ssi-analysis-result-parsers 0.0.9__py3-none-any.whl → 0.0.11__py3-none-any.whl
This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.
- ssi_analysis_result_parsers/Ecoli_parser.py +669 -0
- ssi_analysis_result_parsers/Legionella_parser.py +3 -1
- ssi_analysis_result_parsers/Nmeningitidis_parser.py +178 -0
- ssi_analysis_result_parsers/Spyogenes_parser.py +0 -1
- ssi_analysis_result_parsers/__init__.py +1 -1
- ssi_analysis_result_parsers/_modidx.py +43 -1
- {ssi_analysis_result_parsers-0.0.9.dist-info → ssi_analysis_result_parsers-0.0.11.dist-info}/METADATA +1 -1
- {ssi_analysis_result_parsers-0.0.9.dist-info → ssi_analysis_result_parsers-0.0.11.dist-info}/RECORD +22 -10
- {ssi_analysis_result_parsers-0.0.9.dist-info → ssi_analysis_result_parsers-0.0.11.dist-info}/entry_points.txt +3 -0
- {ssi_analysis_result_parsers-0.0.9.dist-info → ssi_analysis_result_parsers-0.0.11.dist-info}/top_level.txt +1 -0
- test_input/Ecoli/ERR14229029.res +1 -0
- test_input/Ecoli/ERR3528110.res +4 -0
- test_input/Ecoli/samplesheet.tsv +3 -0
- test_input/Legionella/test.tsv +2 -0
- test_input/Nmeningitidis/batch_parser_file_paths.tsv +6 -0
- test_input/Nmeningitidis/meningotype/meningotype1.tsv +2 -0
- test_input/Nmeningitidis/meningotype/meningotype2.tsv +2 -0
- test_input/Nmeningitidis/meningotype/meningotype3.tsv +2 -0
- test_input/Nmeningitidis/neisseria_mlst_scheme.tsv +18415 -0
- test_output/Ecoli/KMA_cases_parser.tsv +3 -0
- {ssi_analysis_result_parsers-0.0.9.dist-info → ssi_analysis_result_parsers-0.0.11.dist-info}/WHEEL +0 -0
- {ssi_analysis_result_parsers-0.0.9.dist-info → ssi_analysis_result_parsers-0.0.11.dist-info}/licenses/LICENSE +0 -0
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# AUTOGENERATED! DO NOT EDIT! File to edit: ../nbs/37_Nmeningitidis_parser.ipynb.
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# %% auto 0
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__all__ = ['extract_meningotype', 'extract_cc_from_mlst', 'NmeningitidisResults', 'Nmeningitidis_parser',
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'Nmeningitidis_batch_parser']
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# %% ../nbs/37_Nmeningitidis_parser.ipynb 3
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# standard libs
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import os
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import re
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# Common to template
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# add into settings.ini, requirements, package name is python-dotenv, for conda build ensure `conda config --add channels conda-forge`
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import dotenv # for loading config from .env files, https://pypi.org/project/python-dotenv/
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import envyaml # Allows to loads env vars into a yaml file, https://github.com/thesimj/envyaml
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import fastcore # To add functionality related to nbdev development, https://github.com/fastai/fastcore/
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from fastcore import (
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test,
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)
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from fastcore.script import (
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call_parse,
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) # for @call_parse, https://fastcore.fast.ai/script
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import json # for nicely printing json and yaml
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# import functions from core module (optional, but most likely needed).
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from ssi_analysis_result_parsers import (
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core,
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blast_parser,
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)
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# from ssi_analysis_result_parsers.blast_parser import extract_presence_absence
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# Project specific libraries
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from pathlib import Path
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import pandas
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import numpy
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import sys
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# %% ../nbs/37_Nmeningitidis_parser.ipynb 6
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def extract_meningotype(meningotype_tsv: Path):
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if meningotype_tsv.exists():
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try:
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df = pandas.read_csv(meningotype_tsv, sep="\t")
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PorA_split = df["PorA"][0].split(",")
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return {
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"SEROGROUP": df["SEROGROUP"][0],
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"VR1": PorA_split[0],
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"VR2": PorA_split[1],
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"FetA": df["FetA"][0],
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}
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except pandas.errors.EmptyDataError:
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print(
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f"Meningotype output file empty at {meningotype_tsv}", file=sys.stderr
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)
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return None
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else:
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print(f"No meningotype output found at {meningotype_tsv}", file=sys.stderr)
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return None
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return None
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def extract_cc_from_mlst(
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MLST: str,
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mlst_scheme_tsv: Path = "/users/data/Projects/MICROBIAL_SURVEILLANCE/Resources/Databases/mlst/neisseria/neisseria.txt",
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):
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CC = {"CC": ""}
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if mlst_scheme_tsv.exists():
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try:
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with open(mlst_scheme_tsv) as f:
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for line in f:
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line = line.strip("\n").split("\t")
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if line[0] == MLST:
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if line[8][:3] == "ST-":
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CC["CC"] = line[8].split(" ")[0][3:]
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return CC
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except Exception as e:
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CC["CC"] = f"Failed to load mlst scheme tsv: {e}"
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else:
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CC["CC"] = "Failed to load mlst scheme tsv, file not found"
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return CC
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class NmeningitidisResults(core.PipelineResults):
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@classmethod
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def from_tool_paths(
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cls, meningotype_tsv: Path, MLST: str, mlst_scheme_tsv: Path, sample_name=None
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):
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"""
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Alternative constructor for initializing results for single sample,
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Initializes NmeningitidisResults instance provided paths to outputs from tools (legionella sbt and lag1 presence blast)
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"""
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mgk_results = cls.summary(
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meningotype_tsv=Path(meningotype_tsv),
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MLST=MLST,
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mlst_scheme_tsv=Path(mlst_scheme_tsv),
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)
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return cls({sample_name: mgk_results})
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@classmethod
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def from_tool_paths_dict(cls, file_paths: dict):
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"""
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Alternative constructor for initializing results for multiple samples,
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Initializes NmeningitidisResults instance by providing a dictionary of paths to outputs from tools (legionella sbt and lag1 presence blast)
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"""
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results_dict = {}
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for sample_name, path_dict in file_paths.items():
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mgk_results = cls.summary(
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meningotype_tsv=Path(path_dict["meningotype_results"]),
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MLST=path_dict["MLST"],
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mlst_scheme_tsv=path_dict["mlst_scheme_tsv"],
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)
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results_dict[sample_name] = mgk_results
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return cls(results_dict)
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@classmethod
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def from_tool_paths_dataframe(cls, file_paths_df: pandas.DataFrame):
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"""
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Alternative constructor for initializing results for multiple samples,
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Initializes NmeningitidisResults instance by providing a DataFrame of paths to outputs from tools (legionella sbt and lag1 presence blast)
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"""
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file_paths = file_paths_df.to_dict(orient="index")
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return cls.from_tool_paths_dict(file_paths=file_paths)
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@classmethod
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def from_tool_paths_tsv(cls, tool_paths_tsv: Path):
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"""
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Alternative constructor for initializing results for multiple samples,
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Initializes NmeningitidisResults instance by providing a tsv-file with paths to outputs from tools (legionella sbt and lag1 presence blast)
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"""
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file_paths_df = pandas.read_csv(tool_paths_tsv, sep="\t")
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file_paths_df.set_index("sample_name", inplace=True, drop=True)
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return cls.from_tool_paths_dataframe(file_paths_df)
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@staticmethod
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def summary(meningotype_tsv: Path, MLST: str, mlst_scheme_tsv: Path) -> dict:
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meningotype_results = extract_meningotype(meningotype_tsv=Path(meningotype_tsv))
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results_dict = meningotype_results
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cc_dict = extract_cc_from_mlst(MLST=MLST, mlst_scheme_tsv=Path(mlst_scheme_tsv))
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results_dict = core.update_results_dict(
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results_dict, cc_dict, old_duplicate_key_prefix="Clonal_complex: "
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)
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if results_dict is None:
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return {}
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return results_dict
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def __repr__(self):
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return f"< Spyogenes analysis results object. {len(self.results_df)} samples with {len(self.results_df.columns)} result variables > "
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# %% ../nbs/37_Nmeningitidis_parser.ipynb 9
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@call_parse
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def Nmeningitidis_parser(
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meningotype_tsv: Path = None, # Blast output from blasting EMM and emm-like genes
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MLST: str = None, # MLST to deduce Clonal complex from
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mlst_scheme_tsv: Path = None, # Path to pubmlst scheme for neisseria for MLST: CC table
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sample_name: str = None,
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output_file: Path = None,
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) -> None:
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""" """
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results = NmeningitidisResults.from_tool_paths(
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meningotype_tsv=meningotype_tsv,
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MLST=MLST,
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mlst_scheme_tsv=mlst_scheme_tsv,
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sample_name=sample_name,
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)
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results.write_tsv(output_file=output_file)
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@call_parse
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def Nmeningitidis_batch_parser(
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file_path_tsv: Path = None, # Path to tsv containing file paths to the outputs from tools to be parsed. Must contain headers "sample_name", "sbt_results", and "lag1_blast_results"
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output_file: Path = None, # Path to output tsv
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) -> None:
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""" """
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results = NmeningitidisResults.from_tool_paths_tsv(tool_paths_tsv=file_path_tsv)
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results.write_tsv(output_file)
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@@ -193,7 +193,6 @@ def extract_emm_type(emm_blast_tsv: Path):
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f"ENN{blast_df_unique.iloc[2]['qseqid'][3:]} with pident {round(blast_df_unique.iloc[2]['pident'],2)} and length {blast_df_unique.iloc[2]['length']}/{blast_df_unique.iloc[2]['qlen']}"
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)
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else:
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note_to_add = "EMM and EMM-like genes found on multiple contigs"
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emm_genes = []
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for index, row in blast_df_unique.iterrows():
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if row["length"] < row["qlen"] or row["pident"] < 100:
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__version__ = "0.0.
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__version__ = "0.0.10"
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@@ -5,7 +5,27 @@ d = { 'settings': { 'branch': 'main',
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'doc_host': 'https://thej-ssi.github.io',
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'git_url': 'https://github.com/thej-ssi/ssi_analysis_result_parsers',
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'lib_path': 'ssi_analysis_result_parsers'},
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'syms': { 'ssi_analysis_result_parsers.
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'syms': { 'ssi_analysis_result_parsers.Ecoli_parser': { 'ssi_analysis_result_parsers.Ecoli_parser.EcoliResults': ( 'ecoli_parser.html#ecoliresults',
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'ssi_analysis_result_parsers/Ecoli_parser.py'),
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'ssi_analysis_result_parsers.Ecoli_parser.EcoliResults.__init__': ( 'ecoli_parser.html#ecoliresults.__init__',
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'ssi_analysis_result_parsers/Ecoli_parser.py'),
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'ssi_analysis_result_parsers.Ecoli_parser.EcoliResults.__repr__': ( 'ecoli_parser.html#ecoliresults.__repr__',
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'ssi_analysis_result_parsers/Ecoli_parser.py'),
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'ssi_analysis_result_parsers.Ecoli_parser.EcoliResults.from_samplesheet': ( 'ecoli_parser.html#ecoliresults.from_samplesheet',
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'ssi_analysis_result_parsers/Ecoli_parser.py'),
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'ssi_analysis_result_parsers.Ecoli_parser.EcoliResults.summarize_single_sample': ( 'ecoli_parser.html#ecoliresults.summarize_single_sample',
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'ssi_analysis_result_parsers/Ecoli_parser.py'),
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'ssi_analysis_result_parsers.Ecoli_parser.EcoliResults.write_tsv': ( 'ecoli_parser.html#ecoliresults.write_tsv',
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'ssi_analysis_result_parsers/Ecoli_parser.py'),
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'ssi_analysis_result_parsers.Ecoli_parser.ecoli_parser': ( 'ecoli_parser.html#ecoli_parser',
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'ssi_analysis_result_parsers/Ecoli_parser.py'),
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'ssi_analysis_result_parsers.Ecoli_parser.get_threshold': ( 'ecoli_parser.html#get_threshold',
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'ssi_analysis_result_parsers/Ecoli_parser.py'),
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'ssi_analysis_result_parsers.Ecoli_parser.process_res_file': ( 'ecoli_parser.html#process_res_file',
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'ssi_analysis_result_parsers/Ecoli_parser.py'),
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'ssi_analysis_result_parsers.Ecoli_parser.setup_logging': ( 'ecoli_parser.html#setup_logging',
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'ssi_analysis_result_parsers/Ecoli_parser.py')},
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'ssi_analysis_result_parsers.Legionella_parser': { 'ssi_analysis_result_parsers.Legionella_parser.LegionellaResults': ( 'legionella_parser.html#legionellaresults',
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'ssi_analysis_result_parsers/Legionella_parser.py'),
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'ssi_analysis_result_parsers.Legionella_parser.LegionellaResults.__repr__': ( 'legionella_parser.html#legionellaresults.__repr__',
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'ssi_analysis_result_parsers/Legionella_parser.py'),
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'ssi_analysis_result_parsers/Legionella_parser.py'),
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'ssi_analysis_result_parsers.Legionella_parser.legionella_parser': ( 'legionella_parser.html#legionella_parser',
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'ssi_analysis_result_parsers/Legionella_parser.py')},
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'ssi_analysis_result_parsers.Nmeningitidis_parser': { 'ssi_analysis_result_parsers.Nmeningitidis_parser.NmeningitidisResults': ( 'nmeningitidis_parser.html#nmeningitidisresults',
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'ssi_analysis_result_parsers/Nmeningitidis_parser.py'),
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'ssi_analysis_result_parsers.Nmeningitidis_parser.NmeningitidisResults.__repr__': ( 'nmeningitidis_parser.html#nmeningitidisresults.__repr__',
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'ssi_analysis_result_parsers/Nmeningitidis_parser.py'),
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'ssi_analysis_result_parsers.Nmeningitidis_parser.NmeningitidisResults.from_tool_paths': ( 'nmeningitidis_parser.html#nmeningitidisresults.from_tool_paths',
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'ssi_analysis_result_parsers/Nmeningitidis_parser.py'),
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'ssi_analysis_result_parsers.Nmeningitidis_parser.NmeningitidisResults.from_tool_paths_dataframe': ( 'nmeningitidis_parser.html#nmeningitidisresults.from_tool_paths_dataframe',
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'ssi_analysis_result_parsers/Nmeningitidis_parser.py'),
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'ssi_analysis_result_parsers.Nmeningitidis_parser.NmeningitidisResults.from_tool_paths_dict': ( 'nmeningitidis_parser.html#nmeningitidisresults.from_tool_paths_dict',
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'ssi_analysis_result_parsers/Nmeningitidis_parser.py'),
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'ssi_analysis_result_parsers.Nmeningitidis_parser.NmeningitidisResults.from_tool_paths_tsv': ( 'nmeningitidis_parser.html#nmeningitidisresults.from_tool_paths_tsv',
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'ssi_analysis_result_parsers/Nmeningitidis_parser.py'),
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'ssi_analysis_result_parsers.Nmeningitidis_parser.NmeningitidisResults.summary': ( 'nmeningitidis_parser.html#nmeningitidisresults.summary',
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'ssi_analysis_result_parsers/Nmeningitidis_parser.py'),
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'ssi_analysis_result_parsers/Nmeningitidis_parser.py'),
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'ssi_analysis_result_parsers/Nmeningitidis_parser.py'),
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'ssi_analysis_result_parsers/Nmeningitidis_parser.py'),
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ssi_analysis_result_parsers/Legionella_parser.py,sha256=Yp14u8xqItrIb-uVk786K6jlIi-HNfn0wnQMo_R_X1c,6950
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ssi_analysis_result_parsers/Nmeningitidis_parser.py,sha256=qZFsYMoa13vPXEVRPivMqVkj179a7LAJ7n18oLcDV_k,6906
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ssi_analysis_result_parsers/Spyogenes_parser.py,sha256=Cjibp7iKGofjSp-igm-jmjBVkQ6-zxYQWVSZT-Vx3Fo,12731
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ssi_analysis_result_parsers/__init__.py,sha256=-nNlMKS9nph3FR78_ZG9RGKrbxseeNp2K6nMr0pVGaU,23
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ssi_analysis_result_parsers-0.0.11.dist-info/licenses/LICENSE,sha256=p6aTb6QIfqyZ2Uux2VjV4F2zthdUSHZOjB4mfwGc7fo,1094
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test_input/Ecoli/ERR14229029.res,sha256=AmVZwbiUTjOQLe7SmSKWt9-URdcrsLSxt9hHUh-nFUY,129
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test_input/Legionella/lag-1_blast.tsv,sha256=MN5QL_iBn9gQ8VTYEcTnT0JwKgpkD8G15-QFOrSWxkU,1133
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test_input/Nmeningitidis/neisseria_mlst_scheme.tsv,sha256=lT2kydH5uthbqHDYCQ1OFTPl5_2olGQ29fZzgZueytA,639270
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test_input/Nmeningitidis/meningotype/meningotype1.tsv,sha256=SgzN8oiN0wurF-0SddmijbxzBBsfUO7CGhzAYP5I2bQ,248
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ssi_analysis_result_parsers-0.0.11.dist-info/METADATA,sha256=n-ciGwjniNsGbVa_xVSeIJGtK5a6k7guU2BSPE1WCQQ,2766
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ssi_analysis_result_parsers-0.0.11.dist-info/WHEEL,sha256=CmyFI0kx5cdEMTLiONQRbGQwjIoR1aIYB7eCAQ4KPJ0,91
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ssi_analysis_result_parsers-0.0.11.dist-info/entry_points.txt,sha256=OixZpyfeqGO7S_8k1ExmGc32EFBt9RX6C1W3H8vZ1K4,913
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blast_parser_allele_matches = ssi_analysis_result_parsers.blast_parser:allele_matches
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blast_parser_presence_absence = ssi_analysis_result_parsers.blast_parser:presence_absence
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get_Nmeningitidis_results = ssi_analysis_result_parsers.Nmeningitidis_parser:Nmeningitidis_parser
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#Template Score Expected Template_length Template_Identity Template_Coverage Query_Identity Query_Coverage Depth q_value p_value
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#Template Score Expected Template_length Template_Identity Template_Coverage Query_Identity Query_Coverage Depth q_value p_value
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1__wzx__O6__AJ426045 20056 153 1257 99.92 100.00 99.92 100.00 16.07 19601.01 1.0e-26
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2__wzy__O6__AJ426423 23540 159 1344 100.00 100.00 100.00 100.00 17.35 23065.87 1.0e-26
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5__fliC__H1__AB028471 107030 73 1788 100.00 100.00 100.00 100.00 62.14 106810.34 1.0e-26
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sample_name Illumina_read_files Nanopore_read_file assembly_file organism variant notes
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ERR3528110 examples/Dataset/reads/ERR3528110_1.fastq.gz,examples/Dataset/reads/ERR3528110_2.fastq.gz Na examples/Dataset/assemblies/ERR3528110.fasta E.coli Na Na
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ERR14229029 examples/Dataset/reads/ERR14229029_1.fastq.gz,examples/Dataset/reads/ERR14229029_2.fastq.gz Na examples/Dataset/assemblies/ERR14229029.fasta E.coli Na Na
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sample_name meningotype_results MLST mlst_scheme_tsv
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sample_1 test_input/Nmeningitidis/meningotype/meningotype1.tsv 1466 test_input/Nmeningitidis/neisseria_mlst_scheme.tsv
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sample_2 test_input/Nmeningitidis/meningotype/meningotype2.tsv 1157 test_input/Nmeningitidis/neisseria_mlst_scheme.tsv
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sample_3 test_input/Nmeningitidis/meningotype/meningotype3.tsv - test_input/Nmeningitidis/neisseria_mlst_scheme.tsv
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sample_4 test_input/Nmeningitidis/meningotype/meningotype4.tsv fdafd test_input/Nmeningitidis/neisseria_mlst_scheme.tsv
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sample_5 test_input/empty_file.txt fdafd test_input/Nmeningitidis/neisseria_mlst_scheme.tsv
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