getVariants.py

import streamlit as st
import pandas as pd
import requests
from st_aggrid import AgGrid

st.set_page_config(
    page_title="Get Variants",
    page_icon="random",
    layout="wide",
    initial_sidebar_state="collapsed"
)


@st.cache
def getFeatureCoordinates(gene):
    url = 'https://fhir-gen-ops.herokuapp.com/utilities/get-feature-coordinates?gene='+gene
    headers = {'Accept': 'application/json'}
    return requests.get(url, headers=headers)


@st.cache
def findSubjectVariants(subject, range):
    url = 'https://fhir-gen-ops.herokuapp.com/subject-operations/genotype-operations/$find-subject-variants?subject='+subject+'&ranges='+range+'&includeVariants=true'
    headers = {'Accept': 'application/json'}
    return requests.get(url, headers=headers)


@st.cache
def findSubjectStructuralIntersectingVariants(subject, range):
    url = 'https://fhir-gen-ops.herokuapp.com/subject-operations/genotype-operations/$find-subject-structural-intersecting-variants?subject='+subject+'&ranges='+range+'&includeVariants=true'
    headers = {'Accept': 'application/json'}
    return requests.get(url, headers=headers)


@st.cache
def findSubjectHaplotypes(subject, geneId):
    url = 'https://fhir-gen-ops.herokuapp.com/subject-operations/genotype-operations/$find-subject-haplotypes?subject='+subject+'&genes='+geneId
    headers = {'Accept': 'application/json'}
    return requests.get(url, headers=headers)


st.title("Get Variants")
st.markdown("This app illustrates [FHIR Genomics Operations](http://build.fhir.org/ig/HL7/genomics-reporting/operations.html) find-subject-variants, find-subject-intersecting-variants, \
    and find-subject-haplotypes; and the get-feature-coordinates utility. Enter patient and gene in the sidebar and click 'run'. All overlapping simple variants, structural variants, \
    and genotypes are returned.")

with st.sidebar:
    subject = st.text_input("Enter patient ID", value="HG00403")
    gene = st.text_input("Enter gene (HGNC gene symbol or code)", value="APC")

if st.sidebar.button("Run"):
    variantList = []
    geneFeatures = getFeatureCoordinates(gene)
    if len(geneFeatures.json()) > 0:
        geneId = geneFeatures.json()[0]["geneId"]
        range = geneFeatures.json()[0]["build38Coordinates"]
        # get and parse simple variants
        response = findSubjectVariants(subject, range)
        if response.status_code == 200:
            for i in response.json()["parameter"]:
                for j in i["part"]:
                    if j["name"] == "variant":
                        dnaChangeType = "simple"
                        sourceClass, allelicState, SPDI, alleleFreq, location, refSeq, start, end, genotype, copyNumber = "", "", "", "", "", "", "", "", "", ""
                        for k in j["resource"]["component"]:
                            if k["code"]["coding"][0]["code"] == "48002-0":
                                sourceClass = k["valueCodeableConcept"]["coding"][0]["display"]
                            elif k["code"]["coding"][0]["code"] == "53034-5":
                                allelicState = k["valueCodeableConcept"]["coding"][0]["display"]
                            elif k["code"]["coding"][0]["code"] == "81252-9":
                                SPDI = k["valueCodeableConcept"]["coding"][0]["display"]
                            elif k["code"]["coding"][0]["code"] == "81258-6":
                                alleleFreq = k["valueQuantity"]["value"]
                        variantList.append({
                            "DNA Change Type": dnaChangeType,
                            "Source Class": sourceClass,
                            "SPDI": SPDI,
                            "Location": location,
                            "Genotype": genotype,
                            "Allelic State": allelicState,
                            "Copy Number": copyNumber,
                            "Allele Frequeny": alleleFreq})
        # get and parse structural variants
        response = findSubjectStructuralIntersectingVariants(subject, range)
        if response.status_code == 200:
            for i in response.json()["parameter"]:
                for j in i["part"]:
                    if j["name"] == "variant":
                        sourceClass, allelicState, SPDI, alleleFreq, location, refSeq, start, end, genotype, dnaChangeType, copyNumber = "", "", "", "", "", "", "", "", "", "", ""
                        for k in j["resource"]["component"]:
                            if k["code"]["coding"][0]["code"] == "48002-0":
                                sourceClass = k["valueCodeableConcept"]["coding"][0]["display"]
                            elif k["code"]["coding"][0]["code"] == "53034-5":
                                allelicState = k["valueCodeableConcept"]["coding"][0]["display"]
                            elif k["code"]["coding"][0]["code"] == "81258-6":
                                alleleFreq = k["valueQuantity"]["value"]
                            elif k["code"]["coding"][0]["code"] == "48013-7":
                                refSeq = k["valueCodeableConcept"]["coding"][0]["code"]
                            elif k["code"]["coding"][0]["code"] == "82155-3":
                                copyNumber = k["valueQuantity"]["value"]
                            elif k["code"]["coding"][0]["code"] == "48019-4":
                                dnaChangeType = k["valueCodeableConcept"]["coding"][0]["display"]
                            elif k["code"]["coding"][0]["code"] == "81302-2":
                                start = k["valueRange"]["low"]["value"]
                                end = k["valueRange"]["high"]["value"]
                            location = f"{refSeq}:{start}-{end}"
                        variantList.append({
                            "DNA Change Type": dnaChangeType,
                            "Source Class": sourceClass,
                            "SPDI": SPDI,
                            "Location": location,
                            "Genotype": genotype,
                            "Allelic State": allelicState,
                            "Copy Number": copyNumber,
                            "Allele Frequeny": alleleFreq})
        # get and parse haplotypes
        response = findSubjectHaplotypes(subject, geneId)
        if response.status_code == 200:
            for i in response.json()["parameter"]:
                for j in i["part"]:
                    if j["name"] == "genotype":
                        dnaChangeType = "genotype"
                        sourceClass, allelicState, SPDI, alleleFreq, location, refSeq, start, end, genotype, copyNumber = "", "", "", "", "", "", "", "", "", ""
                        genotype = j["resource"]["valueCodeableConcept"]["coding"][0]["display"]
                        variantList.append({
                            "DNA Change Type": dnaChangeType,
                            "Source Class": sourceClass,
                            "SPDI": SPDI,
                            "Location": location,
                            "Genotype": genotype,
                            "Allelic State": allelicState,
                            "Copy Number": copyNumber,
                            "Allele Frequeny": alleleFreq})

    data = (pd.DataFrame(variantList))
    AgGrid(data, enable_enterprise_modules=True, update_mode="value_changed", allow_unsafe_jscode=True)
    st.download_button("Download table (json)", data.T.to_json(), mime="application/json")
    st.download_button("Download table (csv)", data.to_csv(), mime="text/csv")