From e15c97e346695e6ecf70222851a4864d741c9045 Mon Sep 17 00:00:00 2001
From: Alex Lubbock <alex.lubbock@rfi.ac.uk>
Date: Wed, 4 Oct 2023 14:53:42 +0100
Subject: [PATCH] WIP: Upload and display sequencing results

---
 backend/Pipfile.lock                          | 1498 +++++++++++------
 backend/antigenapi/bioinformatics.py          |  110 ++
 .../0005_sequencingrunresults_and_more.py     |   61 +
 backend/antigenapi/models.py                  |   24 +
 backend/antigenapi/views.py                   |  150 +-
 backend/antigendjango/settings.py             |    1 +
 frontend/src/App.js                           |   23 +-
 .../src/crudtemplates/SequencingResults.js    |  150 ++
 frontend/src/crudtemplates/ViewObjectPage.js  |    6 +-
 frontend/src/crudtemplates/utils.js           |   78 +-
 10 files changed, 1590 insertions(+), 511 deletions(-)
 create mode 100644 backend/antigenapi/bioinformatics.py
 create mode 100644 backend/antigenapi/migrations/0005_sequencingrunresults_and_more.py
 create mode 100644 frontend/src/crudtemplates/SequencingResults.js

diff --git a/backend/Pipfile.lock b/backend/Pipfile.lock
index e76ef3d..6c8f698 100644
--- a/backend/Pipfile.lock
+++ b/backend/Pipfile.lock
@@ -1,7 +1,7 @@
 {
   "_meta": {
     "hash": {
-      "sha256": "29a063ac4ac82517cddab61324728d516de2c8f70e9951dfe1f1570d638c7e67"
+      "sha256": "1751386876147ec078678949fc665c1d5bbb8e577e7f4e7c512cf8cc5d7c11f1"
     },
     "pipfile-spec": 6,
     "requires": {},
@@ -18,68 +18,232 @@
       "editable": true,
       "path": "."
     },
+    "appdirs": {
+      "hashes": [
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+      ],
+      "version": "==1.4.4"
+    },
     "asgiref": {
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+        "sha256:89b2ef2247e3b562a16eef663bc0e2e703ec6468e2fa8a5cd61cd449786d4f6e",
+        "sha256:9e0ce3aa93a819ba5b45120216b23878cf6e8525eb3848653452b4192b92afed"
       ],
       "markers": "python_version >= '3.7'",
-      "version": "==3.6.0"
+      "version": "==3.7.2"
+    },
+    "beautifulsoup4": {
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+      "markers": "python_full_version >= '3.6.0'",
+      "version": "==4.12.2"
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@@ -91,11 +255,11 @@
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@@ -107,11 +271,11 @@
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@@ -121,6 +285,29 @@
       "markers": "python_version >= '3.6'",
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@@ -129,39 +316,141 @@
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@@ -531,11 +1043,11 @@
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@@ -547,11 +1059,11 @@
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@@ -563,11 +1075,11 @@
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@@ -579,11 +1091,10 @@
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@@ -618,35 +1129,36 @@
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@@ -658,37 +1170,41 @@
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+        "sha256:f7fc5a5acafb7d6ccca13bfa8c90f8c51f13d8fb87d95656d3950f0158d3ce53",
+        "sha256:f9b5571d33660d5009a8b3c25dc1db560206e2d2f89d3df1cb32d72c0d117d52"
       ],
-      "markers": "python_version >= '3.6'",
-      "version": "==2.9.5"
+      "markers": "python_version >= '3.7'",
+      "version": "==2.9.9"
     },
     "pycodestyle": {
       "hashes": [
@@ -866,11 +1378,11 @@
     },
     "pytest": {
       "hashes": [
-        "sha256:130328f552dcfac0b1cec75c12e3f005619dc5f874f0a06e8ff7263f0ee6225e",
-        "sha256:c99ab0c73aceb050f68929bc93af19ab6db0558791c6a0715723abe9d0ade9d4"
+        "sha256:1d881c6124e08ff0a1bb75ba3ec0bfd8b5354a01c194ddd5a0a870a48d99b002",
+        "sha256:a766259cfab564a2ad52cb1aae1b881a75c3eb7e34ca3779697c23ed47c47069"
       ],
       "markers": "python_version >= '3.7'",
-      "version": "==7.2.2"
+      "version": "==7.4.2"
     },
     "pytest-black": {
       "hashes": [
@@ -881,11 +1393,11 @@
     },
     "pytest-cov": {
       "hashes": [
-        "sha256:2feb1b751d66a8bd934e5edfa2e961d11309dc37b73b0eabe73b5945fee20f6b",
-        "sha256:996b79efde6433cdbd0088872dbc5fb3ed7fe1578b68cdbba634f14bb8dd0470"
+        "sha256:3904b13dfbfec47f003b8e77fd5b589cd11904a21ddf1ab38a64f204d6a10ef6",
+        "sha256:6ba70b9e97e69fcc3fb45bfeab2d0a138fb65c4d0d6a41ef33983ad114be8c3a"
       ],
       "markers": "python_version >= '3.6'",
-      "version": "==4.0.0"
+      "version": "==4.1.0"
     },
     "pytest-django": {
       "hashes": [
@@ -927,25 +1439,25 @@
     },
     "pytz": {
       "hashes": [
-        "sha256:01a0681c4b9684a28304615eba55d1ab31ae00bf68ec157ec3708a8182dbbcd0",
-        "sha256:78f4f37d8198e0627c5f1143240bb0206b8691d8d7ac6d78fee88b78733f8c4a"
+        "sha256:7b4fddbeb94a1eba4b557da24f19fdf9db575192544270a9101d8509f9f43d7b",
+        "sha256:ce42d816b81b68506614c11e8937d3aa9e41007ceb50bfdcb0749b921bf646c7"
       ],
-      "version": "==2022.7.1"
+      "version": "==2023.3.post1"
     },
     "s3transfer": {
       "hashes": [
-        "sha256:06176b74f3a15f61f1b4f25a1fc29a4429040b7647133a463da8fa5bd28d5ecd",
-        "sha256:2ed07d3866f523cc561bf4a00fc5535827981b117dd7876f036b0c1aca42c947"
+        "sha256:10d6923c6359175f264811ef4bf6161a3156ce8e350e705396a7557d6293c33a",
+        "sha256:fd3889a66f5fe17299fe75b82eae6cf722554edca744ca5d5fe308b104883d2e"
       ],
       "markers": "python_version >= '3.7'",
-      "version": "==0.6.0"
+      "version": "==0.7.0"
     },
     "sentry-sdk": {
       "hashes": [
-        "sha256:3c4e898f7a3edf5a2042cd0dcab6ee124e2112189228c272c08ad15d3850c201",
-        "sha256:ad40860325c94d1a656da70fba5a7c4dbb2f6809d3cc2d00f74ca0b608330f14"
+        "sha256:64a7141005fb775b9db298a30de93e3b83e0ddd1232dc6f36eb38aebc1553291",
+        "sha256:6de2e88304873484207fed836388e422aeff000609b104c802749fd89d56ba5b"
       ],
-      "version": "==1.17.0"
+      "version": "==1.31.0"
     },
     "six": {
       "hashes": [
@@ -964,11 +1476,11 @@
     },
     "sqlparse": {
       "hashes": [
-        "sha256:0323c0ec29cd52bceabc1b4d9d579e311f3e4961b98d174201d5622a23b85e34",
-        "sha256:69ca804846bb114d2ec380e4360a8a340db83f0ccf3afceeb1404df028f57268"
+        "sha256:5430a4fe2ac7d0f93e66f1efc6e1338a41884b7ddf2a350cedd20ccc4d9d28f3",
+        "sha256:d446183e84b8349fa3061f0fe7f06ca94ba65b426946ffebe6e3e8295332420c"
       ],
       "markers": "python_version >= '3.5'",
-      "version": "==0.4.3"
+      "version": "==0.4.4"
     },
     "toml": {
       "hashes": [
@@ -980,33 +1492,41 @@
     },
     "typing-extensions": {
       "hashes": [
-        "sha256:5cb5f4a79139d699607b3ef622a1dedafa84e115ab0024e0d9c044a9479ca7cb",
-        "sha256:fb33085c39dd998ac16d1431ebc293a8b3eedd00fd4a32de0ff79002c19511b4"
+        "sha256:8f92fc8806f9a6b641eaa5318da32b44d401efaac0f6678c9bc448ba3605faa0",
+        "sha256:df8e4339e9cb77357558cbdbceca33c303714cf861d1eef15e1070055ae8b7ef"
       ],
-      "markers": "python_version >= '3.7'",
-      "version": "==4.5.0"
+      "markers": "python_version >= '3.8'",
+      "version": "==4.8.0"
+    },
+    "tzdata": {
+      "hashes": [
+        "sha256:11ef1e08e54acb0d4f95bdb1be05da659673de4acbd21bf9c69e94cc5e907a3a",
+        "sha256:7e65763eef3120314099b6939b5546db7adce1e7d6f2e179e3df563c70511eda"
+      ],
+      "markers": "python_version >= '2'",
+      "version": "==2023.3"
     },
     "urllib3": {
       "hashes": [
-        "sha256:8a388717b9476f934a21484e8c8e61875ab60644d29b9b39e11e4b9dc1c6b305",
-        "sha256:aa751d169e23c7479ce47a0cb0da579e3ede798f994f5816a74e4f4500dcea42"
+        "sha256:24d6a242c28d29af46c3fae832c36db3bbebcc533dd1bb549172cd739c82df21",
+        "sha256:94a757d178c9be92ef5539b8840d48dc9cf1b2709c9d6b588232a055c524458b"
       ],
-      "markers": "python_version >= '3.6'",
-      "version": "==1.26.15"
+      "markers": "python_version >= '2.7' and python_version not in '3.0, 3.1, 3.2, 3.3, 3.4, 3.5'",
+      "version": "==1.26.17"
     },
     "uwsgi": {
       "hashes": [
-        "sha256:35a30d83791329429bc04fe44183ce4ab512fcf6968070a7bfba42fc5a0552a9"
+        "sha256:4cc4727258671ac5fa17ab422155e9aaef8a2008ebb86e4404b66deaae965db2"
       ],
-      "version": "==2.0.21"
+      "version": "==2.0.22"
     },
     "xmlschema": {
       "hashes": [
-        "sha256:0caa96668807b4b51c42a0fe2b6610752bc59f069615df3e34dcfffb962973fd",
-        "sha256:557f3632b54b6ff10576736bba62e43db84eb60f6465a83818576cd9ffcc1799"
+        "sha256:276a03e0fd3c94c148d528bff4d9482f9b99bf8c7b4056a2e8e703d28149d454",
+        "sha256:f2b29c45485fac414cc1fdb38d18a220c5987d7d3aa996e6df6ff35ee94d5a63"
       ],
       "markers": "python_version >= '3.7'",
-      "version": "==2.2.2"
+      "version": "==2.5.0"
     }
   }
 }
diff --git a/backend/antigenapi/bioinformatics.py b/backend/antigenapi/bioinformatics.py
new file mode 100644
index 0000000..15fd9ed
--- /dev/null
+++ b/backend/antigenapi/bioinformatics.py
@@ -0,0 +1,110 @@
+import itertools
+import os
+import sys
+import zipfile
+
+import vquest.config
+import vquest.vq
+
+START_CODON = "ATG"
+
+
+def file_name_to_sequence_name(fn):
+    """Extract the sequence identifier from the file name (Ray Owens' method)."""
+    # Use whole filename as sequence name, as requested by Lauren
+    return fn[:-4] if fn.endswith(".seq") else fn
+
+
+def trim_sequence(seq):
+    """Trim the sequence after start codon, if present."""
+    try:
+        return seq[seq.index(START_CODON) + len(START_CODON) :]
+    except ValueError:
+        return ""
+
+
+def _load_sequences_zip(zip_file):
+    seq_data = {}
+    with zipfile.ZipFile(zip_file, "r") as zip_ref:
+        for fn in zip_ref.namelist():
+            if not fn.endswith(".seq"):
+                continue
+
+            # Convert the file name to a short sequence identifier
+            seq_name = os.path.basename(file_name_to_sequence_name(fn))
+
+            # Read the .seq file
+            with zip_ref.open(fn, "r") as f:
+                seq = f.read().decode("utf-8")
+
+            # Trim the sequence
+            seq = trim_sequence(seq)
+
+            # Add to dictionary of sequences, if a start codon was present
+            if seq:
+                seq_data[seq_name] = seq
+
+    return seq_data
+
+
+def load_sequences(directory_or_zip):
+    """Load a set of sequences from .seq files from a dictionary or .zip file."""
+    if os.path.isfile(directory_or_zip):
+        return _load_sequences_zip(directory_or_zip)
+
+    seq_data = {}
+    for fn in os.listdir(directory_or_zip):
+        if fn.endswith(".seq"):
+            # Convert the file name to a short sequence identifier
+            seq_name = file_name_to_sequence_name(fn)
+            # Read the .seq file
+            with open(os.path.join(directory_or_zip, fn), "r") as f:
+                seq = f.read()
+            # Trim the sequence
+            seq = trim_sequence(seq)
+            # Add to dictionary of sequences, if a start codon was present
+            if seq:
+                seq_data[seq_name] = seq
+
+    return seq_data
+
+
+def _chunks(data, size=None):
+    """Split a dict into multiple dicts of specified max size (iterator)."""
+    if size is None:
+        size = sys.maxsize
+    it = iter(data)
+    for _ in range(0, len(data), size):
+        yield {k: data[k] for k in itertools.islice(it, size)}
+
+
+def as_fasta_files(seq_data, max_file_size=50):
+    """Convert a dictionary of sequence names and data to FASTA format files.
+
+    max_file_size specifies the maximum number of sequences in each file
+    (For IMGT, this is 50)
+    """
+    fasta_files = []
+    for seq_data_chunk in _chunks(seq_data, max_file_size):
+        fasta_files.append(
+            "\n".join([f"> {name}\n{seq}" for name, seq in seq_data_chunk.items()])
+        )
+    return fasta_files
+
+
+def run_vquest(fasta_data, species="alpaca", receptor="IG"):
+    """Run vquest bioinformatics on a set of fasta files."""
+    conf = vquest.config.DEFAULTS.copy()
+    conf["inputType"] = "inline"
+    conf["species"] = species
+    conf["receptorOrLocusType"] = receptor
+    conf["sequences"] = fasta_data
+
+    # Set vquest logging to DEBUG
+    import logging
+
+    from vquest import LOGGER
+
+    LOGGER.setLevel(logging.DEBUG)
+
+    return vquest.vq.vquest(conf)
diff --git a/backend/antigenapi/migrations/0005_sequencingrunresults_and_more.py b/backend/antigenapi/migrations/0005_sequencingrunresults_and_more.py
new file mode 100644
index 0000000..ccaa36a
--- /dev/null
+++ b/backend/antigenapi/migrations/0005_sequencingrunresults_and_more.py
@@ -0,0 +1,61 @@
+# Generated by Django 4.2.5 on 2023-10-03 20:40
+
+import django.db.models.deletion
+from django.conf import settings
+from django.db import migrations, models
+
+
+class Migration(migrations.Migration):
+
+    dependencies = [
+        migrations.swappable_dependency(settings.AUTH_USER_MODEL),
+        ("antigenapi", "0004_remove_sequencingrun_results_date_and_more"),
+    ]
+
+    operations = [
+        migrations.CreateModel(
+            name="SequencingRunResults",
+            fields=[
+                (
+                    "id",
+                    models.BigAutoField(
+                        auto_created=True,
+                        primary_key=True,
+                        serialize=False,
+                        verbose_name="ID",
+                    ),
+                ),
+                ("seq", models.PositiveSmallIntegerField()),
+                (
+                    "seqres_file",
+                    models.FileField(upload_to="uploads/sequencingresults/"),
+                ),
+                (
+                    "parameters_file",
+                    models.FileField(upload_to="uploads/sequencingresults/"),
+                ),
+                ("airr_file", models.FileField(upload_to="uploads/sequencingresults/")),
+                ("added_date", models.DateTimeField(auto_now_add=True)),
+                (
+                    "added_by",
+                    models.ForeignKey(
+                        on_delete=django.db.models.deletion.PROTECT,
+                        to=settings.AUTH_USER_MODEL,
+                    ),
+                ),
+                (
+                    "sequencing_run",
+                    models.ForeignKey(
+                        on_delete=django.db.models.deletion.PROTECT,
+                        to="antigenapi.sequencingrun",
+                    ),
+                ),
+            ],
+        ),
+        migrations.AddConstraint(
+            model_name="sequencingrunresults",
+            constraint=models.UniqueConstraint(
+                fields=("sequencing_run", "seq"), name="unique_seqrun_seq"
+            ),
+        ),
+    ]
diff --git a/backend/antigenapi/models.py b/backend/antigenapi/models.py
index 454e387..0185d04 100644
--- a/backend/antigenapi/models.py
+++ b/backend/antigenapi/models.py
@@ -164,6 +164,29 @@ class SequencingRun(Model):
     added_date = DateTimeField(auto_now_add=True)
 
 
+class SequencingRunResults(Model):
+    """A results file for a sequencing run."""
+
+    sequencing_run = ForeignKey(SequencingRun, on_delete=PROTECT)
+    seq: int = PositiveSmallIntegerField()
+    seqres_file: File = FileField(
+        upload_to="uploads/sequencingresults/",
+    )
+    parameters_file: File = FileField(
+        upload_to="uploads/sequencingresults/",
+    )
+    airr_file: File = FileField(
+        upload_to="uploads/sequencingresults/",
+    )
+    added_by = ForeignKey(settings.AUTH_USER_MODEL, on_delete=PROTECT)
+    added_date = DateTimeField(auto_now_add=True)
+
+    class Meta:  # noqa: D106
+        constraints = [
+            UniqueConstraint(fields=["sequencing_run", "seq"], name="unique_seqrun_seq")
+        ]
+
+
 auditlog.register(Project)
 auditlog.register(Llama)
 auditlog.register(Antigen)
@@ -171,3 +194,4 @@ class SequencingRun(Model):
 auditlog.register(Library)
 auditlog.register(ElisaPlate)
 auditlog.register(SequencingRun)
+auditlog.register(SequencingRunResults)
diff --git a/backend/antigenapi/views.py b/backend/antigenapi/views.py
index b55fb60..8087ca2 100644
--- a/backend/antigenapi/views.py
+++ b/backend/antigenapi/views.py
@@ -5,13 +5,17 @@
 from tempfile import NamedTemporaryFile
 from wsgiref.util import FileWrapper
 
+import numpy as np
 import openpyxl
+import pandas as pd
 from auditlog.models import LogEntry
+from django.conf import settings
 from django.contrib.contenttypes.models import ContentType
+from django.core.files import File
 from django.db import transaction
 from django.db.models.deletion import ProtectedError
 from django.db.utils import IntegrityError
-from django.http import Http404, HttpResponse
+from django.http import Http404, HttpResponse, JsonResponse
 from rest_framework import status
 from rest_framework.decorators import action
 from rest_framework.response import Response
@@ -25,6 +29,7 @@
 )
 from rest_framework.viewsets import ModelViewSet
 
+from antigenapi.bioinformatics import as_fasta_files, load_sequences, run_vquest
 from antigenapi.models import (
     Antigen,
     Cohort,
@@ -35,6 +40,7 @@
     PlateLocations,
     Project,
     SequencingRun,
+    SequencingRunResults,
 )
 from antigenapi.utils.uniprot import get_protein
 
@@ -379,10 +385,21 @@ class Meta:  # noqa: D106
         fields = ("plate", "location")
 
 
+class SequencingRunResultSerializer(ModelSerializer):
+    """A serializer for sequencing run results."""
+
+    added_by = StringRelatedField()
+
+    class Meta:  # noqa: D106
+        model = SequencingRunResults
+        fields = ("seq", "added_by", "added_date")
+
+
 class SequencingRunSerializer(ModelSerializer):
     """A serializer for sequencing runs."""
 
     added_by = StringRelatedField()
+    sequencingrunresults_set = SequencingRunResultSerializer(many=True, required=False)
 
     def validate_wells(self, data):
         """Check JSONField for wells is valid."""
@@ -562,3 +579,134 @@ def download_submission_xlsx(self, request, pk, submission_idx):
             f'sr{pk}_{submission_idx}.xlsx"'
         )
         return response
+
+    @action(
+        detail=True,
+        methods=["PUT"],
+        name="Upload sequencing run results file (.zip).",
+        url_path="resultsfile/(?P<submission_idx>[0-9]+)",
+    )
+    def upload_sequencing_run_results(self, request, pk, submission_idx):
+        """Upload sequencing run results file (.zip)."""
+        results_file = request.data["file"]
+
+        # TODO: Validate results file in more detail
+        if not results_file.name.endswith(".zip"):
+            raise ValidationError("file", "Results file should be a .zip file")
+
+        # TODO: Validate submission_idx
+
+        # Run bioinformatics using .zip file
+        print("Extracting zip file...")
+        seq_data = load_sequences(results_file.temporary_file_path())
+
+        # Convert to FASTA in-memory (vquest api handles chunking to
+        # max 50 seqs per file)
+        fasta_file = as_fasta_files(seq_data, max_file_size=None)[0]
+
+        # Submit to vquest
+        print("Running vquest...")
+        vquest_results = run_vquest(fasta_file)
+
+        parameters_file_data = vquest_results["Parameters.txt"]
+        vquest_airr_data = vquest_results["vquest_airr.tsv"]
+
+        base_filename = f"SequencingResults_{pk}_{submission_idx}"
+
+        # Create SequencingRunResults object
+        with open(
+            os.path.join(
+                settings.MEDIA_ROOT,
+                SequencingRunResults.parameters_file.field.upload_to,
+                f"{base_filename}_vquestparams.txt",
+            ),
+            "w+",
+        ) as parameters_file, open(
+            os.path.join(
+                settings.MEDIA_ROOT,
+                SequencingRunResults.airr_file.field.upload_to,
+                f"{base_filename}_vquestairr.tsv",
+            ),
+            "w+",
+        ) as airr_file:
+            parameters_file.write(parameters_file_data)
+            parameters_file_wrapped = File(parameters_file)
+            airr_file.write(vquest_airr_data)
+            airr_file_wrapped = File(airr_file)
+
+            SequencingRunResults.objects.update_or_create(
+                sequencing_run=SequencingRun.objects.get(pk=int(pk)),
+                seq=submission_idx,
+                defaults={
+                    "added_by": request.user,
+                    "seqres_file": results_file,
+                    "parameters_file": parameters_file_wrapped,
+                    "airr_file": airr_file_wrapped,
+                },
+            )
+
+        return JsonResponse(
+            SequencingRunSerializer(SequencingRun.objects.get(pk=int(pk))).data
+        )
+
+    @action(
+        detail=True,
+        methods=["GET"],
+        name="Get sequencing results.",
+        url_path="results",
+    )
+    def upload_sequencing_run_results(self, request, pk):
+        """Get sequencing results."""
+        IMPORTANT_COLUMNS = (
+            "sequence_id",
+            "productive",
+            "stop_codon",
+            "fwr1_aa",
+            "cdr1_aa",
+            "fwr2_aa",
+            "cdr2_aa",
+            "fwr3_aa",
+            "cdr3_aa",
+        )
+
+        results = SequencingRunResults.objects.filter(
+            sequencing_run_id=int(pk)
+        ).order_by("seq")
+
+        import io
+
+        csvs = []
+        for r in results:
+            # Clean up the CSVs! They seem to have an extra tab in some cases.
+            buffer = io.StringIO(
+                "\n".join(
+                    line.strip()
+                    for line in r.airr_file.read().decode("utf8").split("\n")
+                )
+            )
+            df = pd.read_csv(buffer, sep="\t", header=0, usecols=IMPORTANT_COLUMNS)
+            csvs.append(df)
+        df = pd.concat(csvs)
+
+        # Get number of matches per CDR3 sequence
+        cdr3_counts = df["cdr3_aa"].value_counts()
+        cdr3_counts.name = "cdr3_aa_count"
+        df = df.merge(cdr3_counts, on="cdr3_aa", how="left")
+
+        # Sort as required - Productive, number of CDR3 matches,
+        # then CDR3 itself, then sequence ID
+        df = df.sort_values(
+            by=["productive", "cdr3_aa_count", "cdr3_aa", "sequence_id"],
+            ascending=[False, False, True, True],
+        )
+
+        # Ensure we have the right columns in the right order
+        df = df.loc[:, IMPORTANT_COLUMNS]
+
+        # Set index and replace NaN with None (null in JSON)
+        df = df.replace({np.nan: None})
+
+        # Indicator to show when cdr3 has changed from previous row
+        df["new_cdr3"] = df["cdr3_aa"].shift(1).ne(df["cdr3_aa"])
+
+        return JsonResponse({"records": df.to_dict(orient="records")})
diff --git a/backend/antigendjango/settings.py b/backend/antigendjango/settings.py
index 3d396f8..134c252 100644
--- a/backend/antigendjango/settings.py
+++ b/backend/antigendjango/settings.py
@@ -49,6 +49,7 @@
     "rest_framework",
     "guardian",
     "auditlog",
+    "django_cleanup.apps.CleanupConfig",
 ]
 
 MIDDLEWARE = [
diff --git a/frontend/src/App.js b/frontend/src/App.js
index 5f075c0..4c05243 100644
--- a/frontend/src/App.js
+++ b/frontend/src/App.js
@@ -19,6 +19,8 @@ import {
 } from "react-router-dom";
 import * as Sentry from "@sentry/react";
 import { BrowserTracing } from "@sentry/tracing";
+import { getCookie } from "./crudtemplates/utils.js";
+import SequencingResults from "./crudtemplates/SequencingResults.js";
 
 if (process.env.REACT_APP_SENTRY_DSN !== undefined) {
   Sentry.init({
@@ -60,22 +62,6 @@ const App = () => {
     username: "",
   });
 
-  const getCookie = (name) => {
-    if (!document.cookie) {
-      return null;
-    }
-
-    const xsrfCookies = document.cookie
-      .split(";")
-      .map((c) => c.trim())
-      .filter((c) => c.startsWith(name + "="));
-
-    if (xsrfCookies.length === 0) {
-      return null;
-    }
-    return decodeURIComponent(xsrfCookies[0].split("=")[1]);
-  };
-
   useEffect(() => {
     const getCSRF = () => {
       // 5 second timeout
@@ -724,6 +710,11 @@ const App = () => {
                       onSetError={setError}
                       csrfToken={csrfToken}
                     ></ViewObjectPage>
+                    <SequencingResults
+                      tabName="Results"
+                      schema={schemas.sequencing}
+                      onSetError={setError}
+                    ></SequencingResults>
                     <AuditLog
                       tabName="Audit Log"
                       schema={schemas.sequencing}
diff --git a/frontend/src/crudtemplates/SequencingResults.js b/frontend/src/crudtemplates/SequencingResults.js
new file mode 100644
index 0000000..979ba6a
--- /dev/null
+++ b/frontend/src/crudtemplates/SequencingResults.js
@@ -0,0 +1,150 @@
+import config from "../config.js";
+import { useState, useEffect } from "react";
+import { useParams } from "react-router-dom";
+import * as Sentry from "@sentry/browser";
+
+const SequencingResults = (props) => {
+  const { recordId } = useParams();
+  const [sequencingResults, setSequencingResults] = useState();
+  // const [activeElisaPlates, setActiveElisaPlates] = useState([]);
+
+  const fetchSequencingResults = () => {
+    fetch(config.url.API_URL + "/sequencingrun/" + recordId + "/results/", {
+      method: "GET",
+      headers: {
+        "Content-Type": "application/json",
+        "X-CSRFToken": props.csrfToken,
+      },
+    })
+      .then((res) => {
+        res.json().then(
+          (data) => {
+            setSequencingResults(data.records);
+          },
+          () => {
+            props.setError("HTTP code " + res.status);
+          },
+        );
+      })
+      .catch((err) => {
+        Sentry.captureException(err);
+        props.setError(err.toString());
+      });
+  };
+
+  useEffect(() => {
+    fetchSequencingResults();
+  }, []); // eslint-disable-line react-hooks/exhaustive-deps
+
+  return (
+    <>
+      {!sequencingResults && "..."}
+      {sequencingResults && (
+        <div className="mt-8 flow-root">
+          <div className="-mx-4 -my-2 overflow-x-auto sm:-mx-6 lg:-mx-8">
+            <div className="inline-block min-w-full py-2 align-middle sm:px-6 lg:px-8">
+              <table className="min-w-full divide-y divide-gray-300">
+                <thead>
+                  <tr>
+                    <th
+                      scope="col"
+                      className="py-3.5 pl-4 pr-3 text-left text-sm font-semibold text-gray-900 sm:pl-3"
+                    >
+                      Sequence ID
+                    </th>
+                    <th
+                      scope="col"
+                      className="px-3 py-3.5 text-left text-sm font-semibold text-gray-900"
+                    >
+                      Productive (T/F)
+                    </th>
+                    <th
+                      scope="col"
+                      className="px-3 py-3.5 text-left text-sm font-semibold text-gray-900"
+                    >
+                      Stop Codon (T/F)
+                    </th>
+                    <th
+                      scope="col"
+                      className="px-3 py-3.5 text-left text-sm font-semibold text-gray-900"
+                    >
+                      FWR1
+                    </th>
+                    <th
+                      scope="col"
+                      className="px-3 py-3.5 text-left text-sm font-semibold text-gray-900"
+                    >
+                      CDR1
+                    </th>
+                    <th
+                      scope="col"
+                      className="px-3 py-3.5 text-left text-sm font-semibold text-gray-900"
+                    >
+                      FWR2
+                    </th>
+                    <th
+                      scope="col"
+                      className="px-3 py-3.5 text-left text-sm font-semibold text-gray-900"
+                    >
+                      CDR2
+                    </th>
+                    <th
+                      scope="col"
+                      className="px-3 py-3.5 text-left text-sm font-semibold text-gray-900"
+                    >
+                      FWR3
+                    </th>
+                    <th
+                      scope="col"
+                      className="px-3 py-3.5 text-left text-sm font-semibold text-gray-900"
+                    >
+                      CDR3
+                    </th>
+                  </tr>
+                </thead>
+                <tbody className="bg-white">
+                  {sequencingResults.map((row) => (
+                    <tr
+                      key={row.sequence_id}
+                      className={row.new_cdr3 ? "border-t-2 border-black" : ""}
+                    >
+                      <td className="whitespace-nowrap py-4 pl-4 pr-3 text-sm font-medium text-gray-900 sm:pl-3">
+                        {row.sequence_id}
+                      </td>
+                      <td className="whitespace-nowrap px-3 py-4 text-sm text-gray-500">
+                        {row.productive}
+                      </td>
+                      <td className="whitespace-nowrap px-3 py-4 text-sm text-gray-500">
+                        {row.stop_codon}
+                      </td>
+                      <td className="whitespace-nowrap px-3 py-4 text-sm text-gray-500">
+                        {row.fwr1_aa}
+                      </td>
+                      <td className="whitespace-nowrap px-3 py-4 text-sm text-gray-500">
+                        {row.cdr1_aa}
+                      </td>
+                      <td className="whitespace-nowrap px-3 py-4 text-sm text-gray-500">
+                        {row.fwr2_aa}
+                      </td>
+                      <td className="whitespace-nowrap px-3 py-4 text-sm text-gray-500">
+                        {row.cdr2_aa}
+                      </td>
+                      <td className="whitespace-nowrap px-3 py-4 text-sm text-gray-500">
+                        {row.fwr3_aa}
+                      </td>
+                      <td className="whitespace-nowrap px-3 py-4 text-sm text-gray-500">
+                        {row.cdr3_aa}
+                      </td>
+                    </tr>
+                  ))}
+                </tbody>
+              </table>
+            </div>
+          </div>
+        </div>
+      )}
+    </>
+  );
+};
+
+export default SequencingResults;
diff --git a/frontend/src/crudtemplates/ViewObjectPage.js b/frontend/src/crudtemplates/ViewObjectPage.js
index cff611d..ae17a74 100644
--- a/frontend/src/crudtemplates/ViewObjectPage.js
+++ b/frontend/src/crudtemplates/ViewObjectPage.js
@@ -143,7 +143,11 @@ const ViewObjectPage = (props) => {
                   {field.label}
                 </dt>
                 <dd className="mt-1 text-sm text-gray-900 sm:col-span-2 sm:mt-0 break-words">
-                  {!loading && displayField(field, record, "ViewObjectPage")}
+                  {!loading &&
+                    displayField(field, record, "ViewObjectPage", {
+                      setRecord: setRecord,
+                      setLoading: setLoading,
+                    })}
                   {loading && (
                     <div className="h-2.5 bg-gray-300 w-12 rounded-full mb-2.5 rounded shadow animate-pulse"></div>
                   )}
diff --git a/frontend/src/crudtemplates/utils.js b/frontend/src/crudtemplates/utils.js
index 47fe458..75a5e2e 100644
--- a/frontend/src/crudtemplates/utils.js
+++ b/frontend/src/crudtemplates/utils.js
@@ -3,6 +3,22 @@ import { LinkIcon } from "@heroicons/react/20/solid";
 import config from "../config.js";
 import schema from "../schema.js";
 
+export const getCookie = (name) => {
+  if (!document.cookie) {
+    return null;
+  }
+
+  const xsrfCookies = document.cookie
+    .split(";")
+    .map((c) => c.trim())
+    .filter((c) => c.startsWith(name + "="));
+
+  if (xsrfCookies.length === 0) {
+    return null;
+  }
+  return decodeURIComponent(xsrfCookies[0].split("=")[1]);
+};
+
 const elisaHeader = [
   "",
   "1",
@@ -105,7 +121,37 @@ const makeExtLink = (value, linkTemplate, context) => {
   }
 };
 
-export const displayFieldSingle = (field, record, context) => {
+export const uploadSequencingResults = (event, props) => {
+  var input = event.target;
+
+  var data = new FormData();
+  data.append("file", input.files[0]);
+
+  props.setLoading(true);
+  fetch(
+    config.url.API_URL +
+      "/sequencingrun/" +
+      input.dataset.seqidx +
+      "/resultsfile/" +
+      input.dataset.residx +
+      "/",
+    {
+      method: "PUT",
+      body: data,
+      headers: {
+        "X-CSRFToken": getCookie("csrftoken"),
+      },
+    },
+  ).then((res) => {
+    props.setLoading(false);
+    res.json().then((json) => {
+      console.log(json);
+      props.setRecord(json);
+    });
+  });
+};
+
+export const displayFieldSingle = (field, record, context, props) => {
   if (field.fkApiField) {
     if (!Array.isArray(record[field.fkApiField])) {
       return record[field.field];
@@ -143,6 +189,7 @@ export const displayFieldSingle = (field, record, context) => {
       retVal.push(<div key={"seqPlate" + p}>{plateFn(p)}</div>);
       retVal.push(
         <a
+          key={"seqPlateLink" + p}
           href={
             config.url.API_URL +
             schema.sequencing.apiUrl +
@@ -155,12 +202,34 @@ export const displayFieldSingle = (field, record, context) => {
         >
           <button
             type="button"
-            className="w-full sm:w-auto mb-2 mt-2 sm:mb-0 relative inline-flex items-center justify-center rounded-md border border-transparent bg-indigo-600 px-4 py-2 text-sm font-medium text-white shadow-sm hover:bg-indigo-700 focus:outline-none focus:ring-2 focus:ring-indigo-500 focus:ring-offset-2"
+            className="w-full sm:w-auto mb-2 mt-2 mr-2 sm:mb-0 relative inline-flex items-center justify-center rounded-md border border-transparent bg-indigo-600 px-4 py-2 text-sm font-medium text-white shadow-sm hover:bg-indigo-700 focus:outline-none focus:ring-2 focus:ring-indigo-500 focus:ring-offset-2"
           >
             Download sequencing submission file
           </button>
         </a>,
       );
+      if (record.sequencingrunresults_set.find((x) => x.seq === p)) {
+        // Sequencing results found
+      } else {
+        // Sequencing results not uploaded yet
+        retVal.push(
+          <label
+            key={"resultsFileUpload" + p}
+            type="button"
+            className="w-full cursor-pointer sm:w-auto mb-2 mt-2 sm:mb-0 relative inline-flex items-center justify-center rounded-md border border-transparent bg-teal-600 px-4 py-2 text-sm font-medium text-white shadow-sm hover:bg-teal-700 focus:outline-none focus:ring-2 focus:ring-teal-500 focus:ring-offset-2"
+          >
+            <input
+              type="file"
+              data-residx={p}
+              data-seqidx={record.id}
+              onChange={(event) => uploadSequencingResults(event, props)}
+              className="hidden"
+              name={"resultsFile" + p}
+            />
+            Upload sequencing results file
+          </label>,
+        );
+      }
     }
     return retVal;
   } else if (field.type === "platethreshold" && record[field.field]) {
@@ -180,7 +249,7 @@ export const displayFieldSingle = (field, record, context) => {
   }
 };
 
-export const displayField = (field, record, context) => {
+export const displayField = (field, record, context, props) => {
   if (
     !displayTogetherFieldTypes.includes(field.type) &&
     Array.isArray(record[field.field])
@@ -191,6 +260,7 @@ export const displayField = (field, record, context) => {
           field,
           { ...record, [field.field]: valEach },
           context,
+          props,
         ),
       )
       .reduce(
@@ -205,7 +275,7 @@ export const displayField = (field, record, context) => {
         null,
       );
   } else {
-    return displayFieldSingle(field, record, context);
+    return displayFieldSingle(field, record, context, props);
   }
 };