virallc 1.0.12__tar.gz

virallc-1.0.12/LICENSE

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+MIT License
+
+Copyright (c) 2024 Chrispin Chaguza
+
+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.

virallc-1.0.12/PKG-INFO

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+Metadata-Version: 2.4
+Name: virallc
+Version: 1.0.12
+Summary: virallc: A Python package for consistent assignment of viral lineages
+Author-email: Chrispin Chaguza <chrispin.chaguza@gmail.com>
+Maintainer-email: Chrispin Chaguza <chrispin.chaguza@gmail.com>
+License: MIT License
+        
+        Copyright (c) 2024 Chrispin Chaguza
+        
+        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.
+        
+Project-URL: Homepage, https://github.com/ChrispinChaguza/virallc/
+Project-URL: Repository, https://github.com/ChrispinChaguza/virallc.git
+Project-URL: Issues, https://github.com/ChrispinChaguza/virallc/issues
+Project-URL: Documentation, https://github.com/ChrispinChaguza/virallc/
+Project-URL: Website, https://github.com/ChrispinChaguza/virallc
+Keywords: Virus,Lineage,Strain typing,Lineage classification,Genotype,Sublineage,Genome
+Classifier: Programming Language :: Python :: 3
+Classifier: License :: OSI Approved :: MIT License
+Classifier: Operating System :: OS Independent
+Classifier: Development Status :: 4 - Beta
+Classifier: Environment :: Console
+Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
+Classifier: Intended Audience :: Science/Research
+Requires-Python: >=3.8
+Description-Content-Type: text/markdown
+License-File: LICENSE
+Requires-Dist: setuptools
+Requires-Dist: toml
+Requires-Dist: biopython
+Requires-Dist: fsspec
+Requires-Dist: pandas
+Dynamic: license-file
+
+# ViralLC: A package rapid assignment of viral lineage nomenclature
+
+## Get the source code
+```
+git clone https://github.com/ChrispinChaguza/virallc.git
+```
+
+## About virallc
+
+## Setup
+
+The easist way to install ViralLC is using Conda (upcoming!).
+```
+conda install -c conda-forge virallc
+conda install -c bioconda virallc
+```
+
+Another way to download ViralLC from GitHub and then manually setup the environment for the package 
+
+```
+git clone https://github.com/ChrispinChaguza/virallc.git
+cd virallc
+```
+
+Install the requirement packages
+```
+#conda env export > environment.yml
+conda env create -n virallc -f environment.yml 
+```
+
+Follow the instructions below to build and install ViralLC
+
+```
+python -m build 
+pip install --force-reinstall dist/virallc-*.whl 
+```
+
+## Basic usage
+
+The simplest way to run virallc is to provide a single or separate multiple input FASTA file containing a single or multiple rotavirus A sequences.
+```
+virallc database --sequences input.fasta --output report.tsv
+```
+Or using the following shorthand options
+```
+virallc assign -s input.fasta -o report.tsv
+```
+
+If you have multiple input FASTA files, you can run virallc as follows:
+```
+virallc assign --sequences input1.fasta input2.fasta input3.fasta --output report.tsv
+```
+
+When running virallc for the first time, it will automatically download and setup the virallc database in the home directory (~/db.rotavirus.lineages/). However, if new lineages or sublineages have been assigned, you can redownload and update your local database as follows:
+```
+virallc assign --sequences input.fasta --output report.tsv --updatedb
+```
+
+Or
+```
+virallc assign -s input.fasta -o report.tsv -u
+```
+
+By default the output report containing the lineage calls will be provided in tab-separated value (TSV) file. To change the format of the output file to comma-separate value (CSV) format, specify "--csv" or "-c" options as follows:
+```
+virallc assign --sequences input.fasta --output report.tsv --csv
+```
+Or
+```
+virallc assign -s input.fasta -o report.tsv -c
+```
+
+In addition, the user can specify "--nucseq" or "-n" option to show nucleotide sequences of the query and closest matching reference sequences in the output report. To silence the output on the terminal, specify 
+"--quiet" or "-q" option.
+
+## Cite
+To be updated!

virallc-1.0.12/README.md

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+# ViralLC: A package rapid assignment of viral lineage nomenclature
+
+## Get the source code
+```
+git clone https://github.com/ChrispinChaguza/virallc.git
+```
+
+## About virallc
+
+## Setup
+
+The easist way to install ViralLC is using Conda (upcoming!).
+```
+conda install -c conda-forge virallc
+conda install -c bioconda virallc
+```
+
+Another way to download ViralLC from GitHub and then manually setup the environment for the package 
+
+```
+git clone https://github.com/ChrispinChaguza/virallc.git
+cd virallc
+```
+
+Install the requirement packages
+```
+#conda env export > environment.yml
+conda env create -n virallc -f environment.yml 
+```
+
+Follow the instructions below to build and install ViralLC
+
+```
+python -m build 
+pip install --force-reinstall dist/virallc-*.whl 
+```
+
+## Basic usage
+
+The simplest way to run virallc is to provide a single or separate multiple input FASTA file containing a single or multiple rotavirus A sequences.
+```
+virallc database --sequences input.fasta --output report.tsv
+```
+Or using the following shorthand options
+```
+virallc assign -s input.fasta -o report.tsv
+```
+
+If you have multiple input FASTA files, you can run virallc as follows:
+```
+virallc assign --sequences input1.fasta input2.fasta input3.fasta --output report.tsv
+```
+
+When running virallc for the first time, it will automatically download and setup the virallc database in the home directory (~/db.rotavirus.lineages/). However, if new lineages or sublineages have been assigned, you can redownload and update your local database as follows:
+```
+virallc assign --sequences input.fasta --output report.tsv --updatedb
+```
+
+Or
+```
+virallc assign -s input.fasta -o report.tsv -u
+```
+
+By default the output report containing the lineage calls will be provided in tab-separated value (TSV) file. To change the format of the output file to comma-separate value (CSV) format, specify "--csv" or "-c" options as follows:
+```
+virallc assign --sequences input.fasta --output report.tsv --csv
+```
+Or
+```
+virallc assign -s input.fasta -o report.tsv -c
+```
+
+In addition, the user can specify "--nucseq" or "-n" option to show nucleotide sequences of the query and closest matching reference sequences in the output report. To silence the output on the terminal, specify 
+"--quiet" or "-q" option.
+
+## Cite
+To be updated!

virallc-1.0.12/pyproject.toml

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+[build-system]
+requires = ["setuptools"]
+
+[project]
+name = "virallc"
+version = "1.0.12"
+authors = [
+  { name="Chrispin Chaguza", email="chrispin.chaguza@gmail.com" },
+]
+
+maintainers = [
+  {name = "Chrispin Chaguza", email = "chrispin.chaguza@gmail.com"},
+]
+
+description = "virallc: A Python package for consistent assignment of viral lineages"
+readme = {file = "README.md", content-type = "text/markdown"}
+license = {file = "LICENSE"}
+requires-python = ">=3.8"
+classifiers = [
+    "Programming Language :: Python :: 3",
+    "License :: OSI Approved :: MIT License",
+    "Operating System :: OS Independent",
+    "Development Status :: 4 - Beta",
+    "Environment :: Console",
+    "Topic :: Scientific/Engineering :: Bio-Informatics",
+    "Intended Audience :: Science/Research",
+]
+
+keywords = ["Virus","Lineage","Strain typing","Lineage classification","Genotype","Sublineage","Genome"]
+dependencies = [
+   "setuptools",
+   "toml",
+   "biopython",
+   "fsspec",
+   "pandas"
+]
+
+[tool.setuptools.packages]
+find = {} 
+
+[tool.setuptools]
+py-modules = ["virallc.SeqLib.SeqLib","virallc"]
+
+[project.scripts]
+virallc = "virallc:main"
+alnPairDist = "virallc.scripts.alnPairDist:main"
+cleanFastaSeqs = "virallc.scripts.cleanFastaSeqs:main"
+virallcLineageChecker = "virallc.scripts.virallcLineageChecker:main"
+alnSeqCov = "virallc.scripts.alnSeqCov:main"
+virallcClusters = "virallc.scripts.virallcClusters:main"
+virallcClusters3L = "virallc.scripts.virallcClusters3L:main"
+
+[project.urls]
+Homepage = "https://github.com/ChrispinChaguza/virallc/"
+Repository = "https://github.com/ChrispinChaguza/virallc.git"
+Issues = "https://github.com/ChrispinChaguza/virallc/issues"
+Documentation = "https://github.com/ChrispinChaguza/virallc/"
+Website = "https://github.com/ChrispinChaguza/virallc"
+

virallc-1.0.12/setup.cfg

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+[egg_info]
+tag_build = 
+tag_date = 0
+