ssi-analysis-result-parsers 0.0.1__py3-none-any.whl

ssi_analysis_result_parsers/some_string.py

@@ -0,0 +1,27 @@
+# AUTOGENERATED! DO NOT EDIT! File to edit: ../nbs/02_template.ipynb.
+
+# %% auto 0
+__all__ = []
+
+# %% ../nbs/02_template.ipynb 3
+# standard libs
+import os
+import re
+
+# Common to template
+# add into settings.ini, requirements, package name is python-dotenv, for conda build ensure `conda config --add channels conda-forge`
+import dotenv  # for loading config from .env files, https://pypi.org/project/python-dotenv/
+import envyaml  # Allows to loads env vars into a yaml file, https://github.com/thesimj/envyaml
+import fastcore  # To add functionality related to nbdev development, https://github.com/fastai/fastcore/
+from fastcore import (
+    test,
+)
+from fastcore.script import (
+    call_parse,
+)  # for @call_parse, https://fastcore.fast.ai/script
+import json  # for nicely printing json and yaml
+
+# import functions from core module (optional, but most likely needed).
+from . import core
+
+# Project specific libraries

ssi_analysis_result_parsers-0.0.1.dist-info/METADATA

@@ -0,0 +1,109 @@
+Metadata-Version: 2.4
+Name: ssi_analysis_result_parsers
+Version: 0.0.1
+Summary: TODO
+Home-page: https://github.com/thej-ssi/ssi_analysis_result_parsers
+Author: thej-ssi
+Author-email: thej@ssi.dk
+License: MIT License
+Keywords: nbdev jupyter notebook python
+Classifier: Development Status :: 4 - Beta
+Classifier: Intended Audience :: Developers
+Classifier: Natural Language :: English
+Classifier: Programming Language :: Python :: 3.9
+Classifier: Programming Language :: Python :: 3.10
+Classifier: Programming Language :: Python :: 3.11
+Classifier: Programming Language :: Python :: 3.12
+Classifier: License :: OSI Approved :: MIT License
+Requires-Python: >=3.9
+Description-Content-Type: text/markdown
+License-File: LICENSE
+Requires-Dist: fastcore
+Requires-Dist: python_dotenv
+Requires-Dist: envyaml
+Requires-Dist: pandas
+Requires-Dist: black
+Provides-Extra: dev
+Dynamic: author
+Dynamic: author-email
+Dynamic: classifier
+Dynamic: description
+Dynamic: description-content-type
+Dynamic: home-page
+Dynamic: keywords
+Dynamic: license
+Dynamic: license-file
+Dynamic: provides-extra
+Dynamic: requires-dist
+Dynamic: requires-python
+Dynamic: summary
+
+# ssi_analysis_result_parsers
+
+
+<!-- WARNING: THIS FILE WAS AUTOGENERATED! DO NOT EDIT! -->
+
+This file will become your README and also the index of your
+documentation.
+
+## Developer Guide
+
+If you are new to using `nbdev` here are some useful pointers to get you
+started.
+
+### Install ssi_analysis_result_parsers in Development mode
+
+``` sh
+# make sure ssi_analysis_result_parsers package is installed in development mode
+$ pip install -e .
+
+# make changes under nbs/ directory
+# ...
+
+# compile to have changes apply to ssi_analysis_result_parsers
+$ nbdev_prepare
+```
+
+## Usage
+
+### Installation
+
+Install latest from the GitHub
+[repository](https://github.com/$GIT_USER_NAME/ssi_analysis_result_parsers):
+
+``` sh
+$ pip install git+https://github.com/$GIT_USER_NAME/ssi_analysis_result_parsers.git
+```
+
+or from
+[conda](https://anaconda.org/$GIT_USER_NAME/ssi_analysis_result_parsers)
+
+``` sh
+$ conda install -c $GIT_USER_NAME ssi_analysis_result_parsers
+```
+
+or from [pypi](https://pypi.org/project/ssi_analysis_result_parsers/)
+
+``` sh
+$ pip install ssi_analysis_result_parsers
+```
+
+### Documentation
+
+Documentation can be found hosted on this GitHub
+[repository](https://github.com/$GIT_USER_NAME/ssi_analysis_result_parsers)’s
+[pages](https://$GIT_USER_NAME.github.io/ssi_analysis_result_parsers/).
+Additionally you can find package manager specific guidelines on
+[conda](https://anaconda.org/$GIT_USER_NAME/ssi_analysis_result_parsers)
+and [pypi](https://pypi.org/project/ssi_analysis_result_parsers/)
+respectively.
+
+## How to use
+
+Fill me in please! Don’t forget code examples:
+
+``` python
+1+1
+```
+
+    2

ssi_analysis_result_parsers-0.0.1.dist-info/RECORD

@@ -0,0 +1,21 @@
+ssi_analysis_result_parsers/Legionella_parser.py,sha256=cDaBYC6UjuXLI1GGSihY6zlVFBcqYDhmhFZ5xfchSSQ,3279
+ssi_analysis_result_parsers/__init__.py,sha256=sXLh7g3KC4QCFxcZGBTpG2scR7hmmBsMjq6LqRptkRg,22
+ssi_analysis_result_parsers/_modidx.py,sha256=Kojwrr-9jPtuKhxTDhjhs5cn1FBm_A-U9J1AND_eujw,5159
+ssi_analysis_result_parsers/blast_parser.py,sha256=Yam04LnF2-eECalVGyyq7DDq3ZYRqrQ6I8dX0Z0V8-w,7389
+ssi_analysis_result_parsers/core.py,sha256=6j6mQQws-mcR2Ef7KY_9F8jenrT9a_DtGYVH-9D9rzw,10335
+ssi_analysis_result_parsers/hello_world.py,sha256=jpN94sqYuNHqUbUZMCJ35qGY5iLPB_emucgnDGDUk_U,1895
+ssi_analysis_result_parsers/some_string.py,sha256=JwmAXKbX_JgY8UGh4FAu5-7ZjezcAEhq4Q2B73pWp2M,923
+ssi_analysis_result_parsers/config/config.default.env,sha256=Zt6bfPbVV3rYCksoebX1ruAdFgeD9wqAnKDtswhtJJM,1390
+ssi_analysis_result_parsers/config/config.default.yaml,sha256=3qgUrUtQpxrzYv7WQaHsvz9dQB0RALKNU0idxv7oRqM,460
+ssi_analysis_result_parsers-0.0.1.dist-info/licenses/LICENSE,sha256=p6aTb6QIfqyZ2Uux2VjV4F2zthdUSHZOjB4mfwGc7fo,1094
+test_input/.DS_Store,sha256=sdTEvl9DTKPHNPYYjMqDepX7q7ZETlonk21tGEuWLao,6148
+test_input/Legionella/lag-1_blast.tsv,sha256=MN5QL_iBn9gQ8VTYEcTnT0JwKgpkD8G15-QFOrSWxkU,1133
+test_input/Legionella/test.sbt.tsv,sha256=ibhaH3is2dxHaABPvR2QM2HAq9bKOs1AwOTmrwSrcd8,168
+test_input/blast_parser/allele_matches_test.tsv,sha256=7vfQAOxz3fKc84HtxN9eoCyQoF9G8MFd-GKH3Krw_Cs,233035
+test_input/blast_parser/gene_presence_absence_test.tsv,sha256=qCvMkBC-1GuXx83RDhnGAuuBXAlIq4e_IW0rrNVn2yA,1447
+test_output/output_with_sample_name.tsv,sha256=NQG7WaxczuWCCsX2a9MUxCCYpbuAirz9gw08OLdEdUo,41
+ssi_analysis_result_parsers-0.0.1.dist-info/METADATA,sha256=lLlQweqBO3vbnxiQdvfIXyOJtDZjJ5Xv4D4fA4lL8Pw,2753
+ssi_analysis_result_parsers-0.0.1.dist-info/WHEEL,sha256=CmyFI0kx5cdEMTLiONQRbGQwjIoR1aIYB7eCAQ4KPJ0,91
+ssi_analysis_result_parsers-0.0.1.dist-info/entry_points.txt,sha256=nR2p-a6E4W1Xg7oR-f4OXXcnR7ohtT64ZdyaCPG7N7k,355
+ssi_analysis_result_parsers-0.0.1.dist-info/top_level.txt,sha256=3q56bBc2Wv2a6ZQ1l_9m66vot2-Qu6tM9tDr3QQ8auM,81
+ssi_analysis_result_parsers-0.0.1.dist-info/RECORD,,

ssi_analysis_result_parsers-0.0.1.dist-info/WHEEL

@@ -0,0 +1,5 @@
+Wheel-Version: 1.0
+Generator: setuptools (78.1.0)
+Root-Is-Purelib: true
+Tag: py3-none-any
+

ssi_analysis_result_parsers-0.0.1.dist-info/entry_points.txt

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+[console_scripts]
+blast_parser_allele_matches = ssi_analysis_result_parsers.blast_parser:allele_matches
+blast_parser_presence_absence = ssi_analysis_result_parsers.blast_parser:presence_absence
+legionella_parser = ssi_analysis_result_parsers.Legionella_parser:legionella_parser
+
+[nbdev]
+ssi_analysis_result_parsers = ssi_analysis_result_parsers._modidx:d

ssi_analysis_result_parsers-0.0.1.dist-info/licenses/LICENSE

@@ -0,0 +1,8 @@
+The MIT License (MIT)
+Copyright © 2023 Statens Serum Institut
+
+Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the “Software”), to deal in the Software without restriction, including without limitation the rights to use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of the Software, and to permit persons to whom the Software is furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in all copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED “AS IS”, WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.

ssi_analysis_result_parsers-0.0.1.dist-info/top_level.txt

@@ -0,0 +1,8 @@
+_proc
+config
+input
+nbs
+output
+ssi_analysis_result_parsers
+test_input
+test_output

test_input/Legionella/lag-1_blast.tsv

@@ -0,0 +1 @@
+lag-1	contig_5	99.907	1074	1074	1	1074	4693	5766	ATGTACAATAAACTCACAGCAAGTCAAGCAGCCTACCTAAATTTTCTTCGAGGGTTTTCAGCTATAATAGTTTTGGCTGGACATACCTTATCAGGCATATCCGGGGTAATTTCATTTGGAAAACAATTGCCTTTCCAATCCTTGGCAGTAAATGCTTTTTTTTGGCTCTCTGGATTTTTGATTACGTATCATTGTATAACAAAGAAACCGTATTCATTTGTAGAATATATGATTGATCGTTTCTGCAGAATTTATGTCATTTACATTCCTGTGTTGATTTTATCAGTTTTTTTGTTAGTGGAGGCAGAGTTGGCATCAATGCCTAAACTTAAAGAGTGGATTGCTAATATTCTCATGATACAACATACTCCTTTTAATCGAATTTTTGAATTTTTACCTACTATTCCACCTTTAGCTCAAATTTCCCCATTGTGGTCAATAGCAGTTGAGTGGTGGTTATATACTTTGTTTGGGATAGCCTTTTTTTTTCATAAAAGCTCTTTTGCTACCAGGCTTATAATGAGCTTATTAATTATTCCTGCTTTGCTAGTTGCTGGATATTTCACATTAAAAGAGTATGTTGCTTTGGTATGGTTTCTGGGTTCTGGGTGCGCCTATCATTTCTGTAATATAAATAGGAAGTATAATAATCACGCGATTTTAATGCTTAGTTTAATCACAGGCGCAGCTTTTCTGGTTAGATTCTATGTCTTAAAGCATTCACTAATGAATATGTATGATTTGCAATTAGTCATTCCTGGCTGTATCTTTTTGTATTCACTGTTGTTATTACTGTCAACAAACAAACAAAACAAAAAAATTGAATTAATTTCAACATTTCTTGCATTTATTTCCTATACACTGTATTTGAGCCATGAGCCAATAAGAAGAGTTGTATCCACATTTATTGAACCGACGAATTTAAAGAGGGGCTTCCTTATTTGTGGAGTTTGTATTGCTTGCGCAACTATCATCGCTTATTTATTAGAGAACAAACATCTCGTAGTTCGCGAGTGGCTAAAAAATAAACTTTTGCAAAAAAATACATCAAACAAGTTGGCTTATTCAACATAA	0.0	1978

test_input/Legionella/test.sbt.tsv

@@ -0,0 +1,2 @@
+sample	ST	flaA	pilE	asd	mip	mompS	proA	neuA	notes
+LEG-2024-R10861.fasta	23	2	3	9	10	2	1	6	Exact ST match, Heterozygous mompS alleles, High confidence mompS allele call