feat: sequencing results upload and bioinformatics

backend/antigenapi/bioinformatics.py

@@ -0,0 +1,107 @@
+import itertools
+import logging
+import os
+import sys
+import zipfile
+
+import vquest.config
+import vquest.vq
+from vquest import LOGGER as VQUEST_LOGGER
+
+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") or fn.startswith("__MACOSX"):
+                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 hasattr(directory_or_zip, "read") or 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
+
+    VQUEST_LOGGER.setLevel(logging.WARNING)
+
+    return vquest.vq.vquest(conf)

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"
+            ),
+        ),
+    ]

backend/antigenapi/models.py

@@ -138,6 +138,14 @@ def __str__(self):  # noqa: D105
 )
 
 
+def _remove_zero_pad_well_name(well_name):
+    """Remove zero padding from well name, e.g. A01 -> A1."""
+    if well_name[1] == "0":
+        return well_name[0] + well_name[2]
+    else:
+        return well_name
+
+
 class ElisaWell(Model):
     """ELISA well model."""
 
@@ -164,10 +172,34 @@ 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)
 auditlog.register(Cohort, m2m_fields={"projects", "antigens"})
 auditlog.register(Library)
 auditlog.register(ElisaPlate)
 auditlog.register(SequencingRun)
+auditlog.register(SequencingRunResults)