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"""SoloSeq folding submission command.""" |
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from datetime import datetime |
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from pathlib import Path |
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from typing import Annotated |
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import typer |
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from rich.panel import Panel |
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from folding_studio.client import Client |
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from folding_studio.commands.utils import ( |
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success_fail_catch_print, |
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success_fail_catch_spinner, |
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) |
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from folding_studio.config import FOLDING_API_KEY |
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from folding_studio.console import console |
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from folding_studio.query.soloseq import SoloSeqQuery |
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def soloseq( |
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source: Annotated[ |
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Path, |
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typer.Argument( |
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help=( |
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"Path to the data source. Either a fasta file or a directory of fasta files." |
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), |
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exists=True, |
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), |
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], |
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project_code: Annotated[ |
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str, |
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typer.Option( |
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help="Project code. If unknown, contact your PM or the Folding Studio team.", |
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envvar="FOLDING_PROJECT_CODE", |
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exists=True, |
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), |
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], |
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seed: Annotated[int, typer.Option(help="Random seed.")] = 0, |
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skip_relaxation: Annotated[ |
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bool, |
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typer.Option(help="Skip the relaxation process."), |
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] = False, |
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subtract_plddt: Annotated[ |
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bool, |
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typer.Option(help="Output (100 - pLDDT) instead of the pLDDT itself."), |
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] = False, |
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output: Annotated[ |
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Path, |
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typer.Option( |
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help="Local path to download the result zip and query parameters to. " |
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"Default to 'soloseq_results'." |
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), |
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] = "soloseq_results", |
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force: Annotated[ |
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bool, |
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typer.Option( |
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help=( |
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"Forces the download to overwrite any existing file " |
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"with the same name in the specified location." |
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) |
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), |
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] = False, |
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unzip: Annotated[ |
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bool, typer.Option(help="Unzip the file after its download.") |
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] = False, |
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spinner: Annotated[ |
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bool, typer.Option(help="Use live spinner in log output.") |
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] = True, |
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): |
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"""Synchronous SoloSeq folding submission""" |
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success_fail_catch = ( |
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success_fail_catch_spinner if spinner else success_fail_catch_print |
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) |
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console.print( |
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Panel("[bold cyan]:dna: SoloSeq Folding submission [/bold cyan]", expand=False) |
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) |
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output_dir = output / f"submission_{datetime.now().strftime('%Y%m%d%H%M%S')}" |
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with success_fail_catch(":key: Authenticating client"): |
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client = Client.authenticate() |
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with success_fail_catch(":package: Generating query"): |
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query_builder = ( |
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SoloSeqQuery.from_file if source.is_file() else SoloSeqQuery.from_directory |
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) |
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query: SoloSeqQuery = query_builder( |
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source, |
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seed=seed, |
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skip_relaxation=skip_relaxation, |
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subtract_plddt=subtract_plddt, |
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) |
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query.save_parameters(output_dir) |
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console.print("[blue]Generated query: [/blue]") |
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console.print_json(data=query.payload) |
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with success_fail_catch(":brain: Processing folding job"): |
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response = client.send_request(query, project_code) |
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console.print("[blue]Confidence Data:[/blue]", end=" ") |
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console.print_json(data=response.confidence_data) |
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with success_fail_catch( |
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f":floppy_disk: Downloading results to `[green]{output_dir}[/green]`" |
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): |
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response.download_results(output_dir=output_dir, force=force, unzip=unzip) |
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