📖 How to Use TSUMUGI

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) to extract and visualize gene modules based on phenotypic similarity.

TSUMUGI (紡ぎ in Japanese) 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).

👉 Phenotype list

Gene

Specify one gene to search for other genes whose KO mice show similar phenotypes.
Gene symbols follow MGI.

👉 Gene list

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:

{"significant": true, "sexual_dimorphism": "Female", "effect_size": 0.0119677350763567, "marker_symbol": "4930447C04Rik", "zygosity": "Homo", "marker_accession_id": "MGI:1923051", "mp_term_id": "MP:0000063", "disease_annotation": ["Male Infertility With Azoospermia Or Oligozoospermia Due To Single Gene Mutation", "Premature Ovarian Failure 18", "Spermatogenic Failure 52"], "life_stage": "Early", "mp_term_name": "decreased bone mineral density"}

`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": "1500009L16Rik", "gene2_symbol": "Aak1", "phenotype_shared_annotations": [{"mp_term_name": "increased circulating enzyme level", "life_stage": "Early", "zygosity": "Homo", "sexual_dimorphism": "None"}], "phenotype_similarity_score": 47}

🌐 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

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; binary list: 👉 here) 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:

conda install -c conda-forge -c bioconda tsumugi

PyPI:

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.

Important

All commands except tsumugi run require either pairwise_similarity_annotation.jsonl.gz or genewise_phenotype_annotation.jsonl.gz. Both files can be downloaded from the TSUMUGI top page.

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.

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.

tsumugi mp [-h] (-i MP_ID | -e MP_ID) [-g | -p] [-m PATH_MP_OBO] [-a PATH_GENEWISE_ANNOTATIONS] [--in PATH_PAIRWISE_ANNOTATIONS]
                  [--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 PATH_MP_OBO`, `--mp_obo PATH_MP_OBO`

Path to Mammalian Phenotype ontology (mp.obo). If omitted, uses the bundled data/mp.obo.

`-a PATH_GENEWISE_ANNOTATIONS`, `--genewise_annotations PATH_GENEWISE_ANNOTATIONS`

Path to the genewise annotation file (JSONL/.gz). Required for --exclude; also specify when using --genewise.

`--in PATH_PAIRWISE_ANNOTATIONS`

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.

# 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`)

tsumugi count [-h] (-g | -p) [--min MIN] [--max MAX] [--in PATH_PAIRWISE_ANNOTATIONS] [-a PATH_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 PATH_PAIRWISE_ANNOTATIONS`

Path to the pairwise annotation file (JSONL/.gz). If omitted, reads from STDIN.

`-a PATH_GENEWISE_ANNOTATIONS`, `--genewise_annotations PATH_GENEWISE_ANNOTATIONS`

Path to the genewise annotation file (JSONL/.gz). Required with --genewise.

Shared phenotypes per pair:

tsumugi count --pairwise --min 3 --max 20 \
  --in pairwise_similarity_annotations.jsonl.gz \
  > pairwise_min3_max20.jsonl

Phenotypes per gene (genewise required):

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`)

tsumugi score [-h] [--min MIN] [--max MAX] [--in PATH_PAIRWISE_ANNOTATIONS]

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 PATH_PAIRWISE_ANNOTATIONS`

Path to the pairwise annotation file (JSONL/.gz). If omitted, reads from STDIN.

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`)

tsumugi genes [-h] (-k GENE_SYMBOL | -d GENE_SYMBOL) [-g | -p] [--in PATH_PAIRWISE_ANNOTATIONS]

`-k GENE_SYMBOL`, `--keep GENE_SYMBOL`

Keep only pairs containing specified genes in a text file.

`-d GENE_SYMBOL`, `--drop GENE_SYMBOL`

Drop pairs containing specified genes in a text file.

`-g, --genewise`

Filter by user-provided gene symbols.

`-p, --pairwise`

Filter by user-provided gene pairs.

`--in PATH_PAIRWISE_ANNOTATIONS`

Path to the pairwise annotation file (JSONL/.gz). If omitted, reads from STDIN.

cat << EOF > genes.txt
Maf
Aamp
Cacna1c
EOF

tsumugi genes --genewise --keep genes.txt \
  --in "$directory"/pairwise_similarity_annotations.jsonl.gz \
  > pairwise_keep_genes.jsonl

cat << EOF > gene_pairs.csv
Maf,Aamp
Maf,Cacna1c
EOF

tsumugi genes --pairwise --drop gene_pairs.csv \
  --in pairwise_similarity_annotations.jsonl.gz \
  > pairwise_drop_genes.jsonl

Filter by life stage (`tsumugi life-stage --keep/--drop`)

tsumugi life-stage [-h] (-k LIFE_STAGE | -d LIFE_STAGE) [--in PATH_PAIRWISE_ANNOTATIONS]

`-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 PATH_PAIRWISE_ANNOTATIONS`

Path to the pairwise annotation file (JSONL/.gz). If omitted, reads from STDIN.

tsumugi life-stage --keep Early \
  --in pairwise_similarity_annotations.jsonl.gz \
  > pairwise_lifestage_early.jsonl

Filter by sex (`tsumugi sex --keep/--drop`)

tsumugi sex [-h] (-k SEX | -d SEX) [--in PATH_PAIRWISE_ANNOTATIONS]

`-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 PATH_PAIRWISE_ANNOTATIONS`

Path to the pairwise annotation file (JSONL/.gz). If omitted, reads from STDIN.

tsumugi sex --drop Male \
  --in pairwise_similarity_annotations.jsonl.gz \
  > pairwise_no_male.jsonl

Filter by zygosity (`tsumugi zygosity --keep/--drop`)

tsumugi zygosity [-h] (-k ZYGOSITY | -d ZYGOSITY) [--in PATH_PAIRWISE_ANNOTATIONS]

`-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 PATH_PAIRWISE_ANNOTATIONS`

Path to the pairwise annotation file (JSONL/.gz). If omitted, reads from STDIN.

tsumugi zygosity --keep Homo \
  --in pairwise_similarity_annotations.jsonl.gz \
  > pairwise_homo.jsonl

Export GraphML / webapp

tsumugi build-graphml [-h] [--in PATH_PAIRWISE_ANNOTATIONS] -a PATH_GENEWISE_ANNOTATIONS

`--in PATH_PAIRWISE_ANNOTATIONS`

Path to the pairwise annotation file (JSONL/.gz). If omitted, reads from STDIN.

`-a PATH_GENEWISE_ANNOTATIONS`, `--genewise_annotations PATH_GENEWISE_ANNOTATIONS`

Path to the genewise annotation file (JSONL/.gz). Required.

tsumugi build-graphml \
  --in pairwise_similarity_annotations.jsonl.gz \
  --genewise genewise_phenotype_annotations.jsonl.gz \
  > network.graphml

tsumugi build-webapp [-h] [--in PATH_PAIRWISE_ANNOTATIONS] -a PATH_GENEWISE_ANNOTATIONS -o OUT

`--in PATH_PAIRWISE_ANNOTATIONS`

Path to the pairwise annotation file (JSONL/.gz). If omitted, reads from STDIN.

`-a PATH_GENEWISE_ANNOTATIONS`, `--genewise_annotations PATH_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.

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

We use the IMPC dataset Release-23.0 statistical-results-ALL.csv.gz.
See dataset columns: Data fields

Preprocessing

Extract gene–phenotype pairs whose KO mouse P-values (p_value, female_ko_effect_p_value, or male_ko_effect_p_value) are ≤ 0.0001.

Annotate genotype-specific phenotypes as homo, hetero, or hemi.
Annotate sex-specific phenotypes as female or male.

Phenotypic similarity

TSUMUGI adopts a Phenodigm-like approach (Smedley D, et al. (2013)).

Note

Differences from the original Phenodigm are as follows.

Terms below the 5th percentile of IC are set to IC=0, so overly general phenotypes (e.g., embryo phenotype) are not evaluated.
We apply weighting based on metadata matches in genotype, life stage, and sex.

1. Definition of MP term-pair similarity

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 IC=0.
For each MP term pair, find the most specific common ancestor (MICA) and use its IC as Resnik similarity.
For two MP terms, compute the Jaccard index of their ancestor sets.
Define MP term-pair similarity as sqrt(Resnik * Jaccard).

2. Weighting by phenotype metadata agreement

Apply weights based on phenotype metadata: genotype, life stage, and sex.
For each gene pair, build an MP-term × MP-term similarity matrix.
Multiply by weights 0.2, 0.5, 0.75, 1.0 for 0, 1, 2, 3 matches of genotype/life stage/sex.

3. Phenodigm scaling

Apply Phenodigm-style scaling to normalize each KO mouse phenotype similarity to 0–100:
Compute observed max/mean, then normalize by theoretical max/mean.
Score = 100 * (normalized_max + normalized_mean) / 2
If the denominator is 0, the score is set to 0.

✉️ Contact

Google Form: https://forms.gle/ME8EJZZHaRNgKZ979
GitHub Issues: https://github.com/akikuno/TSUMUGI-dev/issues/new/choose

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📖 How to Use TSUMUGI

Phenotype

Gene

Gene List

📥 Download data

genewise_phenotype_annotations.jsonl.gz

pairwise_similarity_annotations.jsonl.gz

🌐 Network

Network panel

Control panel

Filter by phenotypic similarity

Filter by phenotype severity

Specify genotype

Specify sex

Specify life stage

Markup panel

Highlight: Human Disease

Search: Specific Gene

Layout & Display

Export

🛠 Command-Line Interface (CLI)

Features

Installation

Available commands

Usage

Recompute from IMPC data (tsumugi run)

Filter by MP term (tsumugi mp --include/--exclude)

-i MP_ID, --include MP_ID

-e MP_ID, --exclude MP_ID

-g, --genewise

-p, --pairwise

-m PATH_MP_OBO, --mp_obo PATH_MP_OBO

-a PATH_GENEWISE_ANNOTATIONS, --genewise_annotations PATH_GENEWISE_ANNOTATIONS

--in PATH_PAIRWISE_ANNOTATIONS

--life_stage LIFE_STAGE

--sex SEX

--zygosity ZYGOSITY

Filter by phenotype counts (tsumugi count)

-g, --genewise

-p, --pairwise

--min MIN, --max MAX

--in PATH_PAIRWISE_ANNOTATIONS

-a PATH_GENEWISE_ANNOTATIONS, --genewise_annotations PATH_GENEWISE_ANNOTATIONS

Filter by similarity score (tsumugi score)

--min MIN, --max MAX

--in PATH_PAIRWISE_ANNOTATIONS

Filter by gene list (tsumugi genes --keep/--drop)

-k GENE_SYMBOL, --keep GENE_SYMBOL

-d GENE_SYMBOL, --drop GENE_SYMBOL

-g, --genewise

-p, --pairwise

--in PATH_PAIRWISE_ANNOTATIONS

Filter by life stage (tsumugi life-stage --keep/--drop)

-k LIFE_STAGE, --keep LIFE_STAGE

-d LIFE_STAGE, --drop LIFE_STAGE

--in PATH_PAIRWISE_ANNOTATIONS

Filter by sex (tsumugi sex --keep/--drop)

-k SEX, --keep SEX

-d SEX, --drop SEX

--in PATH_PAIRWISE_ANNOTATIONS

Filter by zygosity (tsumugi zygosity --keep/--drop)

-k ZYGOSITY, --keep ZYGOSITY

-d ZYGOSITY, --drop ZYGOSITY

--in PATH_PAIRWISE_ANNOTATIONS

Export GraphML / webapp

--in PATH_PAIRWISE_ANNOTATIONS

-a PATH_GENEWISE_ANNOTATIONS, --genewise_annotations PATH_GENEWISE_ANNOTATIONS

--in PATH_PAIRWISE_ANNOTATIONS

-a PATH_GENEWISE_ANNOTATIONS, --genewise_annotations PATH_GENEWISE_ANNOTATIONS

-o OUT, --out OUT

🔍 How We Calculate Phenotypically Similar Genes

Data source

Preprocessing

Phenotypic similarity

`genewise_phenotype_annotations.jsonl.gz`

`pairwise_similarity_annotations.jsonl.gz`

Recompute from IMPC data (`tsumugi run`)

Filter by MP term (`tsumugi mp --include/--exclude`)

`-i MP_ID`, `--include MP_ID`

`-e MP_ID`, `--exclude MP_ID`

`-g`, `--genewise`

`-p`, `--pairwise`

`-m PATH_MP_OBO`, `--mp_obo PATH_MP_OBO`

`-a PATH_GENEWISE_ANNOTATIONS`, `--genewise_annotations PATH_GENEWISE_ANNOTATIONS`

`--in PATH_PAIRWISE_ANNOTATIONS`

`--life_stage LIFE_STAGE`

`--sex SEX`

`--zygosity ZYGOSITY`

Filter by phenotype counts (`tsumugi count`)

`-g`, `--genewise`

`-p`, `--pairwise`

`--min MIN`, `--max MAX`

`--in PATH_PAIRWISE_ANNOTATIONS`

`-a PATH_GENEWISE_ANNOTATIONS`, `--genewise_annotations PATH_GENEWISE_ANNOTATIONS`

Filter by similarity score (`tsumugi score`)

`--min MIN`, `--max MAX`

`--in PATH_PAIRWISE_ANNOTATIONS`

Filter by gene list (`tsumugi genes --keep/--drop`)

`-k GENE_SYMBOL`, `--keep GENE_SYMBOL`

`-d GENE_SYMBOL`, `--drop GENE_SYMBOL`

`-g, --genewise`

`-p, --pairwise`

`--in PATH_PAIRWISE_ANNOTATIONS`

Filter by life stage (`tsumugi life-stage --keep/--drop`)

`-k LIFE_STAGE`, `--keep LIFE_STAGE`

`-d LIFE_STAGE`, `--drop LIFE_STAGE`

`--in PATH_PAIRWISE_ANNOTATIONS`

Filter by sex (`tsumugi sex --keep/--drop`)

`-k SEX`, `--keep SEX`

`-d SEX`, `--drop SEX`

`--in PATH_PAIRWISE_ANNOTATIONS`

Filter by zygosity (`tsumugi zygosity --keep/--drop`)

`-k ZYGOSITY`, `--keep ZYGOSITY`

`-d ZYGOSITY`, `--drop ZYGOSITY`

`--in PATH_PAIRWISE_ANNOTATIONS`

`--in PATH_PAIRWISE_ANNOTATIONS`

`-a PATH_GENEWISE_ANNOTATIONS`, `--genewise_annotations PATH_GENEWISE_ANNOTATIONS`

`--in PATH_PAIRWISE_ANNOTATIONS`

`-a PATH_GENEWISE_ANNOTATIONS`, `--genewise_annotations PATH_GENEWISE_ANNOTATIONS`

`-o OUT`, `--out OUT`