meancure 1.0.0__tar.gz

meancure-1.0.0/LICENSE

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+MIT License
+
+Copyright (c) 2026 Christoph Schomburg
+
+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.

meancure-1.0.0/PKG-INFO

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+Metadata-Version: 2.4
+Name: meancure
+Version: 1.0.0
+Summary: Metabarcoding Analysis with a Custom Reference
+Project-URL: Homepage, https://github.com/cschomb/Metabarcoding-Analysis-with-a-Custom-Reference
+Project-URL: Issues, https://github.com/cschomb/Metabarcoding-Analysis-with-a-Custom-Reference/issues
+Author-email: Christoph Schomburg <c.schomburg@uni-kassel.de>
+License-Expression: MIT
+License-File: LICENSE
+Classifier: Operating System :: OS Independent
+Classifier: Programming Language :: Python :: 3
+Requires-Python: >=3.8
+Requires-Dist: numpy>=2.3.5
+Requires-Dist: openpyxl>=3.1.5
+Requires-Dist: pandas>=2.3.3
+Requires-Dist: pyproj>=3.7.2
+Requires-Dist: requests>=2.31.0
+Requires-Dist: tqdm>=4.67.1
+Requires-Dist: urllib3>=2.0.7
+Description-Content-Type: text/markdown
+
+# MEtabarcoding-ANalysis against a CUstom REference (MEAN-CURE)
+
+## Introduction
+This script is used for the Analysis of Metabarcoding results from the Apscale Pipeline from a custom reference database. It assignes taxonomic information to the ESV sequences and can check the plausibility of these assignments by querying GBIF occurrence records.
+
+### BLAST search
+Performs a BLAST search of ESV sequences against a custom reference database (see Requirements for details). The maximum number of BLAST hits to keep can be set in the settings file. It also incorporates information about the length of the query coverage, which is used in the analysis step.
+
+### Analysis
+Filters the BLAST hits, so that the top 3% of the most identical records remain as candidates. These results are then calculated into a BLAST score.
+
+### GBIF occurrence search
+The resulting analysed esv tabel can further be checked against occurrence records on GBIF. The settings file allows the creation of a circle (point and radius) in which occurrences should be present. Cutoffs for the year since when occurrences are counted and the minimum number of occurrences can be set. The best blast hits (family, genus and species level) from the results file will be labeled as plausible or implausible depending on occurrences in the set parameters. Entries from the other_candidates column will only appear, if they are likely to occur according to GBIF. 

meancure-1.0.0/README.md

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+# MEtabarcoding-ANalysis against a CUstom REference (MEAN-CURE)
+
+## Introduction
+This script is used for the Analysis of Metabarcoding results from the Apscale Pipeline from a custom reference database. It assignes taxonomic information to the ESV sequences and can check the plausibility of these assignments by querying GBIF occurrence records.
+
+### BLAST search
+Performs a BLAST search of ESV sequences against a custom reference database (see Requirements for details). The maximum number of BLAST hits to keep can be set in the settings file. It also incorporates information about the length of the query coverage, which is used in the analysis step.
+
+### Analysis
+Filters the BLAST hits, so that the top 3% of the most identical records remain as candidates. These results are then calculated into a BLAST score.
+
+### GBIF occurrence search
+The resulting analysed esv tabel can further be checked against occurrence records on GBIF. The settings file allows the creation of a circle (point and radius) in which occurrences should be present. Cutoffs for the year since when occurrences are counted and the minimum number of occurrences can be set. The best blast hits (family, genus and species level) from the results file will be labeled as plausible or implausible depending on occurrences in the set parameters. Entries from the other_candidates column will only appear, if they are likely to occur according to GBIF. 

meancure-1.0.0/pyproject.toml

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+[build-system]
+requires = ["hatchling >= 1.26"]
+build-backend = "hatchling.build"
+
+[project]
+name = "meancure"
+version = "1.0.0"
+authors = [
+  { name="Christoph Schomburg", email="c.schomburg@uni-kassel.de" },
+]
+description = "Metabarcoding Analysis with a Custom Reference"
+readme = "README.md"
+requires-python = ">=3.8"
+classifiers = [
+    "Programming Language :: Python :: 3",
+    "Operating System :: OS Independent",
+]
+dependencies = [
+  "numpy>=2.3.5",
+  "pandas>=2.3.3",
+  "requests>=2.31.0",
+  "openpyxl>=3.1.5",
+  "pyproj>=3.7.2",
+  "urllib3>=2.0.7",
+  "tqdm>=4.67.1",
+]
+license = "MIT"
+license-files = ["LICEN[CS]E*"]
+
+[project.urls]
+Homepage = "https://github.com/cschomb/Metabarcoding-Analysis-with-a-Custom-Reference"
+Issues = "https://github.com/cschomb/Metabarcoding-Analysis-with-a-Custom-Reference/issues"
+
+[project.scripts]
+meancure = "meancure_CS5150.meancure:main"