From 207cffd56913ce14a67dd1dbcebc9ad12f557688 Mon Sep 17 00:00:00 2001 From: Alex Lubbock Date: Tue, 15 Oct 2024 15:16:53 +0100 Subject: [PATCH] feat: blast search dataset vs database (#99) * style: fix deprecated dockerfile syntax * feat: add BLAST to backend container * wip: all-vs-all BLAST * wip: blastp * fix: empty state for blast results * fix: ci build of test env * fix: bytes decoding in exception message * ci: ignore flake8 false positives * fix: restore types-pytz in dev env --- .github/workflows/ci.yml | 2 + backend/Dockerfile | 41 ++- backend/Pipfile.lock | 328 +++++++++--------- backend/antigenapi/bioinformatics/__init__.py | 0 backend/antigenapi/bioinformatics/blast.py | 137 ++++++++ .../imgt.py} | 0 backend/antigenapi/models.py | 2 +- backend/antigenapi/tests/test_parsers.py | 2 +- backend/antigenapi/views_old.py | 87 ++++- backend/setup.cfg | 10 +- docker-compose.yml | 4 + frontend/Dockerfile | 2 +- frontend/src/App.js | 6 + frontend/src/LoadingLlama.js | 54 +++ frontend/src/crudtemplates/BlastResults.js | 152 ++++++++ .../src/crudtemplates/SequencingResults.js | 10 +- 16 files changed, 642 insertions(+), 195 deletions(-) create mode 100644 backend/antigenapi/bioinformatics/__init__.py create mode 100644 backend/antigenapi/bioinformatics/blast.py rename backend/antigenapi/{bioinformatics.py => bioinformatics/imgt.py} (100%) create mode 100644 frontend/src/LoadingLlama.js create mode 100644 frontend/src/crudtemplates/BlastResults.js diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml index d9e27bc3..380799e5 100644 --- a/.github/workflows/ci.yml +++ b/.github/workflows/ci.yml @@ -37,6 +37,8 @@ jobs: with: context: ${{ matrix.component }} target: dev + build-args: | + PIPENV_SYNC_FLAGS=--dev platforms: linux/amd64 load: true tags: antigen-app-dev-${{ matrix.component }}:latest diff --git a/backend/Dockerfile b/backend/Dockerfile index 1d7d7098..16035c59 100644 --- a/backend/Dockerfile +++ b/backend/Dockerfile @@ -1,14 +1,21 @@ -FROM python:3.11-bullseye AS builder +FROM quay.io/rosalindfranklininstitute/blast:2.16.0 AS blast -RUN pip install --user wheel pipenv +FROM python:3.13-bookworm AS builder + +RUN pip install --upgrade pip wheel pipenv + +RUN adduser --uid 10191 --group --system --no-create-home nonroot +RUN chown -R nonroot:nonroot /usr/src +USER nonroot +WORKDIR /usr/src # Tell pipenv to create venv in the current directory ENV PIPENV_VENV_IN_PROJECT=1 COPY Pipfile Pipfile.lock pyproject.toml setup.cfg /usr/src/ -WORKDIR /usr/src -RUN /root/.local/bin/pipenv sync +ARG PIPENV_SYNC_FLAGS= +RUN pipenv sync ${PIPENV_SYNC_FLAGS} COPY manage.py /usr/src/ COPY antigendjango /usr/src/antigendjango @@ -16,14 +23,23 @@ COPY antigenapi /usr/src/antigenapi RUN DJANGO_CI=true .venv/bin/python manage.py collectstatic --noinput -FROM python:3.11-slim-bullseye AS prod +FROM python:3.13-slim-bookworm AS prod +# liblmdb-dev required by BLAST RUN apt-get update && apt-get install -y \ libxml2 \ media-types \ + liblmdb-dev \ && rm -rf /var/lib/apt/lists/* -RUN mkdir -v /usr/src/.venv +RUN adduser --uid 10191 --group --system --no-create-home nonroot +RUN chown -R nonroot:nonroot /usr/src +USER nonroot +WORKDIR /usr/src + +# blastp and makeblastdb commands +COPY --from=blast /blast/ReleaseMT/bin/blastp /usr/local/bin/blastp +COPY --from=blast /blast/ReleaseMT/bin/makeblastdb /usr/local/bin/makeblastdb COPY --from=builder /usr/src/.venv/ /usr/src/.venv/ COPY --from=builder /usr/src/static/ /api_data/static/ @@ -34,16 +50,17 @@ COPY uwsgi.ini /usr/src WORKDIR /usr/src -RUN addgroup --gid 10191 nonroot -RUN adduser --uid 10191 --gid 10191 --system --no-create-home nonroot -USER nonroot - CMD [".venv/bin/uwsgi", "--ini", "uwsgi.ini"] FROM builder AS dev -ENV PATH="$PATH:/root/.local/bin:/usr/src/.venv/bin" +# liblmdb-dev required by BLAST +USER root +RUN apt update && apt install -y liblmdb-dev && rm -rf /var/lib/apt/lists/* +USER nonroot -RUN pipenv sync --dev +# blastp and makeblastdb commands +COPY --from=blast /blast/ReleaseMT/bin/blastp /usr/local/bin/blastp +COPY --from=blast /blast/ReleaseMT/bin/makeblastdb /usr/local/bin/makeblastdb CMD ["pipenv", "run", "python", "manage.py", "runserver", "0.0.0.0:8080"] diff --git a/backend/Pipfile.lock b/backend/Pipfile.lock index 839d1ede..26bc531f 100644 --- a/backend/Pipfile.lock +++ b/backend/Pipfile.lock @@ -1,7 +1,7 @@ { "_meta": { "hash": { - "sha256": "418cdcd38a65d5257a15593a3da0757d179fa7a933e775d6b35a23b6197640c6" + "sha256": "125465e4974ab903b494eb09a16831177ac48ac052f095ca2555a027cb6433c0" }, "pipfile-spec": 6, "requires": {}, @@ -74,18 +74,19 @@ }, "boto3": { "hashes": [ - "sha256:385ca77bf8ea4ab2d97f6e2435bdb29f77d9301e2f7ac796c2f465753c2adf3c", - "sha256:470d981583885859fed2fd1c185eeb01cc03e60272d499bafe41b12625b158c8" + "sha256:33c6a7aeab316f7e0b3ad8552afe95a4a10bfd58519d00741c4d4f3047da8382", + "sha256:9352f6d61f15c789231a5d608613f03425059072ed862c32e1ed102b17206abf" ], - "version": "==1.35.37" + "markers": 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"sha256:491feb020dca48ccc562a8c0cbe8df07ee13078df59813b83959cbdada312ea3" ], - "markers": "python_version >= '2.7' and python_version not in '3.0, 3.1, 3.2, 3.3'", - "version": "==2.3.1" + "markers": "python_version >= '3.6'", + "version": "==2.5.0" }, "pytest": { "hashes": [ @@ -1597,10 +1595,10 @@ }, "pytest-flake8": { "hashes": [ - "sha256:358d449ca06b80dbadcb43506cd3e38685d273b4968ac825da871bd4cc436202", - "sha256:f1b19dad0b9f0aa651d391c9527ebc20ac1a0f847aa78581094c747462bfa182" + "sha256:44a805bd7dce16a0de921a1292df639b70d56ca621a68d4bb515e09858e6e429", + "sha256:7b8dfa77be42b5cec901b6b67eafb18d47ae6a05c4deac89399dba4c3591ce4d" ], - "version": "==1.1.0" + "version": "==1.2.2" }, "pytest-mypy": { "hashes": [ diff --git a/backend/antigenapi/bioinformatics/__init__.py b/backend/antigenapi/bioinformatics/__init__.py new file mode 100644 index 00000000..e69de29b diff --git a/backend/antigenapi/bioinformatics/blast.py b/backend/antigenapi/bioinformatics/blast.py new file mode 100644 index 00000000..7e26de38 --- /dev/null +++ b/backend/antigenapi/bioinformatics/blast.py @@ -0,0 +1,137 @@ +import os +import subprocess +from tempfile import TemporaryDirectory +from typing import Optional + +from ..models import SequencingRunResults +from .imgt import read_airr_file + +# https://www.ncbi.nlm.nih.gov/books/NBK279684/table/appendices.T.options_common_to_all_blast/ +BLAST_FMT_MULTIPLE_FILE_BLAST_JSON = "15" +BLAST_NUM_THREADS = 4 + + +def get_db_fasta(include_run: Optional[int] = None, exclude_run: Optional[int] = None): + """Get the sequencing database in fasta format. + + Args: + include_run (int, optional): Sequencing run ID to include. + Defaults to None. + exclude_run (int, optional): Sequencing run ID to exclude. + Defaults to None. + + Returns: + str: Sequencing run as a FASTA format string + """ + fasta_data = "" + query = SequencingRunResults.objects.all() + if include_run: + query = query.filter(sequencing_run_id=include_run) + if exclude_run: + query = query.exclude(sequencing_run_id=exclude_run) + for sr in query: + airr_file = read_airr_file( + sr.airr_file, usecols=("sequence_id", "sequence_alignment_aa") + ) + airr_file = airr_file[airr_file.sequence_alignment_aa.notna()] + if not airr_file.empty: + for _, row in airr_file.iterrows(): + fasta_data += f"> {row.sequence_id}\n" + fasta_data += f"{row.sequence_alignment_aa.replace('.', '')}\n" + return fasta_data + + +def get_sequencing_run_fasta(sequencing_run_id: int): + """Get sequencing run in BLAST format. + + Args: + sequencing_run_id (int): Sequencing run ID + + Returns: + str: Sequencing run as a FASTA format string + """ + return get_db_fasta(include_run=sequencing_run_id) + + +def run_blastp( + sequencing_run_id: int, outfmt: str = BLAST_FMT_MULTIPLE_FILE_BLAST_JSON +): + """Run blastp for a sequencing run vs rest of database. + + Args: + sequencing_run_id (int): Sequencing run ID. + + Returns: + JSONResponse: Single file BLAST JSON + """ + db_data = get_db_fasta() + if not db_data: + return None + query_data = get_sequencing_run_fasta(sequencing_run_id) + if not query_data: + return None + + # Write the DB to disk as .fasta format + with TemporaryDirectory() as tmp_dir: + fasta_filename = os.path.join(tmp_dir, "db.fasta") + with open(fasta_filename, "w") as f: + f.write(db_data) + + # Run makeblastdb + mkdb_proc = subprocess.run( + [ + "makeblastdb", + "-in", + "db.fasta", + "-dbtype", + "prot", + "-out", + "antigen.db", + ], + capture_output=True, + cwd=tmp_dir, + ) + + if mkdb_proc.returncode != 0: + raise Exception( + f"makeblastdb returned exit code of " + f"{mkdb_proc.returncode}\n\n" + f"STDOUT: {mkdb_proc.stdout.decode()}\n\n" + f"STDERR: {mkdb_proc.stderr.decode()}" + ) + + # Write out query file + fasta_filename = os.path.join(tmp_dir, "query.fasta") + with open(fasta_filename, "w") as f: + f.write(query_data) + + # Run blastp + blastp_proc = subprocess.run( + [ + "blastp", + "-db", + "antigen.db", + "-query", + "query.fasta", + "-outfmt", + outfmt, + "-out", + "antigen.results", + "-num_threads", + str(BLAST_NUM_THREADS), + ], + capture_output=True, + cwd=tmp_dir, + ) + + if blastp_proc.returncode != 0: + raise Exception( + f"blastp returned exit code of " + f"{blastp_proc.returncode}\n\n" + f"STDOUT: {blastp_proc.stdout.decode()}\n\n" + f"STDERR: {blastp_proc.stderr.decode()}" + ) + + # Read in the results file + with open(os.path.join(tmp_dir, "antigen.results"), "r") as f: + return f.read() diff --git a/backend/antigenapi/bioinformatics.py b/backend/antigenapi/bioinformatics/imgt.py similarity index 100% rename from backend/antigenapi/bioinformatics.py rename to backend/antigenapi/bioinformatics/imgt.py diff --git a/backend/antigenapi/models.py b/backend/antigenapi/models.py index ed20cf6a..52871f03 100644 --- a/backend/antigenapi/models.py +++ b/backend/antigenapi/models.py @@ -28,7 +28,7 @@ ) from django.db.models.signals import post_init, post_save -from .bioinformatics import read_airr_file +from .bioinformatics.imgt import read_airr_file class Project(Model): diff --git a/backend/antigenapi/tests/test_parsers.py b/backend/antigenapi/tests/test_parsers.py index b8f13d25..563f72c7 100644 --- a/backend/antigenapi/tests/test_parsers.py +++ b/backend/antigenapi/tests/test_parsers.py @@ -2,7 +2,7 @@ import unittest import zipfile -from antigenapi.bioinformatics import load_sequences, trim_sequence +from antigenapi.bioinformatics.imgt import load_sequences, trim_sequence from antigenapi.views_old import _extract_well diff --git a/backend/antigenapi/views_old.py b/backend/antigenapi/views_old.py index ffbc5f21..d82ccce8 100644 --- a/backend/antigenapi/views_old.py +++ b/backend/antigenapi/views_old.py @@ -1,6 +1,7 @@ import collections.abc import datetime import io +import json import math import os import re @@ -36,7 +37,8 @@ from rest_framework.views import APIView from rest_framework.viewsets import ModelViewSet -from antigenapi.bioinformatics import ( +from antigenapi.bioinformatics.blast import get_db_fasta, run_blastp +from antigenapi.bioinformatics.imgt import ( AIRR_IMPORTANT_COLUMNS, as_fasta_files, load_sequences, @@ -1052,20 +1054,83 @@ def search_sequencing_run_results(self, request, query): {"matches": pd.concat(results).to_dict(orient="records") if results else []} ) + @action( + detail=True, + methods=["GET"], + name="BLAST sequencing run results vs DB.", + url_path="blast", + ) + def get_blast_sequencing_run(self, request, pk): + """BLAST sequencing run vs database.""" + blast_str = run_blastp(pk) + if not blast_str: + return JsonResponse({"hits": []}, status=status.HTTP_404_NOT_FOUND) + + # Read query AIRR files for CDRs + results = SequencingRunResults.objects.filter(sequencing_run_id=int(pk)) + + airr_df = pd.concat(read_airr_file(r.airr_file) for r in results) + airr_df = airr_df.set_index("sequence_id") + + ALIGN_PERC_THRESHOLD = 90 + E_VALUE_THRESHOLD = 0.05 + + # Parse the JSON and keep the important bits + blast_result = json.loads(blast_str) + res = [] + for blast_run in blast_result["BlastOutput2"]: + run_res = blast_run["report"]["results"]["search"] + for blast_hit_set in run_res["hits"]: + subject_title = blast_hit_set["description"][0]["title"] + query_title = run_res["query_title"] + query_cdr3 = airr_df.at[query_title, "cdr3_aa"] + if pd.isna(query_cdr3): + query_cdr3 = None + if subject_title.strip() == query_title.strip(): + continue + hsps = blast_hit_set["hsps"][0] + assert len(blast_hit_set["description"]) == 1 + for hsps in blast_hit_set["hsps"]: + align_perc = round( + (hsps["align_len"] / run_res["query_len"]) * 100, 2 + ) + if align_perc < ALIGN_PERC_THRESHOLD: + continue + e_value = hsps["evalue"] + if e_value > E_VALUE_THRESHOLD: + continue + res.append( + { + "query_title": query_title.strip(), + "query_cdr3": query_cdr3, + "subject_title": subject_title.strip(), + "submatch_no": hsps["num"], + "query_seq": hsps["qseq"], + "subject_seq": hsps["hseq"], + "midline": hsps["midline"], + "bit_score": hsps["bit_score"], + "e_value": e_value, + "align_len": hsps["align_len"], + "align_perc": align_perc, + "ident_perc": round( + (hsps["identity"] / hsps["align_len"]) * 100, 2 + ), + } + ) + + # Sort the results + res = sorted( + res, + key=lambda r: (r["query_cdr3"] or "", -r["align_perc"], -r["ident_perc"]), + ) + + return JsonResponse({"hits": res}) + class GlobalFastaView(APIView): def get(self, request, format=None): """Download entire database as .fasta file.""" - fasta_data = "" - for sr in SequencingRunResults.objects.all(): - airr_file = read_airr_file( - sr.airr_file, usecols=("sequence_id", "sequence_alignment_aa") - ) - airr_file = airr_file[airr_file.sequence_alignment_aa.notna()] - if not airr_file.empty: - for _, row in airr_file.iterrows(): - fasta_data += f"> {row.sequence_id}\n" - fasta_data += f"{row.sequence_alignment_aa.replace('.', '')}\n" + fasta_data = get_db_fasta() fasta_filename = ( f"antigenapp_database_{datetime.datetime.now().isoformat()}.fasta" diff --git a/backend/setup.cfg b/backend/setup.cfg index c86716da..fd7776a3 100644 --- a/backend/setup.cfg +++ b/backend/setup.cfg @@ -26,9 +26,9 @@ install_requires = [options.extras_require] dev = - black==24.3.0 - isort>5.0 - flake8<4 + black + isort + flake8 pytest pytest-cov pytest-black @@ -37,6 +37,7 @@ dev = pytest-flake8 pytest-black pytest-pydocstyle + types-pytz flake8-isort @@ -57,6 +58,9 @@ float_to_top=true max-line-length = 88 extend-ignore = E203, + E231, # false positive + E702, # false positive + E713, # false positive F811, F722, exclude = diff --git a/docker-compose.yml b/docker-compose.yml index 86921927..2c1a6f26 100644 --- a/docker-compose.yml +++ b/docker-compose.yml @@ -16,8 +16,11 @@ services: build: context: backend target: dev + args: + PIPENV_SYNC_FLAGS: --dev restart: always volumes: + - api_venv:/usr/src/.venv - ./backend:/usr/src - api_data:/api_data environment: @@ -43,3 +46,4 @@ services: volumes: api_data: + api_venv: diff --git a/frontend/Dockerfile b/frontend/Dockerfile index e87a9b65..6d65a506 100644 --- a/frontend/Dockerfile +++ b/frontend/Dockerfile @@ -1,6 +1,6 @@ FROM registry.hub.docker.com/library/node:22-alpine AS dev -ENV ANTIGENAPP_DIR /antigenapp +ENV ANTIGENAPP_DIR=/antigenapp COPY package-lock.json ${ANTIGENAPP_DIR}/package-lock.json COPY package.json ${ANTIGENAPP_DIR}/package.json diff --git a/frontend/src/App.js b/frontend/src/App.js index 4130fdfb..514c9d53 100644 --- a/frontend/src/App.js +++ b/frontend/src/App.js @@ -23,6 +23,7 @@ import * as Sentry from "@sentry/react"; import { BrowserTracing } from "@sentry/tracing"; import { getCookie } from "./crudtemplates/utils.js"; import SequencingResults from "./crudtemplates/SequencingResults.js"; +import BlastResults from "./crudtemplates/BlastResults.js"; if (process.env.REACT_APP_SENTRY_DSN !== undefined) { Sentry.init({ @@ -737,6 +738,11 @@ const App = () => { schema={schemas.sequencing} onSetError={setError} > + { + const [isShowing] = useState(true); + + useEffect(() => { + // setIsShowing(props.loading); + }, []); + + return ( + +
+
+ + AntigenApp loading indicator + Loading... +
+
+ + ); +}; + +export default LoadingLlama; diff --git a/frontend/src/crudtemplates/BlastResults.js b/frontend/src/crudtemplates/BlastResults.js new file mode 100644 index 00000000..51076d43 --- /dev/null +++ b/frontend/src/crudtemplates/BlastResults.js @@ -0,0 +1,152 @@ +import config from "../config.js"; +import { useState, useEffect } from "react"; +import { useParams } from "react-router-dom"; +import * as Sentry from "@sentry/browser"; +import LoadingLlama from "../LoadingLlama.js"; + +const BlastResults = (props) => { + const { recordId } = useParams(); + const [blastResults, setBlastResults] = useState(); + + function classNames(...classes) { + return classes.filter(Boolean).join(" "); + } + + const extraPad = 2; + + const formatAlignment = (row) => { + let padLength = + Math.max(row.query_title.length, row.subject_title.length) + extraPad; + return ( + 
+        {row.query_title.padEnd(padLength, " ")}
+        {row.query_seq}
+        

+        {"".padEnd(padLength, " ")}
+        {row.midline}
+        

+        {row.subject_title.padEnd(padLength, " ")}
+        {row.subject_seq}
+
+ ); + }; + + const fetchBlastResults = () => { + fetch(config.url.API_URL + "/sequencingrun/" + recordId + "/blast/", { + method: "GET", + headers: { + "Content-Type": "application/json", + "X-CSRFToken": props.csrfToken, + }, + }) + .then((res) => { + res.json().then( + (data) => { + setBlastResults(data); + }, + (err) => { + console.log(res, err); + props.onSetError("HTTP code " + res.status); + }, + ); + }) + .catch((err) => { + Sentry.captureException(err); + props.onSetError(err.toString()); + }); + }; + + useEffect(() => { + fetchBlastResults(); + }, []); // eslint-disable-line react-hooks/exhaustive-deps + + return ( + <> + {!blastResults && } + {blastResults && ( +
+
+
+ + + + + + + + + + + + {!blastResults.hits.length && ( + + + + )} + {blastResults.hits.map((row, rowIdx, arr) => ( + 0 && + arr[rowIdx - 1].query_cdr3 !== row.query_cdr3 + ? "border-t-2 border-black" + : "", + )} + > + + + + + + + ))} + +
+ Query CDR3 + + Align. length + + Alignment + + e-value + + Bit score +
+ No results +
+ {row.query_cdr3 || "None"} + + {row.align_len} ({row.align_perc}%) + + {formatAlignment(row)} + + {row.e_value} + + {row.bit_score} +
+
+
+
+ )} + + ); +}; + +export default BlastResults; diff --git a/frontend/src/crudtemplates/SequencingResults.js b/frontend/src/crudtemplates/SequencingResults.js index 169f95be..01dd1afa 100644 --- a/frontend/src/crudtemplates/SequencingResults.js +++ b/frontend/src/crudtemplates/SequencingResults.js @@ -2,6 +2,7 @@ import config from "../config.js"; import { useState, useEffect } from "react"; import { useParams } from "react-router-dom"; import * as Sentry from "@sentry/browser"; +import LoadingLlama from "../LoadingLlama.js"; const SequencingResults = (props) => { const { recordId } = useParams(); @@ -42,7 +43,7 @@ const SequencingResults = (props) => { return ( <> - {!sequencingResults && "..."} + {!sequencingResults && } {sequencingResults && (
@@ -119,6 +120,13 @@ const SequencingResults = (props) => { + {!sequencingResults.records.length && ( + + + No results + + + )} {sequencingResults.records.map((row) => (