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""" |
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Command-line interface for mandos. |
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""" |
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from __future__ import annotations |
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import logging |
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from pathlib import Path |
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import typer |
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from mandos import logger |
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from mandos.model.settings import MANDOS_SETTINGS |
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from mandos.model.taxonomy import TaxonomyDf |
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from mandos.model.taxonomy_caches import TaxonomyFactories |
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from mandos.entries.entries import Entries, _Typer |
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from mandos.entries.api_singletons import Apis |
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from mandos.entries.multi_searches import MultiSearch |
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from mandos.entries.searcher import SearcherUtils |
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# IMPORTANT! |
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Apis.set_default() |
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cli = typer.Typer() |
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# _old_wrap_text = copy(click.formatting.wrap_text) |
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# def _new_wrap_text( |
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# text, width=100, initial_indent="", subsequent_indent="", preserve_paragraphs=False |
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# ): |
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# return _old_wrap_text(text, 100, initial_indent, subsequent_indent, preserve_paragraphs) |
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# click.formatting.wrap_text = _new_wrap_text |
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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 = _Typer.path, |
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config: Path = typer.Argument( |
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None, |
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help=".toml config file. See docs.", |
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exists=True, |
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dir_okay=False, |
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readable=True, |
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), |
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) -> None: |
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""" |
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Run multiple searches. |
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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 = _Typer.path, |
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pubchem: bool = typer.Option(True, help="Download data from PubChem"), |
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chembl: bool = typer.Option(True, help="Download data from ChEMBL"), |
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hmdb: bool = typer.Option(True, help="Download data from HMDB"), |
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) -> None: |
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""" |
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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, hmdb=hmdb) |
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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 build_taxonomy( |
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taxa: str = typer.Argument( |
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None, |
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help=""" |
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UniProt taxon ID or scientific name, comma-separated. |
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Scientific names are only permitted for subsets of vertebrata. |
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""", |
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), |
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to: Path = typer.Option( |
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None, |
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show_default=False, |
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help=""" |
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Output file; can be CSV, TSV, feather, etc. |
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If it starts with '.', uses the default path but changes the format and filename extension. |
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[default: <taxon-id,<taxon-id>,...>.feather] |
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""", |
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), |
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): |
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""" |
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Writes a CSV file of the descendents of given taxa. |
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""" |
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taxon_ids = [ |
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int(taxon.strip()) if taxon.isdigit() else taxon.strip() for taxon in taxa.split(",") |
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] |
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# get the filename |
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# by default we'll just use the inputs |
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default_path = Path(",".join([str(t).strip() for t in taxa]) + ".tab.gz") |
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if to is None: |
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to = default_path |
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elif str(to).startswith("."): |
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to = default_path.with_suffix(str(to)) |
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to.parent.mkdir(exist_ok=True, parents=True) |
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# TODO: this is quite inefficient |
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# we're potentially reading in the vertebrata file multiple times |
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# we could instead read it in, then concatenate the matching subtrees |
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# however, this is moderately efficient if you ask for, e.g., Mammalia and Plantae |
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# then it'll download Plantae but just get Mammalia from the resource-file Vertebrata |
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taxes = [] |
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for taxon in taxon_ids: |
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tax = TaxonomyFactories.from_uniprot(MANDOS_SETTINGS.taxonomy_cache_path).load(taxon) |
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taxes.append(tax.to_df()) |
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final_tax = TaxonomyDf.concat(taxes, ignore_index=True) |
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final_tax = final_tax.drop_duplicates().sort_values("taxon") |
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final_tax.write_file(to) |
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@staticmethod |
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def dl_tax( |
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taxon: int, |
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) -> None: |
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""" |
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Preps a new taxonomy file for use in mandos. |
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Just returns if a corresponding file already exists in the resources dir or mandos cache (``~/.mandos``). |
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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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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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# 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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for entry in Entries: |
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from typer.models import CommandInfo |
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info = CommandInfo(entry.cmd(), callback=entry.run) |
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cli.registered_commands.append(info) |
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# print(f"Registered {entry.cmd()} to {entry}") |
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setattr(Commands, entry.cmd(), entry.run) |
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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("@tax-tree", callback=Commands.build_taxonomy), |
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CommandInfo("@tax-dl", callback=Commands.dl_tax, hidden=True), |
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] |
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) |
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if __name__ == "__main__": |
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# logging.basicConfig(level=0) |
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import sys |
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root = logging.getLogger() |
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handler = logging.StreamHandler(sys.stdout) |
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handler.setLevel(0) |
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formatter = logging.Formatter("%(levelname)-7s %(asctime)s %(message)s", "%Y%m%d:%H:%M:%S") |
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handler.setFormatter(formatter) |
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root.addHandler(handler) |
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logger.addHandler(handler) |
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# log_factory = PrettyRecordFactory(10, 12, 5, width=100, symbols=True).modifying(logger) |
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# good start; can be changed |
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root.setLevel(logging.WARNING) |
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logger.setLevel(logging.INFO) |
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cli() |
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__all__ = ["Commands"] |
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dmyersturnbull /
mandos
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