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""" |
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Command-line interface for mandos. |
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3
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""" |
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5
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from __future__ import annotations |
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7
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import logging |
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from pathlib import Path |
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from typing import Optional |
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import typer |
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from mandos.model.settings import MANDOS_SETTINGS |
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from mandos.model.taxonomy_caches import TaxonomyFactories |
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from mandos.search.entries import Entries |
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14
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15
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from mandos.search.api_singletons import Apis |
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from mandos.search.multi_searches import MultiSearch |
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from mandos.search.searcher import Searcher, SearcherUtils |
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logger = logging.getLogger(__package__) |
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# IMPORTANT! |
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Apis.set_default() |
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cli = typer.Typer() |
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class Commands: |
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""" |
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Entry points for mandos. |
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""" |
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@staticmethod |
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def search( |
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path: Path, |
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33
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config: Optional[Path] = None, |
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34
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) -> None: |
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""" |
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Runs multiple searches. |
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Args: |
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path: |
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config: |
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""" |
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MultiSearch(path, config).search() |
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@staticmethod |
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def find( |
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path: Path, |
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pubchem: bool = True, |
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48
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chembl: bool = True, |
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49
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) -> None: |
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50
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""" |
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51
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Fetches and caches compound data. |
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Useful to check what you can see before running a search. |
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""" |
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out_path = path.with_suffix(".ids.csv") |
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if out_path.exists(): |
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raise FileExistsError(out_path) |
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inchikeys = SearcherUtils.read(path) |
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df = SearcherUtils.dl(inchikeys, pubchem=pubchem, chembl=chembl) |
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df.to_csv(out_path) |
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typer.echo(f"Wrote to {out_path}") |
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@staticmethod |
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def dl_tax( |
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taxon: int, |
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65
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) -> None: |
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66
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""" |
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67
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Preps a new taxonomy file for use in mandos. |
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68
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Just returns if a corresponding file already exists in the resources dir or mandos cache (``~/.mandos``). |
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69
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Otherwise, downloads a tab-separated file from UniProt. |
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(To find manually, follow the ``All lower taxonomy nodes`` link and click ``Download``.) |
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Then applies fixes and reduces the file size, creating a new file alongside. |
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Puts both the raw data and fixed data in the cache under ``~/.mandos/taxonomy/``. |
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74
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Args: |
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taxon: The **ID** of the UniProt taxon |
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""" |
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TaxonomyFactories.from_uniprot(MANDOS_SETTINGS.taxonomy_cache_path).load(taxon) |
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79
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80
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# Oh dear this is a nightmare |
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# it's really hard to create typer commands with dynamically configured params -- |
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# we really need to rely on its inferring of params |
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# that makes this really hard to do well |
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84
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for entry in Entries: |
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from typer.models import CommandInfo |
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86
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87
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info = CommandInfo(entry.cmd(), callback=entry.run) |
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cli.registered_commands.append(info) |
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setattr(Commands, entry.cmd(), entry.run) |
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91
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cli.registered_commands.extend( |
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[ |
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CommandInfo("search", callback=Commands.search), |
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CommandInfo("dl_tax", callback=Commands.dl_tax, hidden=True), |
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] |
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) |
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99
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if __name__ == "__main__": |
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cli() |
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101
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102
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103
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__all__ = ["Commands", "Searcher"] |
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dmyersturnbull /
mandos
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