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updating hivtrace test to work with new LANL dataset
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@stevenweaver
stevenweaver committed Sep 16, 2016
1 parent 71e8eac commit ae2aa56
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Showing 4 changed files with 1,497,833 additions and 791,007 deletions.
46 changes: 37 additions & 9 deletions test/rsrc/TEST.FASTA_OUTPUT.FASTA
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Original file line number Diff line number Diff line change
@@ -1,4 +1,32 @@
>Z|JP|K03455|2036
>HXB2_prrt
CCTCAGGTCACTCTTTGGCAACGACCCCTCGTCACAATAAAGATAGGGGGGCAACTAAAG
GAAGCTCTATTAGATACAGGAGCAGATGATACAGTATTAGAAGAAATGAGTTTGCCAGGA
AGATGGAAACCAAAAATGATAGGGGGAATTGGAGGTTTTATCAAAGTAAGACAGTATGAT
CAGATACTCATAGAAATCTGTGGACATAAAGCTATAGGTACAGTATTAGTAGGACCTACA
CCTGTCAACATAATTGGAAGAAATCTGTTGACTCAGATTGGTTGCACTTTAAATTTTCCC
ATTAGCCCTATTGAGACTGTACCAGTAAAATTAAAGCCAGGAATGGATGGCCCAAAAGTT
AAACAATGGCCATTGACAGAAGAAAAAATAAAAGCATTAGTAGAAATTTGTACAGAGATG
GAAAAGGAAGGGAAAATTTCAAAAATTGGGCCTGAAAATCCATACAATACTCCAGTATTT
GCCATAAAGAAAAAAGACAGTACTAAATGGAGAAAATTAGTAGATTTCAGAGAACTTAAT
AAGAGAACTCAAGACTTCTGGGAAGTTCAATTAGGAATACCACATCCCGCAGGGTTAAAA
AAGAAAAAATCAGTAACAGTACTGGATGTGGGTGATGCATATTTTTCAGTTCCCTTAGAT
GAAGACTTCAGGAAGTATACTGCATTTACCATACCTAGTATAAACAATGAGACACCAGGG
ATTAGATATCAGTACAATGTGCTTCCACAGGGATGGAAAGGATCACCAGCAATATTCCAA
AGTAGCATGACAAAAATCTTAGAGCCTTTTAGAAAACAAAATCCAGACATAGTTATCTAT
CAATACATGGATGATTTGTATGTAGGATCTGACTTAGAAATAGGGCAGCATAGAACAAAA
ATAGAGGAGCTGAGACAACATCTGTTGAGGTGGGGACTTACCACACCAGACAAAAAACAT
CAGAAAGAACCTCCATTCCTTTGGATGGGTTATGAACTCCATCCTGATAAATGGACAGTA
CAGCCTATAGTGCTGCCAGAAAAAGACAGCTGGACTGTCAATGACATACAGAAGTTAGTG
GGGAAATTGAATTGGGCAAGTCAGATTTACCCAGGGATTAAAGTAAGGCAATTATGTAAA
CTCCTTAGAGGAACCAAAGCACTAACAGAAGTAATACCACTAACAGAAGAAGCAGAGCTA
GAACTGGCAGAAAACAGAGAGATTCTAAAAGAACCAGTACATGGAGTGTATTATGACCCA
TCAAAAGACTTAATAGCAGAAATACAGAAGCAGGGGCAAGGCCAATGGACATATCAAATT
TATCAAGAGCCATTTAAAAATCTGAAAACAGGAAAATATGCAAGAATGAGGGGTGCCCAC
ACTAATGATGTAAAACAATTAACAGAGGCAGTGCAAAAAATAACCACAGAAAGCATAGTA
ATATGGGGAAAGACTCCTAAATTTAAACTGCCCATACAAAAGGAAACATGGGAAACATGG
TGGACAGAGTATTGGCAAGCCACCTGGATTCCTGAGTGGGAGTTTGTTAATACCCCTCCC
TTAGTGAAATTATGGTACCAGTTAGAGAAAGAACCCATAGTAGGAGCAGAAACCTTC
>Z|JP|K03455|2036|DUPLICATE
CCTCAAATCACTCTTTGGCAACGACCCTTAGTTACAGCAAAAATAGGGGAACAGCTAATA
GAAGCCCTATTAGACACAGGAGCAGATGATACAGTATTAGAAGAAATAAATTTACCAGGG
AAATGGAAACCAAAAATGATAGGGGGAATTGGAGGTTTTATCAAAGTAAGACAGTATGAT
Expand All @@ -17,7 +45,7 @@ CAATACATGGATGATTTATATGTAGGATCTGACTTAGAGATAGGGCAGCATAGAACAAAA
ATACAAGAGTTGAGAGAACATCTACTGAAGTGGGGATTAACCACACCAGATAAAAAACAT
CAGAAAGAACCTCCATTTCTTTGGATGGGATATGAACTCCATCCTGACAAATGGACAGTC
CAGCCTATAAAGCTGCCAGAAAAAGACAGCTGGACTGTCAATGATATACAGAAATTAGTG
GGAAAGCTAAATTGGGCAAGTCAGATTTATGCAGGAATTAAAGTAAGGCA-CTGTGTAAA
GGAAAGCTAAATTGGGCAAGTCAGATTTATGCAGGAATTAAAGTAAGGCARCTGTGTAAA
CTCCTCAGGGGAGCCAAAGCACTAACAGAGATAGTAACACTGACTGAGGAAGCAGAATTA
GAATTAGCAGAAAACAGAGAAATTCTAAAAGAACCTGTTCATGGRGTATATTATGATCCA
TTAAAAGACCTAGTAGCAGAAATACAGAAACAAGGGCAAGACCAATGGACATATCAAATT
Expand All @@ -26,7 +54,7 @@ ACTAATGATGTAAAACAATTAACAGAGGTAGTGCAAAAGGTGTCTACAGAAAGCATAGTA
ATATGGGGAAAGACCCCTAAATTTAGACTACCCATACAAAAAGAAACATGGGAAGCA---
------------------------------------------------------------
---------------------------------------------------------
>Z|JP|K03455|2036
>Z|JP|K03455|2036|DUPLICATE|DUPLICATE 2
CCTCAAATCACTCTTTGGCAACGACCCTTAGTTACAGCAAAAATAGGGGAACAGCTAATA
GAAGCCCTATTAGACACAGGAGCAGATGATACAGTATTAGAAGAAATAAATTTACCAGGG
AAATGGAAACCAAAAATGATAGGGGGAATTGGAGGTTTTATCAAAGTAAGACAGTATGAT
Expand Down Expand Up @@ -54,9 +82,9 @@ ACTAATGATGTAAAACAATTAACAGAGGTAGTGCAAAAGGTGTCTACAGAAAGCATAGTA
ATATGGGGAAAGACCCCTAAATTTAGACTACCCATACAAAAAGAAACATGGGAAGCA---
------------------------------------------------------------
---------------------------------------------------------
>Z|JP|K03455|2036
>Z|JP|K03455|2036|DUPLICATE|DUPLICATE 3
CCTCAAATCACTCTTTGGCAACGACCCTTAGTTACAGCAAAAATAGGGGAACAGCTAATA
GAAGCCCTATTAGACACAGGAGCAGATGATACAGTATTAGAAGAAATAAATTTAC-AGGG
GAAGCCCTATTAGACACAGGAGCAGATGATACAGTATTAGAAGAAATAAATTTAYCAGGG
AAATGGAAACCAAAAATGATAGGGGGAATTGGAGGTTTTATCAAAGTAAGACAGTATGAT
CAGATACCTATAGAAATCTGTGGACATAAAACTATAGGTACGATATTAATAGGACCTACA
CCTGTCAACATAATTGGAAGAAATCTGTTGACTCAGCTTGGCTGCACTTTAAATTTTCCC
Expand All @@ -82,7 +110,7 @@ ACTAATGATGTAAAACAATTAACAGAGGTAGTGCAAAAGGTGTCTACAGAAAGCATAGTA
ATATGGGGAAAGACCCCTAAATTTAGACTACCCATACAAAAAGAAACATGGGAAGCA---
------------------------------------------------------------
---------------------------------------------------------
>Z|JP|K03455|2036
>Z|JP|K03455|2036|DUPLICATE|DUPLICATE 4
CCTCAAATCACTCTTTGGCAACGACCCTTAGTTACAGCAAAAATAGGGGAACAGCTAATA
GAAGCCCTATTAGACACAGGAGCAGATGATACAGTATTAGAAGAAATAAATTTACCAGGG
AAATGGAAACCAAAAATGATAGGGGGAATTGGAGGTTTTATCAAGGTAAGACAATATGAT
Expand All @@ -104,13 +132,13 @@ CAGCCTATAAAGCTGCCAGAAAAAGACAGCTGGACTGTCAATGATATACAGAAATTAGTG
GGAAAGCTAAATTGGGCAAGTCAGATTTATGCAGGAATTAAAGTAAGGCAACTGTGTAAA
CTCCTCAGGGGAGCCAAAGCACTAACAGAGATAGTAACACTGACTGAGGAAGCAGAATTA
GAATTAGCAGAAAACAGAGAAATTCTAAAAGAACCTGTTCATGGAGTATATTATGATCCA
TCAAAAGACCTAGTAGCAGAAATACAGAAACAAGGGCAAG-AC-----------------
TCAAAAGACCTAGTAGCAGAAATACAGAAACAAGGGCAAGAC------------------
------------------------------------------------------------
------------------------------------------------------------
------------------------------------------------------------
------------------------------------------------------------
---------------------------------------------------------
>Z|JP|K03455|2036
>Z|JP|K03455|2036|DUPLICATE|DUPLICATE 5
CCTCAAATCACTCTTTGGCAACGACCCTTAGTTACAGCAAAAATAGGGGAACAGCTAATA
GAAGCCCTATTAGACACAGGAGCAGATGATACAGTATTAGAAGAAATAAATTTACCAGGG
AAATGGAAACCAAAAATGATAGGGGGAATTGGAGGTTTTATCAAAGTAAGACAATATGAT
Expand Down Expand Up @@ -138,7 +166,7 @@ ACTAATGATGTAAAACAATTAACAGAGGTAGTGCAAAAGGTGTCTACAGAAAGCATAGTA
ATATGGGGAAAGACCCCTAAATTTAGACTACCCATACAAAAAGAAACATGGGAAGCA---
------------------------------------------------------------
---------------------------------------------------------
>Z|JP|K03455|2036
>Z|JP|K03455|2036|DUPLICATE|DUPLICATE 6
CCTCAGGTCACTCTTTGGCAACGACCCCTCGTCACAATAAAGATAGGGGGGCAACTAAAG
GAAGCTCTATTAGATACAGGAGCAGATGATACAGTATTAGAAGAAATGAGTTTGCCAGGA
AGATGGAAACCAAAAATGATAGGGGGAATTGGAGGTTTTATCAAAGTAAGACAGTATGAT
Expand Down
2 changes: 1 addition & 1 deletion test/rsrc/TEST.FASTA_USER.TRACE.JSON
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Original file line number Diff line number Diff line change
@@ -1 +1 @@
{"Cluster sizes": [2, 3], "HIV Stages": {"E-3": 0, "E-1": 0, "A-2": 0, "E-2": 0, "A-3": 0, "A-1": 0, "Chronic": 5}, "Degrees": {"rho": 6.741657365453795, "rho CI": [1.457751736250405, 798.9933640071333], "Model": "Yule", "Distribution": [4, 1], "fitted": [0.8516685221760777, 0.110011136113623]}, "Nodes": [{"baseline": null, "cluster": 1, "attributes": {"SUBTYPE": "Z", "ACCESSION_NUMBER": "K03455", "YEAR_OF_SAMPLING": "2036", "COUNTRY": "JP", "SOURCE": "TEST.FASTA_output.fasta"}, "id": "Z|JP|K03455|2036|5", "hxb2_linked": "false", "edi": null}, {"baseline": null, "cluster": 1, "attributes": {"SUBTYPE": "Z", "ACCESSION_NUMBER": "K03455", "YEAR_OF_SAMPLING": "2036", "COUNTRY": "JP", "SOURCE": "TEST.FASTA_output.fasta"}, "id": "Z|JP|K03455|2036|4", "hxb2_linked": "false", "edi": null}, {"baseline": null, "cluster": 2, "attributes": {"SUBTYPE": "Z", "ACCESSION_NUMBER": "K03455", "YEAR_OF_SAMPLING": "2036", "COUNTRY": "JP", "SOURCE": "TEST.FASTA_output.fasta"}, "id": "Z|JP|K03455|2036|3", "hxb2_linked": "false", "edi": null}, {"baseline": null, "cluster": 2, "attributes": {"SUBTYPE": "Z", "ACCESSION_NUMBER": "K03455", "YEAR_OF_SAMPLING": "2036", "COUNTRY": "JP", "SOURCE": "TEST.FASTA_output.fasta"}, "id": "Z|JP|K03455|2036", "hxb2_linked": "false", "edi": null}, {"baseline": null, "cluster": 2, "attributes": {"SUBTYPE": "Z", "ACCESSION_NUMBER": "K03455", "YEAR_OF_SAMPLING": "2036", "COUNTRY": "JP", "SOURCE": "TEST.FASTA_output.fasta"}, "id": "Z|JP|K03455|2036|2", "hxb2_linked": "false", "edi": null}], "Edges": [{"sequences": ["Z|JP|K03455|2036|2", "Z|JP|K03455|2036|3"], "length": 0.0101121, "support": 0.0, "directed": false, "removed": false, "target": 2, "source": 4}, {"sequences": ["Z|JP|K03455|2036", "Z|JP|K03455|2036|3"], "length": 0.0146112, "support": 0.0, "directed": false, "removed": false, "target": 2, "source": 3}, {"sequences": ["Z|JP|K03455|2036|4", "Z|JP|K03455|2036|5"], "length": 0.00230851, "support": 0.0, "directed": false, "removed": false, "target": 0, "source": 1}], "Multiple sequences": {"Subjects with": 0, "Followup, days": null}, "Directed Edges": {"Reasons for unresolved directions": {"Missing dates": 3}, "Count": 0}, "Network Summary": {"Edges": 3, "Nodes": 5, "Sequences used to make links": 5, "Clusters": 2}}
{"Cluster sizes": [2, 3], "HIV Stages": {"Chronic": 5, "E-3": 0, "A-3": 0, "A-2": 0, "A-1": 0, "E-1": 0, "E-2": 0}, "Nodes": [{"baseline": null, "hxb2_linked": "false", "attributes": {"ACCESSION_NUMBER": "K03455", "SUBTYPE": "Z", "COUNTRY": "JP", "YEAR_OF_SAMPLING": "2036", "SOURCE": "TEST.FASTA_output.fasta"}, "id": "Z|JP|K03455|2036|5", "cluster": 1, "edi": null}, {"baseline": null, "hxb2_linked": "false", "attributes": {"ACCESSION_NUMBER": "K03455", "SUBTYPE": "Z", "COUNTRY": "JP", "YEAR_OF_SAMPLING": "2036", "SOURCE": "TEST.FASTA_output.fasta"}, "id": "Z|JP|K03455|2036|4", "cluster": 1, "edi": null}, {"baseline": null, "hxb2_linked": "false", "attributes": {"ACCESSION_NUMBER": "K03455", "SUBTYPE": "Z", "COUNTRY": "JP", "YEAR_OF_SAMPLING": "2036", "SOURCE": "TEST.FASTA_output.fasta"}, "id": "Z|JP|K03455|2036|3", "cluster": 2, "edi": null}, {"baseline": null, "hxb2_linked": "false", "attributes": {"ACCESSION_NUMBER": "K03455", "SUBTYPE": "Z", "COUNTRY": "JP", "YEAR_OF_SAMPLING": "2036", "SOURCE": "TEST.FASTA_output.fasta"}, "id": "Z|JP|K03455|2036", "cluster": 2, "edi": null}, {"baseline": null, "hxb2_linked": "false", "attributes": {"ACCESSION_NUMBER": "K03455", "SUBTYPE": "Z", "COUNTRY": "JP", "YEAR_OF_SAMPLING": "2036", "SOURCE": "TEST.FASTA_output.fasta"}, "id": "Z|JP|K03455|2036|2", "cluster": 2, "edi": null}], "Edges": [{"target": 2, "length": 0.0101121, "removed": false, "directed": false, "support": 0.0, "sequences": ["Z|JP|K03455|2036|2", "Z|JP|K03455|2036|3"], "source": 4}, {"target": 2, "length": 0.0146112, "removed": false, "directed": false, "support": 0.0, "sequences": ["Z|JP|K03455|2036", "Z|JP|K03455|2036|3"], "source": 3}, {"target": 0, "length": 0.00230851, "removed": false, "directed": false, "support": 0.0, "sequences": ["Z|JP|K03455|2036|4", "Z|JP|K03455|2036|5"], "source": 1}], "Degrees": {"fitted": [0.8516685221760777, 0.110011136113623], "Distribution": [4, 1], "Model": "Yule", "rho": 6.741657365453795, "rho CI": [1.457751736250405, 798.9933640071333]}, "Directed Edges": {"Reasons for unresolved directions": {"Missing dates": 3}, "Count": 0}, "Network Summary": {"Nodes": 5, "Clusters": 2, "Sequences used to make links": 5, "Edges": 3}, "Multiple sequences": {"Subjects with": 0, "Followup, days": null}}
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