf3D7_09_v3", + "end" : 1437302, + "genome_id" : 0, + "start" : 1437113, + "strand" : "+" + }, + "microhaplotypes" : + [ + { + "seq" : "TAAAACCTGACAGCTTTGTACAGTTATATTTACCCAATTAGAATGTTCAAACATATTTAAGTGTTGCCATTCTTCAAATAATTTTTTTTCATATTCAGTTTTTGGTTGGTTTTTAAATTCTTTTGATAATGTACCTTCTGCGGATGGTATAGGGAAGTTAAAAATTTTATTACTTACTTTGTTTGAT" + } + ], + "target_id" : 87 + }, + { + "mhap_location" : + { + "chrom" : "Pf3D7_01_v3", + "end" : 531899, + "genome_id" : 0, + "start" : 531681, + "strand" : "+" + }, + "microhaplotypes" : + [ + { + "seq" : "AAAGAAAGATGTTAAGAAAAAAAAGATCGATATGATAAATATATTACACATTCCTACAAATAATTATAGCATGCCAAATGAAAAAGATATAAACAGTTATGAATTTTTTGGATCTGAACCTATTGAATTATATGATGGAAAATCTAATAAGAATTGTGTTATAACTAGCCAATCTTATATTTGTATTGAAAACCCGCATGCTGCCATATTATCCGA" + }, + { + "seq" : "AAAGAAAGATGTTAAGAAAAAAAAGATCGATATGATAAATATATTACACATACCTACAAATAATTATAACATGCCAAATGAAAAAGATATAAACAGTTATGAATTTTTTGGATCTGAACCTATTGAATTATATGATGTAAAATCTAATAAGAATTGTGTTATAACTAGCCAATCTTATATTTGTATTGAAAACCCGCATGCTGCCATATTATCCGA" + }, + { + "seq" : "AAAGAAAGATGTTAAGAAAAAAAAGATCGATATGATAAATATATTACACATACCTACAAATAATTATAACATGCCAAATAAAAAAGATATAAACAGTTATGAATTTTTTGGATCTGAACCTATTGAATTATATGATGTAAAATCTAATAAGAATTGTGTTATAACTAGCCAATCTTATATTTGTATTGAAAACCCGCATGCTGCCATATTATCCGA" + } + ], + "target_id" : 24 + }, + { + "mhap_location" : + { + "chrom" : "Pf3D7_10_v3", + "end" : 377208, + "genome_id" : 0, + "start" : 377094, + "strand" : "+" + }, + "microhaplotypes" : + [ + { + "seq" : "ACCAAAAAATGATACCTGTACGTTTTTCTCCAGGAGAAACAAAAAAATTAGAAAGGATTCTCAAAAAAGTAGACGACTTTTTCTGTGCCAATATTAAAGCGCAATATACCTG" + } + ], + "target_id" : 63 + }, + { + "mhap_location" : + { + "chrom" : "Pf3D7_10_v3", + "end" : 992543, + "genome_id" : 0, + "start" : 992370, + "strand" : "+" + }, + "microhaplotypes" : + [ + { + "seq" : "TTTTAAAAAAAAAAATTATGATATAAAATCTTCAATTAATAAAAGATCTATCCAGTTCTTTACAGACACTAATATAGATCATTATATAGCATATGAATATTATAAGGAGGACCGTACAGAATTTATATTAACTATTATGAATGAAAAAAATATTACTCATCAAGAAACTCA" + } + ], + "target_id" : 65 + }, + { + "mhap_location" : + { + "chrom" : "Pf3D7_10_v3", + "end" : 1386868, + "genome_id" : 0, + "start" : 1386699, + "strand" : "+" + }, + "microhaplotypes" : + [ + { + "seq" : "GAGAACAGGTTAAATATATTGAAGACGTGGTTTGATAATCAGGTATTTCTTTAATTAAATATTCATGATATTGTTCGTTAGATACATAAATTAATTCGTCCTCCACATTTTGCTGTTCTGTTATAATTTGTGAAGAAGCTTGGTTTGTCTTATTTGGTAATTGCTCT" + }, + { + "seq" : "GGGAACAGGTTAAATATATTGAAGACGTGGTTTGATAATCAGGTATTTCTTTAATTAAATATTCATGATATTGTTCGTTAGATACATAAATTAATTCGTCCTCCACATTTTGCTGTTCTGTTATAATTTGTGAAGAAGCTTGGTTTGTCTTATTTGGTAATTGCTCT" + } + ], + "target_id" : 34 + }, + { + "mhap_location" : + { + "chrom" : "Pf3D7_10_v3", + "end" : 1399710, + "genome_id" : 0, + "start" : 1399543, + "strand" : "+" + }, + "microhaplotypes" : + [ + { + "seq" : "ACATCAGAACATAGTAAAGATTTAAATAATAATGATTCAAAAAATGAATCTAGTGATATTATTTCAGAAAATAATAAATCAAATAAAGTAGAAAATCATTTTGAATCATTATCAGATTTAGAATTACTTGAAAATTCCTCACAAGATAATTTAGACAAAGATACA" + }, + { + "seq" : "ACATCAGAACATAGTAAAGATTTAAATAATAATGATTCAAAAAATGAATCTAGTGATATTATTTCAGAAAATAATAAATCAAATAAAGTACAAAATCATTTTGAATCATTATCAGATTTAGAATTACTTGAAAATTCCTCACAAGATAATTTAGACAAAGATACA" + } + ], + "target_id" : 71 + }, + { + "mhap_location" : + { + "chrom" : "Pf3D7_10_v3", + "end" : 1436681, + "genome_id" : 0, + "start" : 1436478, + "strand" : "+" + }, + "microhaplotypes" : + [ + { + "seq" : "GAGGAGAAACACGTTTTATCTCATAATTCATATGAGAAAACTAAAAATAATGAAAATAATAAATTTTTCGATAAGGATAAAGAGTTATCGATGTCTAATGTAAAAAATGTGTCACAAACAAATTTCAAAAGTCTTTTAAGAAATCTTGGTGTTTCAGAGAATATATTCCTTAAAGAAAATAAATTAAATAAGGAAGGGAAA" + }, + { + "seq" : "GAGAAGAAACACGTTTTATCTCATAATTCATATGAGAAAACTAAAAATAATGAAAATAATAAATTTTTCGATAAGGATAAAGAGTTAACGATGTCTAATGTAAAAAATGTGTCACAAACAAATTTCAAAAGTCTTTTAAGAAATCTTGGTGTTTCAGAGAATATATTCCTTAAAGAAAATAAATTAAATAAGGAAGGGAAA" + } + ], 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"seq" : "TCTCATTCCTTTGAAAATATGAACTATTCAACTCATCAAGGTTTTCATATGTTATTTCATAACTGCCATCATCTGAATCCTCTTCATCACTACTACTTAAAGAATGCTCTTCTACAGTTATATCTTCATAATGATTATTTTTAGGAAAATATTCTTCAGATCTTTCTATAAATTCTGTTCCATTA" + } + ], + "target_id" : 60 + }, + { + "mhap_location" : + { + "chrom" : "Pf3D7_11_v3", + "end" : 1552639, + "genome_id" : 0, + "start" : 1552429, + "strand" : "+" + }, + "microhaplotypes" : + [ + { + "seq" : "ATATCGACAATTATAAAGAAAAAATAGAAAATTTTAATGAAAGATATTATGAAGATGATTTAAGTTTCTTAAACTTTCCAGGAACCATAACAAGTTATGATAAAAACCATCAAAGAGATAAAAGAAAAAACTGTTTTGAAGAATATCTAGACAATAATAATTATTTTATTGATAGTAATCTAAAGGAAGTTATAGAAAATAATATATA" + } + ], + "target_id" : 19 + }, + { + "mhap_location" : + { + "chrom" : "Pf3D7_01_v3", + "end" : 532843, + "genome_id" : 0, + "start" : 532689, + "strand" : "+" + }, + "microhaplotypes" : + [ + { + "seq" : "CTTTCTTAATTCTATGAATGAAGAATATACGCATATTAATTTAAATAACTTTATACATAATGATAACAATGATAAAGACGAAAATTATACATTAGATCAGGTGGAAGAATATCCTATGACTAGTTATCAAAATAATATATACAAGGATTTTT" + }, + { + "seq" : "CTTTCTTAATTCTATGAATGAAGAATATACGCATATTAATTTAAATAACTTTATACATAATAATAACCATGATAATGACGAAAATTATACATTAGATCAGGTGGAAGGATATCCTATGACTAGTTATCAAAATAATATATACAAGGATTTTT" + } + ], + "target_id" : 40 + }, + { + "mhap_location" : + { + "chrom" : "Pf3D7_11_v3", + "end" : 1751054, + "genome_id" : 0, + "start" : 1750864, + "strand" : "+" + }, + "microhaplotypes" : + [ + { + "seq" : "TATTAAAAACAACAAATAAATTACCAAGGTCATGGAAAAAACTCTTGTTAAATCTATCCATTAGATTTCAAACAATACCTATAGGTGGTTCTATCGAAATCATATCAAAGGATGAGAAAAATATTTCTGTGACACGATCCAGTGAATATAATGCAACAACATATGAGCATTACACATTTCCCAAATGG" + }, + { + "seq" : "TATTAAAAACAACAGATAAATTACCAAGGTCATGGAAAAAACTCTTGTTAAATCTATCCATTAGATTTCAAACAATACCTATAGGTGGTTCTATCGAAATCATATCAAAGGATGAGAAAAATATTTCTATGACACGATCCAGTGAATATAATGCAACAACATATGAGCATTACACATTTCCCAAATGG" + } + ], + "target_id" : 21 + }, + { + "mhap_location" : + { + "chrom" : "Pf3D7_11_v3", + "end" : 1816424, + "genome_id" : 0, + "start" : 1816210, + "strand" : "+" + }, + "microhaplotypes" : + [ + { + "seq" : "TTGACTTCTCCGGGTTTGTTACATTATCATTACAACCAATATTATTAAGGTTAATATTATTTTTATCATTATTATTGTTGTTTTCATTTGTGTGGTTATATAATAACAATGATGTGTCGTCTATTGGATCATTTTGCACAAGGTCAATATCATTAGAATTATGTTTCATATTATTTGTATACATTTTTTTGTAATTATCATTTTTTCTTACT" + }, + { + "seq" : "TTGACTTCTCCGGGTTTGTTACATTATCATTACAACCAATATTATTAAGGTTAATATTATTTTTATCATTATTATTGTTGTTTTCATTTGTGTGGTTATATAATAACAATGATGTGTCGTCTATTGGATCATTTTGCACAAGGTCAATATCATTAGAATTATGTTTCCTATTATTTGTATACATTTTTTTGTAATTATCATTTTTTCTTACT" + } + ], + "target_id" : 18 + }, + { + "mhap_location" : + { + "chrom" : "Pf3D7_12_v3", + "end" : 63279, + "genome_id" : 0, + "start" : 63165, + "strand" : "+" + }, + "microhaplotypes" : + [ + { + "seq" : "ATAATTTCACCTTTTGAATTACATATGTCTGTATTCAAAAATTTTATATCTCTACTCCATATATTTATCTTTACACCCAAAAACAAAGCAATGAAAAAAACAACCCTTTCAT" + }, + { + "seq" : "ATAATTTCACCTTTTGAATTACATATGTCTGTATTCAAAAATTTTATATCTCTACTCCATATATTTATCTTTACACCCAAAAACAAAGTAATGAAAAAAATAACCCTTTCAT" + } + ], + "target_id" : 69 + }, + { + "mhap_location" : + { + "chrom" : "Pf3D7_12_v3", + "end" : 660009, + "genome_id" : 0, + "start" : 659890, + "strand" : "+" + }, + "microhaplotypes" : + [ + { + "seq" : "GGTCGACTTTTGGTGGTTTAACATTTTCAGCTATGAGTTTTTCGACTGATGGCAATCCTACTTTGATTAATTCCTTTAACATAAGTTTTGCGTGTTTTTTTACTTCTGATTTGATAT" + }, + { + "seq" : "GGTCGACTTTTGGTGGTTTAACATTTTCAGCTACGAGTTTTTCGACTGATGGCAATCCTACTTTGATTAATTCCTTTAACATAAGTTTTGCGTGTCTTTTTACTTCTGATTTGATAT" + } + ], + "target_id" : 16 + }, + { + "mhap_location" : + { + "chrom" : "Pf3D7_12_v3", + "end" : 684260, + "genome_id" : 0, + "start" : 684087, + "strand" : "+" + }, + "microhaplotypes" : + [ + { + "seq" : "ATATCAAGATGGTAGTATTGTTTTAGATGTTAGTAGTACGAGAGATAAACTTTATGGAGAAGTTGAGTGGGAAGGATATAAATTTGAACTTGTGGATACAGGAGGTTTAGTTTTTGAACAAGAAAAGTTTTCAAAAGAAATAAAGGATCAAATTCTTATGGCTCTAAAAGA" + }, + { + "seq" : "ATATCAAGATGGTAGTATTGTTTTAGATGTTAGTAGTACGAGAGATAAACTTTATGGAGAAGTTGAGTGGGAAGGATATAAATTTGAACTTGTGGATACAGGAGGTTTAGTTTTTGAACAAGAAAAGTTTTCAAAAGAAATAAAGGATCAAATTTTTATGGCTCTAAAAGA" + } + ], + "target_id" : 14 + }, + { + "mhap_location" : + 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"genome_id" : 0, + "start" : 2050129, + "strand" : "+" + }, + "microhaplotypes" : + [ + { + "seq" : "TTTAAACTTTGAATCTGTTCAATTAATAACACTTCATCATTGTCTTCGCCTTTTATAATATCTCCATGATTATGTGCTCCTCTAATTAAGGTATCACTAACCTGTTGTTCATCTGTCGCATGAGAACTAGTAGATATATCTGGTTTATTTTTTTTCTTTCTTTTTGTTATTTCTAATTTTTT" + }, + { + "seq" : "TTTAAACTTTGAATCTGTTCAATTAATAACACTTCATCATTGTCTTCTCCTTTTATAATATCCCCATGATTATGTGCTCCTCTAATTAAGGTATCACTAACCTGTTGTTCATCTGTCGCATGAGAACTAGTAGATATATCTGGTTTATTTTTTTTCTTTCTTTTTGTTATTTCTAATTTTTT" + } + ], + "target_id" : 36 + }, + { + "mhap_location" : + { + "chrom" : "Pf3D7_13_v3", + "end" : 103878, + "genome_id" : 0, + "start" : 103658, + "strand" : "+" + }, + "microhaplotypes" : + [ + { + "seq" : "ACTGATGTTAATGAAGGCCAAAATGGAAAAAGTTTAACACAAGAAAAAACCCTAAAACAAATTCCTTCGACATCACCAAATAATTTAGAACAAAAATTACAACAAACACATATTTCTTCTTCCCAACAAAAACATTTAATAAAAACTACTCCTACTTCAGATTCAACTACAACTTCATCAAGCTCTTCTGTTCCTCTTACAAAACAATCCCTTCATTC" + }, + { + "seq" : "ACTGATGTTAATGAAGGCCAAAATGGAAAACGTTTAACACAAGAAAAAACCCTAAAACAAATTCCTTCGACATCACCAAATAATTTAGAACAAAAATTACAACAAACACATATTTCTTCTTCCCAACAAAAACATTTAATAAAAACTACTCCTACTTCAGATTCAACTACAACTTCATCAAGCTCTTCTGTTCCTCTTACAAAACAATCCCTTCATTC" + } + ], + "target_id" : 13 + }, + { + "mhap_location" : + { + "chrom" : "Pf3D7_13_v3", + "end" : 156721, + "genome_id" : 0, + "start" : 156565, + "strand" : "+" + }, + "microhaplotypes" : + [ + { + "seq" : "ATAGAGTTATTATGTTCGAATTAATGACCAGATTGTTTCGATTTTATACAAAACCAATAGACCTTATTATTACTATGAATACACACAGATATGACACACCTATATTGTTAAAACATTCAAACAGCTTACAACTTATCTTATCAAATCAACAAAA" + } + ], + "target_id" : 17 + }, + { + "mhap_location" : + { + "chrom" : "Pf3D7_01_v3", + "end" : 534367, + "genome_id" : 0, + "start" : 534214, + "strand" : "+" + }, + "microhaplotypes" : + [ + { + "seq" : "GATAAAAAAAGAAAATGTAACAATCTACCTTGTGATTGTATCTTATGTAAAAAAAAGCACAATGTTTGTTATTGTAATATGTGTAAAAAGAAAGAAAAAAATATGAGAGAAGATTTATCGGTTGTAAAATATAATGAATATCCGATTAGTG" + }, + { + "seq" : "GATAAAAAAAGAAAATGTAATAATCTACTTTGTGATTGTATCTTATGTAAAAAAAAGCACAATGTTTGTTATTGTAATATGTGTAAAAAGAAAGAGAAAAATATGAGAGAAGATTTATCGGTTGTAAAATATAATGAATATCCGATTAGTG" + }, + { + "seq" : "GATAAAAAAAGAAAATGTAATAATCTACCTTGTGATTGTATCTTATGTAAAAAAAAGCACAATGTTTGTTATTGTAATATGTGTAAAAAGAAAGAAAAAAATATGAGAGAAGATTTATCGGTTGTAAAATATAATGAATATCCGATTAGTG" + } + ], + "target_id" : 84 + }, + { + "mhap_location" : + { + "chrom" : "Pf3D7_13_v3", + "end" : 1150492, + "genome_id" : 0, + "start" : 1150302, + "strand" : "+" + }, + "microhaplotypes" : + [ + { + "seq" : "TAAAAAAAGCAAACAAAAAGAAAAGAGAATGGAAGATTTAAGTATTGAGGAAAATTTGAAAGAGAAATTAATAAACCTAAATATTCAGAAACAGTATAGTGGTTTCCATATGAAAGAAATGGAGGAACAAAATATTCCTGAATTAAATATTCCACAACTTTCAGCTATTCATAATAGAGAAGATATGA" + }, + { + "seq" : "TAAAAAAAGCAAACAAAAAGAAAAGAGAATGGAAGATTTAAGTATTGAGGAAAATTTGAAAGAGAAATTAATAAACCTAAATATTCAGAAACAGTATAGTGGTTTCCATATGAAAGAAATGGAGGAACAAAATATTCCTGAATTAAATATTCCACAACTTTCAGCTACTCATAATAGAGAAGATATGA" + } + ], + "target_id" : 9 + }, + { + "mhap_location" : + { + "chrom" : "Pf3D7_13_v3", + "end" : 1419669, + "genome_id" : 0, + "start" : 1419542, + "strand" : "+" + }, + "microhaplotypes" : + [ + { + "seq" : "TGGTTTTTGTACTTTTTGTCCTTGTGTTGATATCTCTTGTTCATTTTTAGATTGAGTATCTGTTTCACTTTGTGCCTTTACCTTTGATAATACGTTTTTACCGAATAATCCTAAATTTTGGAATA" + }, + { + "seq" : "TGGTTTTTGTACTTCTTTTCCTTGTGTTGATATCTCTTGTTCATTTTTAGATTGAGTATCTGTTTCACTTTGTGCCTTTACCTTTGATAATACGTTTTTACCGAATAATCCTAAATTTTGGAATA" + } + ], + "target_id" : 8 + }, + { + "mhap_location" : + { + "chrom" : "Pf3D7_13_v3", + "end" : 1725569, + "genome_id" : 0, + "start" : 1725364, + "strand" : "+" + }, + "microhaplotypes" : + [ + { + "seq" : "CCAATACAATAAATTCTACCATTTGACGTAACACCACAATTATTTCTTCTAGGTATATTTAAATTACTTGAAACATACCATACATCTCTTAAACGATCATACACCTCAGTTTCAAATAAAGCCTTATAATCATAGTTATTACCACCAAAAACGTATAAGAAATTATTCAATACAGCACTTCCAAAATAAGCTTTTTTGGTAGA" + } + ], + "target_id" : 10 + }, + { + "mhap_location" : + { + "chrom" : "Pf3D7_13_v3", + "end" : 1876533, + "genome_id" : 0, + "start" : 1876351, + "strand" : "+" + 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"ATGGAAAAATGGAATATGAAGTATTAAGTGATGATAAAATAGTGTATGAAAATATACAACATGATTTATTAAAAACAATAGAAGATGATGAAGAAATGTTAAAAGGAACTGAAAGGAAGGATAATATAGATATACTGAGGACTCCTGGAAGGGGAGAATATGATATGTGGTCTACTTCTGGACTAGGGTTCTATGAAT" + } + ], + "target_id" : 31 + } + ] + }, + "sequencing_info" : + [ + { + "library_layout" : "paired-end", + "library_selection" : "RANDOM", + "library_source" : "GENOMIC", + "library_strategy" : "WGS", + "seq_date" : "2020-01-01", + "seq_instrument_model" : "Multiple", + "seq_platform" : "ILLUMINA", + "sequencing_info_name" : "Pf7Plus" + } + ], + "specimen_info" : + [ + { + "collection_country" : "India", + "collection_date" : "2012-08-25", + "geo_admin3" : "NA", + "host_taxon_id" : 9606, + "project_id" : 0, + "specimen_collect_device" : "Dried Blood spot", + "specimen_name" : "5tbx", + "specimen_store_loc" : "Multiple", + "specimen_taxon_id" : + [ + 5833 + ] + }, + { + "collection_country" : "Papua New Guinea", + "collection_date" : "2015", + "geo_admin3" : "NA", + "host_taxon_id" : 9606, + "project_id" : 0, + "specimen_collect_device" : "Dried Blood spot", + "specimen_name" : "XUC009", + "specimen_store_loc" : "Multiple", + "specimen_taxon_id" : + [ + 5833 + ] + } + ], + "target_info" : + [ + { + "forward_primer" : + { + "location" : + { + "chrom" : "Pf3D7_14_v3", + "end" : 1956129, + "genome_id" : 0, + "start" : 1956096, + "strand" : "+" + }, + "seq" : "TTTTTCTCCACTTTGTAATTTTTATTGTTGAAT" + }, + "gene_name" : "PF3D7_1447900", + "insert_location" : + { + "chrom" : "Pf3D7_14_v3", + "end" : 1956286, + "genome_id" : 0, + "ref_seq" : "ATATATATAAAGTTAAACCTATAAATAATACACTACCTAATAAACTATTCTTATATTTAAAAATAAATATAATACATGTTATTAATCCTTCTATTGTTGCCGGAATAATATACATTAAAACAGAACTCATCAAATTATTAGCACTCTCGGTACCTCT", + "start" : 1956129, + "strand" : "+" + }, + "reverse_primer" : + { + "location" : + { + "chrom" : "Pf3D7_14_v3", + "end" : 1956129, + "genome_id" : 0, + "start" : 1956096, + "strand" : "+" + }, + "seq" : "CGGGTGGTATCATGAGAATAGTTGAT" + }, + "target_attributes" : + [ + "Included", 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"CTTACAATGTTCTTCGCATTCGAAATTTTTTTCAGGATTACTTGAAAAGCCTTCTGGACAATTACAATATTCATATCCATGAGTATTCTTACAAACACCTTTTCCACAATTTAAAAAACATTTTTCTTCATTTAAA", + "start" : 120215, + "strand" : "+" + }, + "reverse_primer" : + { + "location" : + { + "chrom" : "Pf3D7_14_v3", + "end" : 120215, + "genome_id" : 0, + "start" : 120188, + "strand" : "+" + }, + "seq" : "ACAGAAAGAATGGTTTAGAAATGTACGAAT" + }, + "target_attributes" : + [ + "Included", + "Microhaplotype" + ], + "target_name" : "t90" + }, + { + "forward_primer" : + { + "location" : + { + "chrom" : "Pf3D7_01_v3", + "end" : 534215, + "genome_id" : 0, + "start" : 534182, + "strand" : "+" + }, + "seq" : "TTCAGATGTGATAAATATATGTGACATTTGTAA" + }, + "gene_name" : "PF3D7_0113800", + "insert_location" : + { + "chrom" : "Pf3D7_01_v3", + "end" : 534368, + "genome_id" : 0, + "ref_seq" : "TGATAAAAAAAGAAAATGTAACAATCTACCTTGTGATTGTATCTTATGTAAAAAAAAGCACAATGTTTGTTATTGTAATATGTGTAAAAAGAAAGAAAAAAATATGAGAGAAGATTTATCGGTTGTAAAATATAATGAATATCCGATTAGTGT", + "start" : 534215, + "strand" : "+" + }, + "reverse_primer" : + { + "location" : + { + "chrom" : "Pf3D7_01_v3", + "end" : 534215, + "genome_id" : 0, + "start" : 534182, + "strand" : "+" + }, + "seq" : "AAAAATATAAGAGATTCAAAGGGTCAGAC" + }, + "target_attributes" : + [ + "Included", + "Microhaplotype" + ], + "target_name" : "t8" + }, + { + "forward_primer" : + { + "location" : + { + "chrom" : "Pf3D7_08_v3", + "end" : 336468, + "genome_id" : 0, + "start" : 336438, + "strand" : "+" + }, + "seq" : "AATACATGAATATGATTAACAACGAACCCA" + }, + "gene_name" : "PF3D7_0806200", + "insert_location" : + { + "chrom" : "Pf3D7_08_v3", + "end" : 336647, + "genome_id" : 0, + "ref_seq" : "TAAATTTACAGAAAAATTTAGATTTAATCATATGGCTAAAAAAGAATATAAAAGAAGGAGAAGCTTTAATTTCTGATATACCCACATCAAGTTTTTTAAGGTGTACTACAAATTATAAATTTGTATTGCATCCACAATATGAAGATAGTAACTTGAGAAAGAGGGTTCAAGATTATTAT", + "start" : 336468, + "strand" : "+" + }, + "reverse_primer" : + { + "location" : + { + "chrom" : "Pf3D7_08_v3", + "end" : 336468, + "genome_id" : 0, + "start" : 336438, + "strand" : "+" + }, + "seq" : "ACTAAAAGGAAGACAAGCTGAAAACAT" + }, + "target_attributes" : + [ + "Included", + "Microhaplotype" + ], + "target_name" : "t47" + }, + { + "forward_primer" : + { + "location" : + { + "chrom" : "Pf3D7_08_v3", + "end" : 102326, + "genome_id" : 0, + "start" : 102298, + "strand" : "+" + }, + "seq" : "ACTTGTCGCTATACCTTCATCTATTGAA" + }, + "gene_name" : "PF3D7_0801300", + "insert_location" : + { + "chrom" : "Pf3D7_08_v3", + "end" : 102500, + "genome_id" : 0, + "ref_seq" : "TTAATTTTCTCAAGTAACATATTTTTGTCTTGACTACTTTCATCTGTAAATGGAACGACTACTCTTTGCTTACCTGCAAAAAGGACAACTGACATATGAGCCTTATCCTTACTTACATTCGAATTAAAGACCATAGATTCTAAAAATGGTATAGTTCCTTTTAACCAATAATCC", + "start" : 102326, + "strand" : "+" + }, + "reverse_primer" : + { + "location" : + { + "chrom" : "Pf3D7_08_v3", + "end" : 102326, + "genome_id" : 0, + "start" : 102298, + "strand" : "+" + }, + "seq" : "TGTTGAAGAGTCAAGTTTTGTTCAGAA" + }, + "target_attributes" : + [ + "Included", + "Microhaplotype" + ], + "target_name" : "t46" + }, + { + "forward_primer" : + { + "location" : + { + "chrom" : "Pf3D7_09_v3", + "end" : 1437114, + "genome_id" : 0, + "start" : 1437081, + "strand" : "+" + }, + "seq" : "CATCATAATCATCTAATGATGTTAATCCTTGTA" + }, + "gene_name" : "PF3D7_0936300", + "insert_location" : + { + "chrom" : "Pf3D7_09_v3", + "end" : 1437303, + "genome_id" : 0, + "ref_seq" : "CTAAAACCTGACAGCTTTGTACAGTTATATTTACCCAATTAGAATGTTCAAACATATTTAAGTGTTGCCATTCTTCAAATAATTTTTTTTCATATTCAGTTTTTGGTTGGTTTTTAAATTCTTTTGATACTGTACCTTCTGCGGATGGTATAGGGAAGTTAAAAATTTTATTACGTACTTTGTTTGATT", + "start" : 1437114, + "strand" : "+" + }, + "reverse_primer" : + { + "location" : + { + "chrom" : "Pf3D7_09_v3", + "end" : 1437114, + "genome_id" : 0, + "start" : 1437081, + "strand" : "+" + }, + "seq" : "GCACCATCATTAAATTTAGAAGAAACCC" + }, + "target_attributes" : + [ + "Included", + "Microhaplotype" + ], + "target_name" : "t59" + }, + { + "forward_primer" : + { + "location" : + { + "chrom" : "Pf3D7_14_v3", + "end" : 279663, + "genome_id" : 0, + "start" : 279635, + "strand" : "+" + }, + "seq" : "CGGATAAATGTTTAGTTATTAGCCAGGT" + }, + "gene_name" : "PF3D7_1407700", + "insert_location" : + { + "chrom" : "Pf3D7_14_v3", + "end" : 279786, + "genome_id" : 0, + "ref_seq" : "GAGTAATAGTGATTCATATAAGGTAAATTGTATTAATTTCTCTGAAGGATTTTGTTGCTGTCATCCAATAAATAATTTAGCACTATTATATGGAGAGTATCAACAAAATCAAGAATCAAAAAT", + "start" : 279663, + "strand" : "+" + }, + "reverse_primer" : + { + "location" : + { + "chrom" : "Pf3D7_14_v3", + "end" : 279663, + "genome_id" : 0, + "start" : 279635, + "strand" : "+" + }, + "seq" : "CATTACTTATGGGAAGTTTCGGTAATTTCATA" + }, + "target_attributes" : + [ + "Included", + "Microhaplotype" + ], + "target_name" : "t92" + }, + { + "forward_primer" : + { + "location" : + { + "chrom" : "Pf3D7_09_v3", + "end" : 1178894, + "genome_id" : 0, + "start" : 1178862, + "strand" : "+" + }, + "seq" : "GAACGTTGAGAAATTACCTTTAGAAGATTACT" + }, + "gene_name" : "PF3D7_0929400", + "insert_location" : + { + "chrom" : "Pf3D7_09_v3", + "end" : 1179078, + "genome_id" : 0, + "ref_seq" : "ACAAATTATCCTTAGCCCCAGATATGGTAAAGACATATCACTGTTATAAATTAGGAAAGCAAGCAGCTGAATTATTAGAATCTATCATTTTAAAGAAAAAGTTCGTAAGATTTAGAGTTACTGATGCTATTGATGTATATGATTTCTTTTATATAAAGAAAGTTTTATCCAGTCGTATTAAGAA", + "start" : 1178894, + "strand" : "+" + }, + "reverse_primer" : + { + "location" : + { + "chrom" : "Pf3D7_09_v3", + "end" : 1178894, + "genome_id" : 0, + "start" : 1178862, + "strand" : "+" + }, + "seq" : "GCTCTTTTGTCTTGTAAAAATTCATTATATTCT" + }, + "target_attributes" : + [ + "Included", + "Microhaplotype" + ], + "target_name" : "t57" + }, + { + "forward_primer" : + { + "location" : + { + "chrom" : "Pf3D7_03_v3", + "end" : 654002, + "genome_id" : 0, + "start" : 653972, + "strand" : "+" + }, + "seq" : "TCACCTAACGGTATATTTTTATCTCGTACA" + }, + "gene_name" : "PF3D7_0316200", + "insert_location" : + { + "chrom" : "Pf3D7_03_v3", + "end" : 654175, + "genome_id" : 0, + "ref_seq" : "ATATTTTTATAATTTCCTTTCATCTTATTTTTTTCTTTATATTTTTTTTTTTCATATGTAAGATTTATATAATCACTTTCGCTTTTTCTAACCCTTTTGAACTTTTTAAATGTACTTCGTTCATTATTTCTAATTCTCGTAAACACAAGAATAAATATTTTGATATATCTTAT", + "start" : 654002, + "strand" : "+" + }, + "reverse_primer" : + { + "location" : + { + "chrom" : "Pf3D7_03_v3", + "end" : 654002, + "genome_id" : 0, + "start" : 653972, + "strand" : "+" + }, + "seq" : "TTATGTATTTTTCAAAAATCGGCACGTTT" + }, + "target_attributes" : + [ + "Included", + "Microhaplotype" + ], + "target_name" : "t18" + }, + { + "forward_primer" : + { + "location" : + { + "chrom" : "Pf3D7_12_v3", + "end" : 943258, + "genome_id" : 0, + "start" : 943227, + "strand" : "+" + }, + "seq" : "ACCCTACTTATACAAAGAGATAAAGAAGTAG" + }, + "gene_name" : "PF3D7_1223400", + "insert_location" : + { + "chrom" : "Pf3D7_12_v3", + "end" : 943428, + "genome_id" : 0, + "ref_seq" : "AATCAACTATAATTAAAAATAGTGGAATTATTGAAAACTTTGGAGATATTGATTATATCTTTACGGATAAAACAGGAACACTAACAGAAAATGTCATGGTGCTTAAAGTTATACATATAGGTTTTGATGTTATACATGCAGAAAATGAAAAAAATTCCATACAAGGTAAT", + "start" : 943258, + "strand" : "+" + }, + "reverse_primer" : + { + "location" : + { + "chrom" : "Pf3D7_12_v3", + "end" : 943258, + "genome_id" : 0, + "start" : 943227, + "strand" : "+" + }, + "seq" : "AATTCCCTTTTTGTTTGGTTTCCATATT" + }, + "target_attributes" : + [ + "Included", + "Microhaplotype" + ], + "target_name" : "t75" + }, + { + "forward_primer" : + { + "location" : + { + "chrom" : "Pf3D7_04_v3", + "end" : 802525, + "genome_id" : 0, + "start" : 802494, + "strand" : "+" + }, + "seq" : "AAGCATCTGAACATTAAAGTTCAAACAAATA" + }, + "gene_name" : "PF3D7_0418000", + "insert_location" : + { + "chrom" : "Pf3D7_04_v3", + "end" : 802713, + "genome_id" : 0, + "ref_seq" : "TAAATTATTATAGAAAGATAGAAGTTATTTTATATGAATGGTTATATTTTCATTATAATAATGTATATAACACCAAAGTAAAAAAACAAAAATTTATATTTACCCAACAAAAAAAAGACATATCAAAACATAACAAGTTATATCTTCAGTATGATCAAAATAAAAGAAACTCTGAAATAGAACATACA", + "start" : 802525, + "strand" : "+" + }, + "reverse_primer" : + { + "location" : + { + "chrom" : "Pf3D7_04_v3", + "end" : 802525, + "genome_id" : 0, + "start" : 802494, + "strand" : "+" + }, + "seq" : "GCACATCGAATAATCTTCTTTGTGATT" + }, + "target_attributes" : + [ + "Included", + "Microhaplotype" + ], + "target_name" : "t27" + }, + { + "forward_primer" : + { + "location" : + { + "chrom" : "Pf3D7_08_v3", + "end" : 549993, + "genome_id" : 0, + "start" : 549962, + "strand" : "+" + }, + "seq" : "CATAAAAGAGGAAATCCACATACAATGGATA" + }, + "gene_name" : "PF3D7_0810800", + "insert_location" : + { + "chrom" : "Pf3D7_08_v3", + "end" : 550218, + "genome_id" : 0, + "ref_seq" : "AACTAACAAATTATGATAATCTAGTTTATGATATAAAAAATTATTTAGAACAAAGATTAAATTTTCTTGTATTAAATGGAATACCTCGTTATAGGATACTATTTGATATTGGATTAGGATTTGCGAAGAAACATGATCAATCTATTAAACTCTTACAAAATATACATGTATATGATGAGTATCCACTTTTTATTGGATATTCAAGAAAAAGATTTATTGCCCATT", + "start" : 549993, + "strand" : "+" + }, + "reverse_primer" : + { + "location" : + { + "chrom" : "Pf3D7_08_v3", + "end" : 549993, + "genome_id" : 0, + "start" : 549962, + "strand" : "+" + }, + "seq" : "GTGTATTTATTACAACATTTTGATCATTCATGC" + }, + "target_attributes" : + [ + "Included", + "DrugResistance" + ], + "target_name" : "t49" + }, + { + "forward_primer" : + { + "location" : + { + "chrom" : "Pf3D7_03_v3", + "end" : 618396, + "genome_id" : 0, + "start" : 618367, + "strand" : "+" + }, + "seq" : "GGGACACTACAGACAAAAATAAATGATCT" + }, + "gene_name" : "PF3D7_0315200", + "insert_location" : + { + "chrom" : "Pf3D7_03_v3", + "end" : 618581, + "genome_id" : 0, + "ref_seq" : "AAAAAGAGATTATAGAAGTGGAAAGAAGACATATATAATACAAGCTCTACAATATGCATTAACATATTATAGCAAACTTTCAAATAGAAAGGAAGCACCTAAAGTAACCATGTTATTTACAGATGGAAATGATTCCTATGAATCAGAAAAGGGATTACAGGATATTGCATTATTATATAGAAAAG", + "start" : 618396, + "strand" : "+" + }, + "reverse_primer" : + { + "location" : + { + "chrom" : "Pf3D7_03_v3", + "end" : 618396, + "genome_id" : 0, + "start" : 618367, + "strand" : "+" + }, + "seq" : "AGAAACTCCTACTACCAATAATTTGACATTTT" + }, + "target_attributes" : + [ + "Included", + "Microhaplotype" + ], + "target_name" : "t17" + }, + { + "forward_primer" : + { + "location" : + { + "chrom" : "Pf3D7_02_v3", + "end" : 805822, + "genome_id" : 0, + "start" : 805795, + "strand" : "+" + }, + "seq" : "TTGGAAAATTTGAGAATCCTATGTGCT" + }, + "gene_name" : "PF3D7_0220100", + "insert_location" : + { + "chrom" : "Pf3D7_02_v3", + "end" : 805942, + "genome_id" : 0, + "ref_seq" : "TTAATTATGAAGACAGTCTCACGACTTCATGTTATATTGATGAAAACAAATCCGATTCATCCTATGAAACTGAAGAAAATGTAAACTATAATAATAAAATGGGTAAACGCAAAAATTTAG", + "start" : 805822, + "strand" : "+" + }, + "reverse_primer" : + { + "location" : + { + "chrom" : "Pf3D7_02_v3", + "end" : 805822, + "genome_id" : 0, + "start" : 805795, + "strand" : "+" + }, + "seq" : "TTCGATTTGCCTACAATTTGTGATTCTA" + }, + "target_attributes" : + [ + "Included", + "Microhaplotype" + ], + "target_name" : "t13" + }, + { + "forward_primer" : + { + "location" : + { + "chrom" : "Pf3D7_04_v3", + "end" : 544718, + "genome_id" : 0, + "start" : 544686, + "strand" : "+" + }, + "seq" : "AACCCAGATAATCATTTATTAAATACAGACAC" + }, + "gene_name" : "PF3D7_0412300", + "insert_location" : + { + "chrom" : "Pf3D7_04_v3", + "end" : 544861, + "genome_id" : 0, + "ref_seq" : "ATATATTTTACATAATAACAATCCTTCATGTAATGATTATAATTTAAATAATCTTTCATTTAATATAAATAAATATATTAATGAAGAAAAAGGCAAAAATAAAAAAACAAATCAACATATATCAGAACAATTTTTATTTCCTA", + "start" : 544718, + "strand" : "+" + }, + "reverse_primer" : + { + "location" : + { + "chrom" : "Pf3D7_04_v3", + "end" : 544718, + "genome_id" : 0, + "start" : 544686, + "strand" : "+" + }, + "seq" : "CTGCAGCACACATTATAACTAAATGTG" + }, + "target_attributes" : + [ + "Included", + "Microhaplotype" + ], + "target_name" : "t24" + }, + { + "forward_primer" : + { + "location" : + { + "chrom" : "Pf3D7_14_v3", + "end" : 150105, + "genome_id" : 0, + "start" : 150075, + "strand" : "+" + }, + "seq" : "CCGAAAATAGAACTCCATATGTTCATTACC" + }, + "gene_name" : "PF3D7_1404300", + "insert_location" : + { + "chrom" : "Pf3D7_14_v3", + "end" : 150294, + "genome_id" : 0, + "ref_seq" : "ATAATAATAGTAATATAAAGAATTATTCAGCTGTAGATATATTCTCACCCAAAAAAACTGGAAAGGAATGTATTAAATGTCTCCCAGATAATTTTTGTGAATGCGAATGTAGTTGTAAAAATAAAACAGGTTTTTCAATGAAATATAGACATGCCAGTAAGGGATCTAAAGGATATAGTAAAAAAATGA", + "start" : 150105, + "strand" : "+" + }, + "reverse_primer" : + { + "location" : + { + "chrom" : "Pf3D7_14_v3", + "end" : 150105, + "genome_id" : 0, + "start" : 150075, + "strand" : "+" + }, + "seq" : "GTCTGGAACGAGAAGATGTCTTTG" + }, + "target_attributes" : + [ + "Included", + "Microhaplotype" + ], + "target_name" : "t91" + }, + { + "forward_primer" : + { + "location" : + { + "chrom" : "Pf3D7_02_v3", + "end" : 109807, + "genome_id" : 0, + "start" : 109776, + "strand" : "+" + }, + "seq" : "CCACCATTTCTTCATTTTAATTTTGAATGGT" + }, + "gene_name" : "PF3D7_0202100", + "insert_location" : + { + "chrom" : "Pf3D7_02_v3", + "end" : 109982, + "genome_id" : 0, + "ref_seq" : "AACTTATGTTCATGAGCTAATTTCCCACAAATACTCCATAACGAACTTTTCATTTTATTAAATTTATCTCTCAAAAGAGAATGACTATAATGCCATATTAAATACATATCTTTCCTTTCTAATTTTCCTGGTAATTCTATTATCATTCTTTCTAAATCTTCTTCTGTAACTTTTC", + "start" : 109807, + "strand" : "+" + }, + "reverse_primer" : + { + "location" : + { + "chrom" : "Pf3D7_02_v3", + "end" : 109807, + "genome_id" : 0, + "start" : 109776, + "strand" : "+" + }, + "seq" : "ACCATTTGGATTAAAACCTTCAGATTTAAATA" + }, + "target_attributes" : + [ + "Included", + "Microhaplotype" + ], + "target_name" : "t10" + }, + { + "forward_primer" : + { + "location" : + { + "chrom" : "Pf3D7_14_v3", + "end" : 3214351, + "genome_id" : 0, + "start" : 3214318, + "strand" : "+" + }, + "seq" : "TGTTAAAATATTTTCCAAAGAATTCAATTAGCG" + }, + "gene_name" : "PF3D7_1478000", + "insert_location" : + { + "chrom" : "Pf3D7_14_v3", + "end" : 3214478, + "genome_id" : 0, + "ref_seq" : "ATCGTTTTGAATTGTTAGAATTTAAAATGACGGAGGATTGTTATACAAAAATGTGGTTTGATTTTATGAGTGATTTTGGAATAGCTACAATGAATGAAACCGAACATACTAGATCTTTTTATGGATT", + "start" : 3214351, + "strand" : "+" + }, + "reverse_primer" : + { + "location" : + { + "chrom" : "Pf3D7_14_v3", + "end" : 3214351, + "genome_id" : 0, + "start" : 3214318, + "strand" : "+" + }, + "seq" : "TCAATTGATGGTTGCCTTTCGATT" + }, + "target_attributes" : + [ + "Included", + "Microhaplotype" + ], + "target_name" : "t100" + } + ], + "targeted_genomes" : + [ + { + "chromosomes" : + [ + "Pf3D7_01_v3", + "Pf3D7_02_v3", + "Pf3D7_03_v3", + "Pf3D7_04_v3", + "Pf3D7_05_v3", + "Pf3D7_06_v3", + "Pf3D7_07_v3", + "Pf3D7_08_v3", + "Pf3D7_09_v3", + "Pf3D7_10_v3", + "Pf3D7_11_v3", + "Pf3D7_12_v3", + "Pf3D7_13_v3", + "Pf3D7_14_v3", + "Pf3D7_API_v3", + "Pf3D7_MIT_v3" + ], + "genome_version" : "2020-09-01", + "gff_url" : "https://plasmodb.org/common/downloads/release-65/Pfalciparum3D7/gff/data/PlasmoDB-65_Pfalciparum3D7.gff", + "name" : "3D7", + "taxon_id" : + [ + 5833 + ], + "url" : "https://plasmodb.org/common/downloads/release-65/Pfalciparum3D7/fasta/data/PlasmoDB-65_Pfalciparum3D7_Genome.fasta" + } + ] +} diff --git a/tests/test_pmo_engine/test_pmo_reader.py b/tests/test_pmo_engine/test_pmo_reader.py index 5cef258..d8d4eb4 100755 --- a/tests/test_pmo_engine/test_pmo_reader.py +++ b/tests/test_pmo_engine/test_pmo_reader.py @@ -102,6 +102,48 @@ def test_combine_multiple_pmos(self): self.assertEqual(expected_pmo, combined_pmo) + def test_combine_multiple_pmos_fail_dup_specimen_names(self): + # the two files below have same specimen_names but have different meta so will fail when trying to combine + pmo_data_list = PMOReader.read_in_pmos( + [ + os.path.join( + os.path.dirname(self.working_dir), + "data/minimum_pmo_example_2_for_spec_dup_testing.json", + ), + os.path.join( + os.path.dirname(self.working_dir), "data/minimum_pmo_example_2.json" + ), + ] + ) + self.assertRaises(Exception, PMOReader.combine_multiple_pmos, pmo_data_list) + + def test_combine_multiple_pmos_fail_dup_library_sample_names(self): + # the two files below have same library sample names so will fail for duplicated library_sample_names + pmo_data_list_2 = PMOReader.read_in_pmos( + [ + os.path.join( + os.path.dirname(self.working_dir), + "data/minimum_pmo_example_2_for_library_sample_dup_testing.json", + ), + os.path.join( + os.path.dirname(self.working_dir), "data/minimum_pmo_example_2.json" + ), + ] + ) + self.assertRaises(Exception, PMOReader.combine_multiple_pmos, pmo_data_list_2) + + def test_combine_multiple_pmos_fail_for_combine_only_one_file(self): + # will fail for only having 1 PMO + pmo_data_list_2 = PMOReader.read_in_pmos( + [ + os.path.join( + os.path.dirname(self.working_dir), + "data/minimum_pmo_example_2_for_library_sample_dup_testing.json", + ) + ] + ) + self.assertRaises(Exception, PMOReader.combine_multiple_pmos, pmo_data_list_2) + if __name__ == "__main__": unittest.main()