Plan return object (data structure) from scoring script

ArtPoon commented 7 years ago

This should be a dictionary. We can base the structure of this on the XML output of the HIVdb algorithm:

<?xml version="1.0" encoding="UTF-8" standalone="no"?>
<DrugResistance_Interpretation xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:noNamespaceSchemaLocation="http://hivdb.stanford.edu/DR/schema/sierra.xsd">
    <algorithmName>HIVDB</algorithmName>
    <algorithmVersion>8.4</algorithmVersion>
    <webServiceVersion>2.0</webServiceVersion>
    <schemaVersion>1.1</schemaVersion>
    <submissionName/>
    <dateTime>2017-08-22 18:19:47.978</dateTime>
    <result>
        <success>true</success>
        <inputSequence>
            <md5sum>f8a9b4e6cfb7de1b4be1cb0eabd1a1cd</md5sum>
            <name>userinput unamed sample: 1</name>
            <sequence>CCTCAGGTCACTCTTTGGCAACGACCCCTCGTCACAATAAAGATAGGGGGGCAACTAAAGGAAGCTCTATTAGATACAGGAGCAGATGATACAGTATTAGAAGAAATGAGTTTGCCAGGAAGATGGAAACCAAAAATGATAGGGGGAATTGGAGGTTTTATCAAAGTAAGACAGTATGATCAGATACTCATAGAAATCTGTGGACATAAAGCTATAGGTACAGTATTAGTAGGACCTACACCTGTCAACATAATTGGAAGAAATCTGTTGACTCAGATTGGTTGCACTTTAAATTTTCCCATTAGCCCTATTGAGACTGTACCAGTAAAATTAAAGCCAGGAATGGATGGCCCAAAAGTTAAACAATGGCCATTGACAGAAGAAAAAATAAAAGCATTAGTAGAAATTTGTACAGAGATGGAAAAGGAAGGGAAAATTTCAAAAATTGGGCCTGAAAATCCATACAATACTCCAGTATTTGCCATAAAGAAAAAAGACAGTACTAAATGGAGAAAATTAGTAGATTTCAGAGAACTTAATAAGAGAACTCAAGACTTCTGGGAAGTTCAATTAGGAATACCACATCCCGCAGGGTTAAAAAAGAAAAAATCAGTAACAGTACTGGATGTGGGTGATGCATATTTTTCAGTTCCCTTAGATGAAGACTTCAGGAAGTATACTGCATTTACCATACCTAGTATAAACAATGAGACACCAGGGATTAGATATCAGTACAATGTGCTTCCACAGGGATGGAAAGGATCACCAGCAATATTCCAAAGTAGCATGACAAAAATCTTAGAGCCTTTTAGAAAACAAAATCCAGACATAGTTATCTATCAATACATGGATGATTTGTATGTAGGATCTGACTTAGAAATAGGGCAGCATAGAACAAAAATAGAGGAGCTGAGACAACATCTGTTGAGGTGGGGACTTACCACACCAGACAAAAAACATCAGAAAGAACCTCCATTCCTTTGGATGGGTTATGAACTCCATCCTGATAAATGGACAGTACAGCCTATAGTGCTGCCAGAAAAAGACAGCTGGACTGTCAATGACATACAGAAGTTAGTGGGGAAATTGAATTGGGCAAGTCAGATTTACCCAGGGATTAAAGTAAGGCAATTATGTAAACTCCTTAGAGGAACCAAAGCACTAACAGAAGTAATACCACTAACAGAAGAAGCAGAG</sequence>
        </inputSequence>
        <GAHypermutated>false</GAHypermutated>
        <geneData>
            <gene>PR</gene>
            <present>true</present>
            <consensus>PQITLWQRPLVTIKIGGQLKEALLDTGADDTVLEEMNLPGRWKPKMIGGIGGFIKVRQYDQILIEICGHKAIGTVLVGPTPVNIIGRNLLTQIGCTLNF</consensus>
            <alignedNASequence>CCTCAGGTCACTCTTTGGCAACGACCCCTCGTCACAATAAAGATAGGGGGGCAACTAAAGGAAGCTCTATTAGATACAGGAGCAGATGATACAGTATTAGAAGAAATGAGTTTGCCAGGAAGATGGAAACCAAAAATGATAGGGGGAATTGGAGGTTTTATCAAAGTAAGACAGTATGATCAGATACTCATAGAAATCTGTGGACATAAAGCTATAGGTACAGTATTAGTAGGACCTACACCTGTCAACATAATTGGAAGAAATCTGTTGACTCAGATTGGTTGCACTTTAAATTTT</alignedNASequence>
            <alignedAASequence>PQVTLWQRPLVTIKIGGQLKEALLDTGADDTVLEEMSLPGRWKPKMIGGIGGFIKVRQYDQILIEICGHKAIGTVLVGPTPVNIIGRNLLTQIGCTLNF</alignedAASequence>
            <firstAA>1</firstAA>
            <lastAA>99</lastAA>
            <subtype>
                <type>B (0.00%)</type>
                <percentSimilarity>100</percentSimilarity>
            </subtype>
            <mutation>
                <classification>OTHER</classification>
                <type>mutation</type>
                <mutationString>I3V</mutationString>
                <wildType>I</wildType>
                <position>3</position>
                <nucleicAcid>GTC</nucleicAcid>
                <translatedNA>V</translatedNA>
            </mutation>
            <mutation>
                <classification>OTHER</classification>
                <type>mutation</type>
                <mutationString>N37S</mutationString>
                <wildType>N</wildType>
                <position>37</position>
                <nucleicAcid>AGT</nucleicAcid>
                <translatedNA>S</translatedNA>
            </mutation>
            <quality/>
        </geneData>
        <geneData>
            <gene>RT</gene>
            <present>true</present>
            <consensus>PISPIETVPVKLKPGMDGPKVKQWPLTEEKIKALVEICTEMEKEGKISKIGPENPYNTPVFAIKKKDSTKWRKLVDFRELNKRTQDFWEVQLGIPHPAGLKKKKSVTVLDVGDAYFSVPLDKDFRKYTAFTIPSINNETPGIRYQYNVLPQGWKGSPAIFQSSMTKILEPFRKQNPDIVIYQYMDDLYVGSDLEIGQHRTKIEELRQHLLRWGFTTPDKKHQKEPPFLWMGYELHPDKWTVQPIVLPEKDSWTVNDIQKLVGKLNWASQIYAGIKVKQLCKLLRGTKALTEVIPLTEEAELELAENREILKEPVHGVYYDPSKDLIAEIQKQGQGQWTYQIYQEPFKNLKTGKYARMRGAHTNDVKQLTEAVQKIATESIVIWGKTPKFKLPIQKETWEAWWTEYWQATWIPEWEFVNTPPLVKLWYQLEKEPIVGAETFYVDGAANRETKLGKAGYVTDRGRQKVVSLTDTTNQKTELQAIHLALQDSGLEVNIVTDSQYALGIIQAQPDKSESELVSQIIEQLIKKEKVYLAWVPAHKGIGGNEQVDKLVSAGIRKVL</consensus>
            <alignedNASequence>CCCATTAGCCCTATTGAGACTGTACCAGTAAAATTAAAGCCAGGAATGGATGGCCCAAAAGTTAAACAATGGCCATTGACAGAAGAAAAAATAAAAGCATTAGTAGAAATTTGTACAGAGATGGAAAAGGAAGGGAAAATTTCAAAAATTGGGCCTGAAAATCCATACAATACTCCAGTATTTGCCATAAAGAAAAAAGACAGTACTAAATGGAGAAAATTAGTAGATTTCAGAGAACTTAATAAGAGAACTCAAGACTTCTGGGAAGTTCAATTAGGAATACCACATCCCGCAGGGTTAAAAAAGAAAAAATCAGTAACAGTACTGGATGTGGGTGATGCATATTTTTCAGTTCCCTTAGATGAAGACTTCAGGAAGTATACTGCATTTACCATACCTAGTATAAACAATGAGACACCAGGGATTAGATATCAGTACAATGTGCTTCCACAGGGATGGAAAGGATCACCAGCAATATTCCAAAGTAGCATGACAAAAATCTTAGAGCCTTTTAGAAAACAAAATCCAGACATAGTTATCTATCAATACATGGATGATTTGTATGTAGGATCTGACTTAGAAATAGGGCAGCATAGAACAAAAATAGAGGAGCTGAGACAACATCTGTTGAGGTGGGGACTTACCACACCAGACAAAAAACATCAGAAAGAACCTCCATTCCTTTGGATGGGTTATGAACTCCATCCTGATAAATGGACAGTACAGCCTATAGTGCTGCCAGAAAAAGACAGCTGGACTGTCAATGACATACAGAAGTTAGTGGGGAAATTGAATTGGGCAAGTCAGATTTACCCAGGGATTAAAGTAAGGCAATTATGTAAACTCCTTAGAGGAACCAAAGCACTAACAGAAGTAATACCACTAACAGAAGAAGCAGAG</alignedNASequence>
            <alignedAASequence>PISPIETVPVKLKPGMDGPKVKQWPLTEEKIKALVEICTEMEKEGKISKIGPENPYNTPVFAIKKKDSTKWRKLVDFRELNKRTQDFWEVQLGIPHPAGLKKKKSVTVLDVGDAYFSVPLDEDFRKYTAFTIPSINNETPGIRYQYNVLPQGWKGSPAIFQSSMTKILEPFRKQNPDIVIYQYMDDLYVGSDLEIGQHRTKIEELRQHLLRWGLTTPDKKHQKEPPFLWMGYELHPDKWTVQPIVLPEKDSWTVNDIQKLVGKLNWASQIYPGIKVRQLCKLLRGTKALTEVIPLTEEAE</alignedAASequence>
            <firstAA>1</firstAA>
            <lastAA>300</lastAA>
            <subtype>
                <type>B (0.00%)</type>
                <percentSimilarity>100</percentSimilarity>
            </subtype>
            <mutation>
                <classification>OTHER</classification>
                <type>mutation</type>
                <mutationString>K122E</mutationString>
                <wildType>K</wildType>
                <position>122</position>
                <nucleicAcid>GAA</nucleicAcid>
                <translatedNA>E</translatedNA>
            </mutation>
            <mutation>
                <classification>OTHER</classification>
                <type>mutation</type>
                <mutationString>F214L</mutationString>
                <wildType>F</wildType>
                <position>214</position>
                <nucleicAcid>CTT</nucleicAcid>
                <translatedNA>L</translatedNA>
            </mutation>
            <mutation>
                <classification>OTHER</classification>
                <type>mutation</type>
                <mutationString>A272P</mutationString>
                <wildType>A</wildType>
                <position>272</position>
                <nucleicAcid>CCA</nucleicAcid>
                <translatedNA>P</translatedNA>
            </mutation>
            <mutation>
                <classification>OTHER</classification>
                <type>mutation</type>
                <mutationString>K277R</mutationString>
                <wildType>K</wildType>
                <position>277</position>
                <nucleicAcid>AGG</nucleicAcid>
                <translatedNA>R</translatedNA>
            </mutation>
            <quality/>
        </geneData>
        <geneData>
            <gene>IN</gene>
            <present>false</present>
        </geneData>
        <sequenceQualityCounts>
            <insertions>0</insertions>
            <deletions>0</deletions>
            <ambiguous>0</ambiguous>
            <stops>0</stops>
            <frameshifts>0</frameshifts>
        </sequenceQualityCounts>
        <drugScore>
            <drugCode>ATV/r</drugCode>
            <genericName>atazanavir/r</genericName>
            <type>PI</type>
            <score>0</score>
            <resistanceLevel>1</resistanceLevel>
            <resistanceLevelText>Susceptible</resistanceLevelText>
            <threeStepResistanceLevel>S</threeStepResistanceLevel>
        </drugScore>
        <drugScore>
            <drugCode>DRV/r</drugCode>
            <genericName>darunavir/r</genericName>
            <type>PI</type>
            <score>0</score>
            <resistanceLevel>1</resistanceLevel>
            <resistanceLevelText>Susceptible</resistanceLevelText>
            <threeStepResistanceLevel>S</threeStepResistanceLevel>
        </drugScore>
        <drugScore>
            <drugCode>FPV/r</drugCode>
            <genericName>fosamprenavir/r</genericName>
            <type>PI</type>
            <score>0</score>
            <resistanceLevel>1</resistanceLevel>
            <resistanceLevelText>Susceptible</resistanceLevelText>
            <threeStepResistanceLevel>S</threeStepResistanceLevel>
        </drugScore>
        <drugScore>
            <drugCode>IDV/r</drugCode>
            <genericName>indinavir/r</genericName>
            <type>PI</type>
            <score>0</score>
            <resistanceLevel>1</resistanceLevel>
            <resistanceLevelText>Susceptible</resistanceLevelText>
            <threeStepResistanceLevel>S</threeStepResistanceLevel>
        </drugScore>
        <drugScore>
            <drugCode>LPV/r</drugCode>
            <genericName>lopinavir/r</genericName>
            <type>PI</type>
            <score>0</score>
            <resistanceLevel>1</resistanceLevel>
            <resistanceLevelText>Susceptible</resistanceLevelText>
            <threeStepResistanceLevel>S</threeStepResistanceLevel>
        </drugScore>
        <drugScore>
            <drugCode>NFV</drugCode>
            <genericName>nelfinavir</genericName>
            <type>PI</type>
            <score>0</score>
            <resistanceLevel>1</resistanceLevel>
            <resistanceLevelText>Susceptible</resistanceLevelText>
            <threeStepResistanceLevel>S</threeStepResistanceLevel>
        </drugScore>
        <drugScore>
            <drugCode>SQV/r</drugCode>
            <genericName>saquinavir/r</genericName>
            <type>PI</type>
            <score>0</score>
            <resistanceLevel>1</resistanceLevel>
            <resistanceLevelText>Susceptible</resistanceLevelText>
            <threeStepResistanceLevel>S</threeStepResistanceLevel>
        </drugScore>
        <drugScore>
            <drugCode>TPV/r</drugCode>
            <genericName>tipranavir/r</genericName>
            <type>PI</type>
            <score>0</score>
            <resistanceLevel>1</resistanceLevel>
            <resistanceLevelText>Susceptible</resistanceLevelText>
            <threeStepResistanceLevel>S</threeStepResistanceLevel>
        </drugScore>
        <drugScore>
            <drugCode>ABC</drugCode>
            <genericName>abacavir</genericName>
            <type>NRTI</type>
            <score>0</score>
            <resistanceLevel>1</resistanceLevel>
            <resistanceLevelText>Susceptible</resistanceLevelText>
            <threeStepResistanceLevel>S</threeStepResistanceLevel>
        </drugScore>
        <drugScore>
            <drugCode>AZT</drugCode>
            <genericName>zidovudine</genericName>
            <type>NRTI</type>
            <score>0</score>
            <resistanceLevel>1</resistanceLevel>
            <resistanceLevelText>Susceptible</resistanceLevelText>
            <threeStepResistanceLevel>S</threeStepResistanceLevel>
        </drugScore>
        <drugScore>
            <drugCode>D4T</drugCode>
            <genericName>stavudine</genericName>
            <type>NRTI</type>
            <score>0</score>
            <resistanceLevel>1</resistanceLevel>
            <resistanceLevelText>Susceptible</resistanceLevelText>
            <threeStepResistanceLevel>S</threeStepResistanceLevel>
        </drugScore>
        <drugScore>
            <drugCode>DDI</drugCode>
            <genericName>didanosine</genericName>
            <type>NRTI</type>
            <score>0</score>
            <resistanceLevel>1</resistanceLevel>
            <resistanceLevelText>Susceptible</resistanceLevelText>
            <threeStepResistanceLevel>S</threeStepResistanceLevel>
        </drugScore>
        <drugScore>
            <drugCode>FTC</drugCode>
            <genericName>emtricitabine</genericName>
            <type>NRTI</type>
            <score>0</score>
            <resistanceLevel>1</resistanceLevel>
            <resistanceLevelText>Susceptible</resistanceLevelText>
            <threeStepResistanceLevel>S</threeStepResistanceLevel>
        </drugScore>
        <drugScore>
            <drugCode>3TC</drugCode>
            <genericName>lamivudine</genericName>
            <type>NRTI</type>
            <score>0</score>
            <resistanceLevel>1</resistanceLevel>
            <resistanceLevelText>Susceptible</resistanceLevelText>
            <threeStepResistanceLevel>S</threeStepResistanceLevel>
        </drugScore>
        <drugScore>
            <drugCode>TDF</drugCode>
            <genericName>tenofovir</genericName>
            <type>NRTI</type>
            <score>0</score>
            <resistanceLevel>1</resistanceLevel>
            <resistanceLevelText>Susceptible</resistanceLevelText>
            <threeStepResistanceLevel>S</threeStepResistanceLevel>
        </drugScore>
        <drugScore>
            <drugCode>EFV</drugCode>
            <genericName>efavirenz</genericName>
            <type>NNRTI</type>
            <score>0</score>
            <resistanceLevel>1</resistanceLevel>
            <resistanceLevelText>Susceptible</resistanceLevelText>
            <threeStepResistanceLevel>S</threeStepResistanceLevel>
        </drugScore>
        <drugScore>
            <drugCode>ETR</drugCode>
            <genericName>etravirine</genericName>
            <type>NNRTI</type>
            <score>0</score>
            <resistanceLevel>1</resistanceLevel>
            <resistanceLevelText>Susceptible</resistanceLevelText>
            <threeStepResistanceLevel>S</threeStepResistanceLevel>
        </drugScore>
        <drugScore>
            <drugCode>NVP</drugCode>
            <genericName>nevirapine</genericName>
            <type>NNRTI</type>
            <score>0</score>
            <resistanceLevel>1</resistanceLevel>
            <resistanceLevelText>Susceptible</resistanceLevelText>
            <threeStepResistanceLevel>S</threeStepResistanceLevel>
        </drugScore>
        <drugScore>
            <drugCode>RPV</drugCode>
            <genericName>rilpivirine</genericName>
            <type>NNRTI</type>
            <score>0</score>
            <resistanceLevel>1</resistanceLevel>
            <resistanceLevelText>Susceptible</resistanceLevelText>
            <threeStepResistanceLevel>S</threeStepResistanceLevel>
        </drugScore>
        <scoreTable>
            <scoreRow>
                <score value="PI"/>
                <score value="ATV/r"/>
                <score value="DRV/r"/>
                <score value="FPV/r"/>
                <score value="IDV/r"/>
                <score value="LPV/r"/>
                <score value="NFV"/>
                <score value="SQV/r"/>
                <score value="TPV/r"/>
            </scoreRow>
            <scoreRow>
                <score value="Total:"/>
                <score class="PI" drug="ATV/r" value="0"/>
                <score class="PI" drug="DRV/r" value="0"/>
                <score class="PI" drug="FPV/r" value="0"/>
                <score class="PI" drug="IDV/r" value="0"/>
                <score class="PI" drug="LPV/r" value="0"/>
                <score class="PI" drug="NFV" value="0"/>
                <score class="PI" drug="SQV/r" value="0"/>
                <score class="PI" drug="TPV/r" value="0"/>
            </scoreRow>
        </scoreTable>
        <scoreTable>
            <scoreRow>
                <score value="NRTI"/>
                <score value="ABC"/>
                <score value="AZT"/>
                <score value="D4T"/>
                <score value="DDI"/>
                <score value="FTC"/>
                <score value="3TC"/>
                <score value="TDF"/>
            </scoreRow>
            <scoreRow>
                <score value="Total:"/>
                <score class="NRTI" drug="ABC" value="0"/>
                <score class="NRTI" drug="AZT" value="0"/>
                <score class="NRTI" drug="D4T" value="0"/>
                <score class="NRTI" drug="DDI" value="0"/>
                <score class="NRTI" drug="FTC" value="0"/>
                <score class="NRTI" drug="3TC" value="0"/>
                <score class="NRTI" drug="TDF" value="0"/>
            </scoreRow>
        </scoreTable>
        <scoreTable>
            <scoreRow>
                <score value="NNRTI"/>
                <score value="EFV"/>
                <score value="ETR"/>
                <score value="NVP"/>
                <score value="RPV"/>
            </scoreRow>
            <scoreRow>
                <score value="Total:"/>
                <score class="NNRTI" drug="EFV" value="0"/>
                <score class="NNRTI" drug="ETR" value="0"/>
                <score class="NNRTI" drug="NVP" value="0"/>
                <score class="NNRTI" drug="RPV" value="0"/>
            </scoreRow>
        </scoreTable>
    </result>
</DrugResistance_Interpretation>

ArtPoon commented 7 years ago

Proposed key-value pairs:

success: True or False
input sequence
gene data:
- protease
- consensus
- aligned sequence
- mutations (relative to reference)
- RT
- integrase
sequence quality counts
- in/dels
- frameshifts/stops
drugscore
- drug code (ie. ABC)
- generic name (ie. abacavir)
- type (ie. NRTI)
- score (ie. 0)
- resistance level (ie. 1)
- resistance level text (ie. "Susceptible")
- three step resistance level (ie. "S")
score table

ArtPoon commented 7 years ago

Output JSON like sierra-client.

jzpero commented 7 years ago

Progress on the output (which is really nested)

[x] drug resistance
- [x] drug scores
- [x] partial scores
- [x] mutation descriptions
[ ] aligned gene sequence
- [x] pretty pairwise mutation line
- [ ] alignedNAs

Progress on the program:

modified algorithm to output partial scores and mutation combinations associated with these scores

Other todo:

figure out which gene on pol an arbitrary sequence is, or contains
output subtype based on the sequence?
refactor and make sure errors are caught
clean up code, it's very messy right now
modify some data structures so it's easier to navigate and think about

ArtPoon commented 7 years ago

We cannot exactly duplicate the content of the JSON output from sierra-client because NucAmino does not return aligned sequences. In addition we do not know how subtype classifications are being generated.

make quick subtype prediction with TN93 (or similar genetic distance) to LANL subtype references, selecting the minimum.
do not return aligned sequences
compose script for comparing the important features of the JSONs produced by sierra-client and sierra-local

PoonLab / sierra-local

Plan return object (data structure) from scoring script #6