TSUMUGI 1.0.1__py3-none-any.whl

tsumugi-1.0.1.dist-info/METADATA

@@ -0,0 +1,504 @@
+Metadata-Version: 2.4
+Name: TSUMUGI
+Version: 1.0.1
+Summary: TSUMUGI: Phenotype-Driven Gene Network Identifier
+License: MIT
+License-File: LICENSE
+Author: Akihiro Kuno
+Author-email: akuno@md.tsukuba.ac.jp
+Requires-Python: >=3.10
+Classifier: License :: OSI Approved :: MIT License
+Classifier: Operating System :: OS Independent
+Classifier: Programming Language :: Python :: 3
+Classifier: Programming Language :: Python :: 3.10
+Classifier: Programming Language :: Python :: 3.11
+Classifier: Programming Language :: Python :: 3.12
+Classifier: Programming Language :: Python :: 3.13
+Classifier: Programming Language :: Python :: 3.14
+Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
+Requires-Dist: networkx (>=3.3)
+Requires-Dist: numpy (>=1.21.0)
+Requires-Dist: tqdm (>=4.64.0)
+Project-URL: Homepage, https://github.com/akikuno/TSUMUGI
+Description-Content-Type: text/markdown
+
+<p align="center">
+    <a href="https://larc-tsukuba.github.io/tsumugi/" target="_blank">
+        <img src="https://raw.githubusercontent.com/akikuno/TSUMUGI-dev/refs/heads/main/image/tsumugi-logo.jpg" alt="Tsumugi Logo" width="80%">
+    </a>
+</p>
+
+[![License](https://img.shields.io/badge/License-MIT-9cf.svg)](https://choosealicense.com/licenses/mit/)
+[![Test](https://img.shields.io/github/actions/workflow/status/akikuno/tsumugi-dev/pytest.yml?branch=main&label=Test&color=brightgreen)](https://github.com/akikuno/tsumugi-dev/actions)
+[![PyPI](https://img.shields.io/pypi/v/tsumugi.svg?label=PyPI&color=orange)](https://pypi.org/project/tsumugi/)
+[![Bioconda](https://img.shields.io/conda/v/bioconda/tsumugi?label=Bioconda&color=orange)](https://anaconda.org/bioconda/tsumugi)
+[![DOI](https://zenodo.org/badge/441025227.svg)](https://doi.org/10.5281/zenodo.14957711)
+[![Contact](https://img.shields.io/badge/Contact-923DE2)](https://forms.gle/ME8EJZZHaRNgKZ979)
+
+Translations: [日本語](https://github.com/akikuno/TSUMUGI-dev/blob/main/doc/README_JP.md) | [한국어](https://github.com/akikuno/TSUMUGI-dev/blob/main/doc/README_KR.md) | [简体中文](https://github.com/akikuno/TSUMUGI-dev/blob/main/doc/README_ZH_CN.md) | [繁體中文](https://github.com/akikuno/TSUMUGI-dev/blob/main/doc/README_ZH_TW.md) | [हिन्दी](https://github.com/akikuno/TSUMUGI-dev/blob/main/doc/README_HI.md) | [Bahasa Indonesia](https://github.com/akikuno/TSUMUGI-dev/blob/main/doc/README_ID.md) | [Tiếng Việt](https://github.com/akikuno/TSUMUGI-dev/blob/main/doc/README_VN.md) | [Español](https://github.com/akikuno/TSUMUGI-dev/blob/main/doc/README_ES.md) | [Français](https://github.com/akikuno/TSUMUGI-dev/blob/main/doc/README_FR.md) | [Deutsch](https://github.com/akikuno/TSUMUGI-dev/blob/main/doc/README_DE.md) | [Português](https://github.com/akikuno/TSUMUGI-dev/blob/main/doc/README_PT.md)
+
+**TSUMUGI (Trait-driven Surveillance for Mutation-based Gene module Identification)** is a web tool that uses knockout (KO) mouse phenotype data from the [International Mouse Phenotyping Consortium (IMPC)](https://www.mousephenotype.org/) to **extract and visualize gene modules based on phenotypic similarity**.  
+
+**TSUMUGI (紡ぎ)** comes from the idea of “weaving together gene groups that form phenotypes.”
+
+This web app is available to everyone online👇️  
+
+🔗https://larc-tsukuba.github.io/tsumugi/
+
+# 📖 How to Use TSUMUGI
+
+TSUMUGI supports three kinds of input.
+
+### Phenotype
+Enter a phenotype of interest to search for **genes whose KO mice have similar overall phenotype profiles**.  
+Phenotype names follow [Mammalian Phenotype Ontology (MPO)](https://www.informatics.jax.org/vocab/mp_ontology).
+
+👉 [Phenotype list](https://github.com/larc-tsukuba/tsumugi/blob/main/data/available_mp_terms.txt)
+
+### Gene
+Specify one gene to search for **other genes whose KO mice show similar phenotypes**.  
+Gene symbols follow [MGI](http://www.informatics.jax.org/).
+
+👉 [Gene list](https://github.com/larc-tsukuba/tsumugi/blob/main/data/available_gene_symbols.txt)
+
+### Gene List
+Paste multiple genes (one per line). This extracts phenotypically similar genes **among the genes in the list**.
+
+> [!CAUTION]  
+> If no similar genes are found: `No similar phenotypes were found among the entered genes.`  
+> If more than 200 similar genes are found: `Too many genes submitted. Please limit the number to 200 or fewer.`
+
+### 📥 Download data
+
+TSUMUGI reports gzipped JSONL files.
+
+#### `genewise_phenotype_annotations.jsonl.gz`
+- Gene symbol (e.g., "1110059G10Rik")  
+- Marker accession ID (e.g., "MGI:1913452")  
+- Phenotype term name/ID (e.g., "fused joints", "MP:0000137")  
+- Effect size (e.g., 0.0, 1.324)  
+- Significance flag (true/false)  
+- Zygosity ("Homo", "Hetero", "Hemi")  
+- Life stage ("Embryo", "Early", "Interval", "Late")  
+- Sexual dimorphism ("None", "Male", "Female")  
+- Disease annotation (e.g., [] or "Premature Ovarian Failure 18")
+
+Example:
+```
+{"life_stage": "Early", "marker_symbol": "1110059G10Rik", "marker_accession_id": "MGI:1913452", "effect_size": 0.0, "mp_term_name": "fused joints", "disease_annotation": [], "significant": false, "zygosity": "Homo", "sexual_dimorphism": "None", "mp_term_id": "MP:0000137"}
+```
+
+#### `pairwise_similarity_annotations.jsonl.gz`
+- Gene pair (`gene1_symbol`, `gene2_symbol`)  
+- `phenotype_shared_annotations` (per-phenotype metadata: life stage, zygosity, sexual dimorphism)  
+- `phenotype_similarity_score` (Phenodigm score, 0–100)
+
+Example:
+```
+{"gene1_symbol": "1110059G10Rik", "gene2_symbol": "Cog6", "phenotype_shared_annotations": {"vertebral transformation": {"zygosity": "Homo", "life_stage": "Early", "sexual_dimorphism": "Male"}}, "phenotype_similarity_score": 42}
+```
+
+# 🌐 Network
+
+The page transitions and draws the network automatically.
+
+> [!IMPORTANT]  
+> Gene pairs with **3 or more shared abnormal phenotypes** and **phenotypic similarity > 0.0** are visualized.
+
+### Network panel
+**Nodes** represent genes. Click to see the list of abnormal phenotypes observed in that KO mouse; drag to rearrange positions.  
+**Edges** show shared phenotypes; click to view details.
+**Modules** outline subnetworks of genes. Click a module to list phenotypes involving its member genes; drag modules to reposition them and avoid overlap.
+
+### Control panel
+Adjust network display from the left panel.
+
+#### Filter by phenotypic similarity
+`Phenotypes similarity` slider thresholds edges by Resnik→Phenodigm score.  
+
+> [!NOTE]
+> For how we compute similarity, see: 👉 [🔍 How We Calculate Phenotypically Similar Genes](#-how-we-calculate-phenotypically-similar-genes)
+
+#### Filter by phenotype severity
+`Phenotype severity` slider filters nodes by effect size (severity in KO mice). Higher values mean stronger impact.  
+
+> [!NOTE]
+> Hidden for binary phenotypes (e.g., [abnormal embryo development](https://larc-tsukuba.github.io/tsumugi/app/phenotype/abnormal_embryo_development.html); binary list: 👉 [here](https://github.com/larc-tsukuba/tsumugi/blob/main/data/binary_phenotypes.txt)) or gene(s) input.
+
+#### Specify genotype
+Choose the genotype in which phenotypes appear:
+- `Homo`: homozygous
+- `Hetero`: heterozygous
+- `Hemi`: hemizygous
+
+#### Specify sex
+Extract sex-specific phenotypes:
+- `Female`
+- `Male`
+
+#### Specify life stage
+Filter by life stage in which phenotypes appear:
+- `Embryo`
+- `Early` (0–16 weeks)
+- `Interval` (17–48 weeks)
+- `Late` (49+ weeks)
+
+### Markup panel
+
+#### Highlight: Human Disease
+Highlight genes linked to human disease (IMPC Disease Models Portal data).
+
+#### Search: Specific Gene
+Search gene names within the network.
+
+#### Layout & Display
+Adjust layout, font size, edge width, and node repulsion (Cose layout).
+
+#### Export
+Export the current network as PNG/CSV/GraphML.  
+CSV includes connected-component (module) IDs and phenotype lists per gene; GraphML is Cytoscape-compatible.
+
+# 🛠 Command-Line Interface (CLI)
+
+The TSUMUGI CLI allows you to use the latest IMPC data downloaded locally, and provides more fine-grained filtering and output options than the web tool.
+
+## Features
+
+- Recompute with IMPC `statistical-results-ALL.csv.gz` (optionally `mp.obo`, `impc_phenodigm.csv`).  
+- Filter by presence/absence of MP terms.  
+- Filter by gene list (comma-separated or text file).  
+- Outputs: GraphML (`tsumugi build-graphml`), offline webapp bundle (`tsumugi build-webapp`).
+
+## Installation
+
+BioConda:
+```bash
+conda install -c conda-forge -c bioconda tsumugi
+```
+
+PyPI:
+```bash
+pip install tsumugi
+```
+
+You are ready if `tsumugi --version` prints the version.
+
+## Available commands
+
+- `tsumugi run`: Recompute the network from IMPC data  
+- `tsumugi mp --include/--exclude (--pairwise/--genewise)`: Filter gene pairs or genes that contain / do not show an MP term  
+- `tsumugi count --pairwise/--genewise (--min/--max)`: Filter by phenotype counts (pairwise or per gene)  
+- `tsumugi score (--min/--max)`: Filter by phenotype similarity score (pairwise)  
+- `tsumugi genes --keep/--drop`: Keep/drop by gene list (comma-separated or text file)  
+- `tsumugi life-stage --keep/--drop`: Filter by life stage (Embryo/Early/Interval/Late)  
+- `tsumugi sex --keep/--drop`: Filter by sex (Male/Female/None)  
+- `tsumugi zygosity --keep/--drop`: Filter by zygosity (Homo/Hetero/Hemi)  
+- `tsumugi build-graphml`: Generate GraphML (Cytoscape, etc.)  
+- `tsumugi build-webapp`: Generate TSUMUGI webapp assets (local HTML/CSS/JS)
+
+> [!NOTE]
+> All filtering subcommands stream JSONL to STDOUT.  
+> Redirect with `>` if you want to save results to a file.
+
+
+## Usage
+
+### Recompute from IMPC data (`tsumugi run`)
+If `--mp_obo` is omitted, TSUMUGI uses the bundled `data-version: releases/2025-08-27/mp.obo`.  
+If `--impc_phenodigm` is omitted, it uses the file fetched on 2025-10-01 from the [IMPC Disease Models Portal](https://diseasemodels.research.its.qmul.ac.uk/).
+```bash
+tsumugi run \
+  --output_dir ./tsumugi-output \
+  --statistical_results ./statistical-results-ALL.csv.gz \
+  --threads 8
+```
+Outputs: `./tsumugi-output` contains genewise annotations (genewise_phenotype_annotations.jsonl.gz), pairwise similarity data (pairwise_similarity_annotations.jsonl.gz), and visualization assets (`TSUMUGI-webapp`).
+
+> [!IMPORTANT]  
+> The `TSUMUGI-webapp` directory includes OS-specific launch scripts; double-click to open the local web app:  
+> - Windows: `open_webapp_windows.bat`  
+> - macOS: `open_webapp_mac.command`  
+> - Linux: `open_webapp_linux.sh`
+
+### Filter by MP term (`tsumugi mp --include/--exclude`)
+Extract gene pairs (or genes) that include phenotypes of interest, or pairs whose relevant phenotypes were measured but did not show significant abnormalities.
+
+```txt
+tsumugi mp [-h] (-i MP_ID | -e MP_ID) [-g | -p] [-m MP_OBO] [-a GENEWISE_ANNOTATIONS] [--in IN] [--life_stage LIFE_STAGE] [--sex SEX] [--zygosity ZYGOSITY]
+```
+
+#### `-i MP_ID`, `--include MP_ID`
+Include genes/gene pairs that have the specified MP term (descendants included).
+
+#### `-e MP_ID`, `--exclude MP_ID`
+Return genes/gene pairs that were measured for the specified MP term (descendants included) and did **not** show a significant phenotype. Requires `-a/--genewise_annotations`.
+
+#### `-g`, `--genewise`
+Filter at gene level. Reads `genewise_phenotype_annotations.jsonl(.gz)`. When using `--genewise`, specify `-a/--genewise_annotations`.
+
+#### `-p`, `--pairwise`
+Filter at gene-pair level. Targets `pairwise_similarity_annotations.jsonl(.gz)`. If `--in` is omitted, reads from STDIN.
+
+#### `-m MP_OBO`, `--mp_obo MP_OBO`
+Path to Mammalian Phenotype ontology (mp.obo). If omitted, uses the bundled `data/mp.obo`.
+
+#### `-a GENEWISE_ANNOTATIONS`, `--genewise_annotations GENEWISE_ANNOTATIONS`
+Path to the genewise annotation file (JSONL/.gz). Required for `--exclude`; also specify when using `--genewise`.
+
+#### `--in IN`
+Path to the pairwise annotation file (JSONL/.gz). If omitted, reads from STDIN.
+
+#### `--life_stage LIFE_STAGE`
+Additional filter by life stage. Available values: `Embryo`, `Early`, `Interval`, `Late`.
+
+#### `--sex SEX`
+Additional filter by sexual dimorphism. Use the values present in annotations (e.g., `Male`, `Female`, `None`).
+
+#### `--zygosity ZYGOSITY`
+Additional filter by zygosity. Available values: `Homo`, `Hetero`, `Hemi`.
+
+```bash
+# Extract only gene pairs that include MP:0001146 (abnormal testis morphology) or descendant terms (e.g., MP:0004849 abnormal testis size)
+tsumugi mp --include MP:0001146 \
+  --in pairwise_similarity_annotations.jsonl.gz \
+  > pairwise_filtered.jsonl
+
+# Extract gene pairs whose measured genes include MP:0001146 and descendant terms and did not show a significant abnormality
+tsumugi mp --exclude MP:0001146 \
+  --genewise genewise_phenotype_annotations.jsonl.gz \
+  --in pairwise_similarity_annotations.jsonl.gz \
+  > pairwise_filtered.jsonl
+
+# Extract significant gene-level annotations containing MP:0001146 (descendants included)
+tsumugi mp --include MP:0001146 \
+  --genewise \
+  --genewise_annotations genewise_phenotype_annotations.jsonl.gz \
+  > genewise_filtered.jsonl
+
+# Extract genes measured for MP:0001146 (descendants included) that did not show a significant abnormality
+tsumugi mp --exclude MP:0001146 \
+  --genewise \
+  --genewise_annotations genewise_phenotype_annotations.jsonl.gz \
+  > genewise_no_phenotype.jsonl
+```
+
+> [!IMPORTANT]
+> **Descendant MP terms of the specified ID are also handled.**  
+> For example, if you specify `MP:0001146 (abnormal testis morphology)`, descendant terms such as `MP:0004849 (abnormal testis size)` are considered as well.
+
+### Filter by phenotype counts (`tsumugi count`)
+```txt
+tsumugi count [-h] (-g | -p) [--min MIN] [--max MAX] [--in IN] [-a GENEWISE_ANNOTATIONS]
+```
+
+Filter genes or gene pairs by the number of phenotypes. At least one of `--min` or `--max` is required.
+
+#### `-g`, `--genewise`
+Filter by the number of significant phenotypes per gene. Requires `-a/--genewise_annotations` with `genewise_phenotype_annotations.jsonl(.gz)`.
+
+#### `-p`, `--pairwise`
+Filter by the number of shared phenotypes per gene pair. If `--in` is omitted, reads `pairwise_similarity_annotations.jsonl(.gz)` from STDIN.
+
+#### `--min MIN`, `--max MAX`
+Lower/upper bounds for phenotype counts. Use either flag alone for one-sided filtering.
+
+#### `--in IN`
+Path to the pairwise annotation file (JSONL/.gz). If omitted, reads from STDIN.
+
+#### `-a GENEWISE_ANNOTATIONS`, `--genewise_annotations GENEWISE_ANNOTATIONS`
+Path to the genewise annotation file (JSONL/.gz). Required with `--genewise`.
+
+- Shared phenotypes per pair:
+```bash
+tsumugi count --pairwise --min 3 --max 20 \
+  --in pairwise_similarity_annotations.jsonl.gz \
+  > pairwise_min3_max20.jsonl
+```
+- Phenotypes per gene (genewise required):
+```bash
+tsumugi count --genewise --min 5 --max 50 \
+  --genewise genewise_phenotype_annotations.jsonl.gz \
+  --in pairwise_similarity_annotations.jsonl.gz \
+  > genewise_min5_max50.jsonl
+```
+`--min` or `--max` alone is fine.
+
+### Filter by similarity score (`tsumugi score`)
+```txt
+tsumugi score [-h] [--min MIN] [--max MAX] [--in IN]
+```
+
+Filter gene pairs by `phenotype_similarity_score` (0–100). At least one of `--min` or `--max` is required.
+
+#### `--min MIN`, `--max MAX`
+Lower/upper bounds for phenotype similarity score. Use either flag alone for one-sided filtering.
+
+#### `--in IN`
+Path to the pairwise annotation file (JSONL/.gz). If omitted, reads from STDIN.
+
+```bash
+tsumugi score --min 50 --max 80 \
+  --in pairwise_similarity_annotations.jsonl.gz \
+  > pairwise_score50_80.jsonl
+```
+
+`--min` or `--max` alone is fine.
+
+### Filter by gene list (`tsumugi genes --keep/--drop`)
+```txt
+tsumugi genes [-h] (-k GENE_SYMBOL | -d GENE_SYMBOL) [--in IN]
+```
+
+#### `-k GENE_SYMBOL`, `--keep GENE_SYMBOL`
+Keep only pairs containing specified genes (comma-separated list or text file).
+
+#### `-d GENE_SYMBOL`, `--drop GENE_SYMBOL`
+Drop pairs containing specified genes (comma-separated list or text file).
+
+#### `--in IN`
+Path to the pairwise annotation file (JSONL/.gz). If omitted, reads from STDIN.
+
+```bash
+tsumugi genes --keep genes.txt \
+  --in pairwise_similarity_annotations.jsonl.gz \
+  > pairwise_keep_genes.jsonl
+
+tsumugi genes --drop geneA,geneB \
+  --in pairwise_similarity_annotations.jsonl.gz \
+  > pairwise_drop_genes.jsonl
+```
+
+### Filter by life stage (`tsumugi life-stage --keep/--drop`)
+```txt
+tsumugi life-stage [-h] (-k LIFE_STAGE | -d LIFE_STAGE) [--in IN]
+```
+
+#### `-k LIFE_STAGE`, `--keep LIFE_STAGE`
+Keep only annotations with the specified life stage (`Embryo`, `Early`, `Interval`, `Late`).
+
+#### `-d LIFE_STAGE`, `--drop LIFE_STAGE`
+Drop annotations with the specified life stage.
+
+#### `--in IN`
+Path to the pairwise annotation file (JSONL/.gz). If omitted, reads from STDIN.
+
+```bash
+tsumugi life-stage --keep Early \
+  --in pairwise_similarity_annotations.jsonl.gz \
+  > pairwise_lifestage_early.jsonl
+```
+
+### Filter by sex (`tsumugi sex --keep/--drop`)
+```txt
+tsumugi sex [-h] (-k SEX | -d SEX) [--in IN]
+```
+
+#### `-k SEX`, `--keep SEX`
+Keep only annotations with the specified sexual dimorphism (`Male`, `Female`, `None`).
+
+#### `-d SEX`, `--drop SEX`
+Drop annotations with the specified sexual dimorphism.
+
+#### `--in IN`
+Path to the pairwise annotation file (JSONL/.gz). If omitted, reads from STDIN.
+
+```bash
+tsumugi sex --drop Male \
+  --in pairwise_similarity_annotations.jsonl.gz \
+  > pairwise_no_male.jsonl
+```
+
+### Filter by zygosity (`tsumugi zygosity --keep/--drop`)
+```txt
+tsumugi zygosity [-h] (-k ZYGOSITY | -d ZYGOSITY) [--in IN]
+```
+
+#### `-k ZYGOSITY`, `--keep ZYGOSITY`
+Keep only annotations with the specified zygosity (`Homo`, `Hetero`, `Hemi`).
+
+#### `-d ZYGOSITY`, `--drop ZYGOSITY`
+Drop annotations with the specified zygosity.
+
+#### `--in IN`
+Path to the pairwise annotation file (JSONL/.gz). If omitted, reads from STDIN.
+
+```bash
+tsumugi zygosity --keep Homo \
+  --in pairwise_similarity_annotations.jsonl.gz \
+  > pairwise_homo.jsonl
+```
+
+### Export GraphML / webapp
+```txt
+tsumugi build-graphml [-h] [--in IN] -a GENEWISE_ANNOTATIONS
+```
+
+#### `--in IN`
+Path to the pairwise annotation file (JSONL/.gz). If omitted, reads from STDIN.
+
+#### `-a GENEWISE_ANNOTATIONS`, `--genewise_annotations GENEWISE_ANNOTATIONS`
+Path to the genewise annotation file (JSONL/.gz). Required.
+
+```bash
+tsumugi build-graphml \
+  --in pairwise_similarity_annotations.jsonl.gz \
+  --genewise genewise_phenotype_annotations.jsonl.gz \
+  > network.graphml
+```
+
+```txt
+tsumugi build-webapp [-h] [--in IN] -a GENEWISE_ANNOTATIONS -o OUT
+```
+
+#### `--in IN`
+Path to the pairwise annotation file (JSONL/.gz). If omitted, reads from STDIN.
+
+#### `-a GENEWISE_ANNOTATIONS`, `--genewise_annotations GENEWISE_ANNOTATIONS`
+Path to the genewise annotation file (JSONL/.gz). Required.
+
+#### `-o OUT`, `--out OUT`
+Output directory for the webapp bundle (HTML/CSS/JS + network data). Do not specify a filename with an extension.
+
+```bash
+tsumugi build-webapp \
+  --in pairwise_similarity_annotations.jsonl.gz \
+  --genewise genewise_phenotype_annotations.jsonl.gz \
+  --output_dir ./webapp_output
+```
+
+CLI supports STDIN/STDOUT, so you can chain commands:  
+`zcat pairwise_similarity_annotations.jsonl.gz | tsumugi mp ... | tsumugi genes ... > out.jsonl`
+
+# 🔍 How We Calculate Phenotypically Similar Genes
+
+## Data source
+[IMPC Release-23.0](https://ftp.ebi.ac.uk/pub/databases/impc/all-data-releases/release-23.0/results) `statistical-results-ALL.csv.gz`  
+Columns: [Data fields](https://www.mousephenotype.org/help/programmatic-data-access/data-fields/)
+
+## Preprocessing
+Extract gene–phenotype pairs with KO mouse P-value (`p_value`, `female_ko_effect_p_value`, or `male_ko_effect_p_value`) ≤ 0.0001.  
+- Annotate genotype-specific phenotypes: `homo`, `hetero`, `hemi`  
+- Annotate sex-specific phenotypes: `female`, `male`
+
+## Phenotypic similarity
+TSUMUGI currently follows a **Phenodigm-like** approach ([Smedley D, et al. (2013)](https://doi.org/10.1093/database/bat025)). We compute **Resnik similarity** between MP terms and **Jaccard similarity** between term sets, then combine them by the **geometric mean**. The key difference from the original Phenodigm is that TSUMUGI adds **metadata weighting** (zygosity, life stage, sexual dimorphism) when aggregating similarities.
+
+1. Build the MP ontology and compute Information Content(IC) for each term:  
+   `IC(term) = -log((|Descendants(term)| + 1) / |All MP terms|)`  
+   Terms below the 5th percentile of IC are set to 0.
+2. For each MP term pair, find the most specific common ancestor and compute Resnik similarity as its IC.  
+   Compute Jaccard index over the ancestor sets.  
+   Pairwise term similarity = `sqrt(Resnik * Jaccard)`.
+3. For each gene pair, build a term-by-term similarity matrix and apply metadata weighting.  
+   Zygosity, life stage, and sexual dimorphism matches contribute weights of 0.25/0.5/0.75/1.0 for 0/1/2/3 matches.
+4. Apply Phenodigm-style scaling to 0–100:  
+   Use row/column maxima to get actual max and mean similarity.  
+   Normalize by theoretical max/mean based on IC, then compute  
+   `Score = 100 * (normalized_max + normalized_mean) / 2`.  
+   If a theoretical denominator is 0, that term is set to 0.
+
+
+# ✉️ Contact
+- Google Form: https://forms.gle/ME8EJZZHaRNgKZ979  
+- GitHub Issues: https://github.com/akikuno/TSUMUGI-dev/issues/new/choose
+

tsumugi-1.0.1.dist-info/RECORD

@@ -0,0 +1,64 @@
+TSUMUGI/annotator.py,sha256=-t-gneApB-TywJ50OJtiSHP4DBOcdNEnL9Bo-NozbQo,3759
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tsumugi-1.0.1.dist-info/WHEEL

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+Wheel-Version: 1.0
+Generator: poetry-core 2.3.0
+Root-Is-Purelib: true
+Tag: py3-none-any

tsumugi-1.0.1.dist-info/entry_points.txt

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+[console_scripts]
+tsumugi=TSUMUGI.main:main
+

tsumugi-1.0.1.dist-info/licenses/LICENSE

@@ -0,0 +1,21 @@
+MIT License
+
+Copyright (c) 2021 Akihiro Kuno
+
+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.