validate.py

from collections import defaultdict
from dotenv import load_dotenv
from langchain_google_genai import ChatGoogleGenerativeAI
from langchain_openai import ChatOpenAI
from prompt import *
from utils import call, permutate
from io import StringIO

import os
import pandas as pd
import re
import requests

load_dotenv()

raw_url = "https://www.ebi.ac.uk/gwas/api/search/downloads/alternative"
gwas_path = "resources/gwas_catalog.tsv"


if os.path.exists(gwas_path):
    gwas = pd.read_csv(gwas_path, delimiter='\t')[['DISEASE/TRAIT', 'CHR_ID', 'MAPPED_GENE', 'SNPS', 'P-VALUE', 'OR or BETA']]
else:
    data = requests.get(raw_url).content.decode('utf-8')
    gwas = pd.read_csv(StringIO(data), delimiter='\t')[['DISEASE/TRAIT', 'CHR_ID', 'MAPPED_GENE', 'SNPS', 'P-VALUE', 'OR or BETA']]

gwas_gene_rsid = gwas[['MAPPED_GENE', 'SNPS']]
gwas_gene_rsid.dropna(inplace=True, ignore_index=True)
gwas_gene_rsid['MAPPED_GENE'] = gwas_gene_rsid['MAPPED_GENE'].apply(lambda x: x.replace(' ', '').upper())


ground_truth = defaultdict(list)
for i in gwas_gene_rsid.index:
    gene = gwas_gene_rsid.loc[i, 'MAPPED_GENE']
    snp = gwas_gene_rsid.loc[i, 'SNPS']

    ground_truth[gene].append(snp)
    ground_truth[snp].append(gene)

    while '-' in gene:
        genes = gene.split('-')
        for gene in genes:
            ground_truth[gene].append(snp)
            ground_truth[snp].append(gene)
        gene = genes[-1]

class Validation():

    def __init__(self, llm):

        if llm.startswith('gpt'):
            self.llm = ChatOpenAI(temperature=0, model_name=llm)
        elif llm.startswith('gemini'):
            self.llm = ChatGoogleGenerativeAI(temperature=0, model=llm)
        else:
            self.llm = ChatOpenAI(temperature=0, model_name=llm, api_key=os.environ['PERPLEXITY_API_KEY'], base_url="https://api.perplexity.ai")

    def validate(self, df, api):

        df = df.fillna('')
        df['Genes'] = df['Genes'].str.replace(' ', '').str.upper()
        df['rsID'] = df['rsID'].str.lower()

        # Check if there is two gene names
        sym = [',', '/', '|', '-']
        for i in df.index:
            gene = df.loc[i, 'Genes']
            for s in sym:
                if s in gene:
                    genes = gene.split(s)
                    df.loc[i + 0.1], df.loc[i + 0.9] = df.loc[i], df.loc[i]
                    df = df.sort_index().reset_index(drop=True)
                    df.loc[i + 1, 'Genes'], df.loc[i + 2, 'Genes'] = genes[0], s.join(genes[1:])
                    break

        # Check if there is SNPs without 'rs'
        for i in df.index:
            safe = True
            snp = df.loc[i, 'rsID']
            snp = snp.replace('l', '1')
            if re.fullmatch('rs(\d)+|', snp):
                pass
            elif re.fullmatch('ts(\d)+', snp):
                snp = 'r' + snp[1:]
            elif re.fullmatch('s(\d)+', snp):
                snp = 'r' + snp
            elif re.fullmatch('(\d)+', snp):
                snp = 'rs' + snp
            else:
                safe = False
                df = df.drop(i)

            if safe:
                df.loc[i, 'rsID'] = snp

        df.reset_index(drop=True, inplace=True)
        df_clean = df.copy()

        # Validate genes and SNPs with APIs
        if api:
            dbsnp = {}
            for i in df.index:
                snp = df.loc[i, 'SNPs']
                gene = df.loc[i, 'Genes']

                if snp not in dbsnp:
                    try:
                        res = call(f'https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esummary.fcgi?db=snp&retmode=json&id={snp[2:]}').json()['result'][snp[2:]]
                        if 'error' not in res:
                            dbsnp[snp].extend([r['name'] for r in res['genes']])
                    except Exception as e:
                        print("Error at API", e)
                        pass

                    dbsnp[snp] = list(set(dbsnp[snp]))

                if gene not in dbsnp[snp]:
                    for other in permutate(gene):
                        if other in dbsnp[snp]:
                            df.loc[i, 'Genes'] = other
                            print(f'{gene} corrected to {other}')
                            break
                    else:
                        df = df.drop(i)

        # Check with GWAS ground truth
        for i in df.index:
            gene = df.loc[i, 'Genes']
            snp = df.loc[i, 'rsID']
            perms = permutate(gene)

            for perm in perms:
                if perm in ground_truth and snp in ground_truth[perm]:
                    df.loc[i, 'Genes'] = perm
                    if gene != perm:
                        print(f'{gene} corrected to {perm}')
                    else:
                        print(f'{gene} and {snp} safe')
                    break
            else:
                print(f'{gene} and {snp} not found')
                df = df.drop(i)

        df.reset_index(drop=True, inplace=True)

        return df, df_clean