| import os |
| import re |
| import shutil |
| import tempfile |
| import base64 |
| from io import StringIO |
| from Bio import Entrez, SeqIO |
| from Bio.SeqFeature import SeqFeature, FeatureLocation |
|
|
| Entrez.email = "user@example.com" |
|
|
|
|
| def fetch_genbank(accession, out_dir): |
| handle = Entrez.efetch(db="nuccore", id=accession, rettype="gbwithparts", retmode="text") |
| record = SeqIO.read(handle, "genbank") |
| handle.close() |
| path = os.path.join(out_dir, f"{accession}.gbk") |
| SeqIO.write(record, path, "genbank") |
| return path |
|
|
|
|
| def fasta_to_gbk(fasta_text, out_dir): |
| records = list(SeqIO.parse(StringIO(fasta_text), "fasta")) |
| if not records: |
| return [], ["Could not parse any sequences from the FASTA input."] |
|
|
| try: |
| import pyrodigal |
| orf_finder = pyrodigal.GeneFinder(meta=True) |
| except ImportError: |
| orf_finder = None |
|
|
| gbk_files, warnings = [], [] |
|
|
| for record in records: |
| record.annotations["molecule_type"] = "DNA" |
|
|
| if orf_finder is not None: |
| try: |
| genes = orf_finder.find_genes(str(record.seq).encode()) |
| for i, gene in enumerate(genes, 1): |
| record.features.append( |
| SeqFeature( |
| FeatureLocation(gene.begin - 1, gene.end, strand=gene.strand), |
| type="CDS", |
| qualifiers={"locus_tag": [f"{record.id}_{i:04d}"]}, |
| ) |
| ) |
| if not list(genes): |
| warnings.append(f"{record.id}: no ORFs predicted (sequence may be too short).") |
| except Exception as e: |
| warnings.append(f"{record.id}: ORF prediction failed — {e}") |
| else: |
| warnings.append(f"{record.id}: pyrodigal not installed, saving without gene annotation.") |
|
|
| safe_id = re.sub(r"[^\w\-]", "_", record.id) |
| path = os.path.join(out_dir, f"{safe_id}.gbk") |
| SeqIO.write(record, path, "genbank") |
| gbk_files.append(path) |
|
|
| return gbk_files, warnings |
|
|
|
|
| def _wrap_in_iframe(html_content): |
| html_b64 = base64.b64encode(html_content.encode("utf-8")).decode("ascii") |
| return ( |
| f'<iframe src="data:text/html;base64,{html_b64}"' |
| ' style="width:100%;height:800px;border:0;" allowfullscreen></iframe>' |
| ) |
|
|
|
|
| def _error_html(msg): |
| return f'<p style="color:#c0392b;font-family:sans-serif;padding:1rem">{msg}</p>' |
|
|
|
|
| def run_clinker(accessions_text, fasta_text=""): |
| accessions = [a.strip() for a in accessions_text.strip().splitlines() if a.strip()] |
| has_fasta = bool(fasta_text.strip()) |
|
|
| if not accessions and not has_fasta: |
| return _error_html("Please enter at least one accession or a FASTA sequence.") |
|
|
| work_dir = tempfile.mkdtemp() |
| gbk_files, errors = [], [] |
|
|
| for acc in accessions: |
| try: |
| gbk_files.append(fetch_genbank(acc, work_dir)) |
| except Exception as e: |
| errors.append(f"{acc}: {e}") |
|
|
| if has_fasta: |
| fasta_gbks, fasta_warnings = fasta_to_gbk(fasta_text, work_dir) |
| gbk_files.extend(fasta_gbks) |
| errors.extend(fasta_warnings) |
|
|
| if not gbk_files: |
| shutil.rmtree(work_dir) |
| return _error_html("No usable input files.<br>" + "<br>".join(errors)) |
|
|
| html_path = os.path.join(work_dir, "output.html") |
| try: |
| try: |
| from clinker.main import clinker as clinker_api |
| clinker_api(gbk_files, plot=html_path, force=True) |
| except ImportError: |
| import subprocess |
| r = subprocess.run( |
| ["clinker", "-f", "-i", "0.225", "-p", html_path] + gbk_files, |
| capture_output=True, text=True, |
| ) |
| if r.returncode != 0 and not os.path.exists(html_path): |
| raise RuntimeError(r.stderr) |
| except Exception as e: |
| shutil.rmtree(work_dir) |
| return _error_html(f"clinker error: {e}") |
|
|
| if not os.path.exists(html_path): |
| shutil.rmtree(work_dir) |
| return _error_html("clinker ran but produced no HTML output.") |
|
|
| with open(html_path, encoding="utf-8") as f: |
| html_content = f.read() |
|
|
| shutil.rmtree(work_dir) |
| return _wrap_in_iframe(html_content) |
|
|
