krakenparser 0.6.0__tar.gz

krakenparser-0.6.0/KrakenParser.egg-info/PKG-INFO

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+Metadata-Version: 2.2
+Name: krakenparser
+Version: 0.6.0
+Summary: A collection of scripts designed to process Kraken2 reports and convert them into CSV format.
+Home-page: https://github.com/PopovIILab/KrakenParser
+Author: Ilia Popov
+Author-email: iljapopov17@gmail.com
+Requires-Python: >=3.6
+Description-Content-Type: text/markdown
+License-File: LICENSE
+Requires-Dist: pandas==2.2.3
+Requires-Dist: matplotlib==3.10.0
+Requires-Dist: numpy==2.2.0
+Requires-Dist: pandas==2.2.3
+Requires-Dist: plotly==5.24.1
+Requires-Dist: seaborn==0.13.2
+Requires-Dist: scipy==1.14.1
+Requires-Dist: scikit-bio==0.6.3
+Dynamic: author
+Dynamic: author-email
+Dynamic: description
+Dynamic: description-content-type
+Dynamic: home-page
+Dynamic: requires-dist
+Dynamic: requires-python
+Dynamic: summary
+
+# KrakenParser: Convert Kraken2 Reports to CSV
+
+## Overview
+KrakenParser is a collection of scripts designed to process Kraken2 reports and convert them into CSV format. This pipeline extracts taxonomic abundance data at six levels:
+- **Phylum**
+- **Class**
+- **Order**
+- **Family**
+- **Genus**
+- **Species**
+
+You can run the entire pipeline with **a single command**, or use the scripts **individually** depending on your needs.
+
+🔗 Please visit [KrakenParser wiki](https://github.com/PopovIILab/KrakenParser/wiki) page
+
+## Output example
+
+### Total abundance output
+
+`counts_phylum.csv` parsed from 7 kraken2 reports of metagenomic samples using `KrakenParser`:
+
+```
+Sample_id,Calditrichota,Caldisericota,Thermosulfidibacterota,Elusimicrobiota,Candidatus Fervidibacterota,Lentisphaerota,Kiritimatiellota,Vulcanimicrobiota,Thermodesulfobiota,Atribacterota,Dictyoglomota,Nitrospinota,Chrysiogenota,Coprothermobacterota,Aquificota,Thermotogota,Bdellovibrionota,Nitrospirota,Deferribacterota,Synergistota,Myxococcota,Acidobacteriota,Candidatus Bipolaricaulota,Candidatus Saccharibacteria,Candidatus Absconditabacteria,Fusobacteriota,Spirochaetota,Candidatus Omnitrophota,Chlamydiota,Verrucomicrobiota,Planctomycetota,Thermodesulfobacteriota,Campylobacterota,Candidatus Cloacimonadota,Fibrobacterota,Gemmatimonadota,Balneolota,Rhodothermota,Ignavibacteriota,Chlorobiota,Bacteroidota,Deinococcota,Thermomicrobiota,Armatimonadota,Chloroflexota,Cyanobacteriota,Mycoplasmatota,Actinomycetota,Bacillota,Pseudomonadota,Heterolobosea,Parabasalia,Fornicata,Evosea,Bacillariophyta,Cercozoa,Euglenozoa,Apicomplexa,Microsporidia,Basidiomycota,Ascomycota,Nanoarchaeota,Candidatus Micrarchaeota,Candidatus Thermoplasmatota,Candidatus Lokiarchaeota,Nitrososphaerota,Euryarchaeota,Thermoproteota,Hofneiviricota,Artverviricota,Nucleocytoviricota,Cossaviricota,Kitrinoviricota,Negarnaviricota,Lenarviricota,Pisuviricota,Peploviricota,Uroviricota
+X1,0,0,0,0,0,0,0,0,1,1,1,1,2,3,4,5,7,8,9,17,23,25,5,13,22,47,54,1,6,27,31,128,151,2,6,13,1,3,7,44,14991,7,9,11,61,414,449,3551,55304,438645,0,0,0,0,0,0,1,22,0,4,15,0,0,0,0,0,3,191,0,0,1,88,0,0,0,161,0,1241
+X2,1,4,14,20,5,12,15,6,8,15,2,15,109,68,182,97,79,196,70,272,331,149,36,77,35,562,1237,21,33,129,427,1044,543,8,98,25,16,45,11,1043,41374,160,28,161,1348,1196,2709,15864,431170,2747842,22,7,301,373,134,136,107,3239,54,1151,2905,0,0,3,5,6,7,410,0,0,0,736,0,3,11,26,1,1552
+...
+X8,1,19,0,47,0,1,6,20,28,0,1,1,47,7,336,110,30,32,10,93,85,48,9,7,7,154,386,0,14,19,106,358,242,14,5,134,15,11,7,18,54057,106,10,24,212,340,1128,16220,567908,650264,95,4,193,402,314,300,187,4376,37,9796,8653,0,1,0,1,5,23,1778,1,1,0,1,1,4,66,30,4,1263
+X9,0,3,2,16,7,1,23,12,10,9,1,2,134,40,390,289,29,372,27,81,150,90,9,88,32,287,881,14,33,60,319,1045,328,15,22,22,10,72,8,63,35301,127,15,48,412,935,2343,11500,380765,2613854,0,0,0,0,0,0,5,74,0,38,40,3,0,0,0,1,3,275,0,0,0,0,0,2,118,25,0,1675
+
+```
+
+### Relative abundance output
+
+`ra_phylum.csv` calculated from 7 kraken2 reports of metagenomic samples using `KrakenParser`:
+
+```
+Sample_id,taxon,rel_abund_perc
+X1,Pseudomonadota,85.03558294577552
+X1,Bacillota,10.72121619814011
+X1,Other (<4.0%),4.243200856084384
+X2,Pseudomonadota,84.28702055549813
+X2,Bacillota,13.225663867469137
+X2,Other (<4.0%),2.487315577032736
+...
+X8,Pseudomonadota,49.25373021277305
+X8,Bacillota,43.01574040339849
+X8,Bacteroidota,4.094504530639667
+X8,Other (<4.0%),3.6360248531887933
+X9,Pseudomonadota,85.62839981589192
+X9,Bacillota,12.473649123439218
+X9,Other (<4.0%),1.8979510606688494
+```
+
+### α-diversity output
+
+`alpha_div.csv` calculated from 7 kraken2 reports of metagenomic samples using `KrakenParser`:
+
+```
+Sample,Shannon,Pielou,Chao1
+X1,3.911345447107001,0.5269245043289149,2274.533185840708
+X2,3.9944130792536563,0.4906424221265042,4155.0
+...
+X8,3.442077115880119,0.42753293021330063,4177.251358695652
+X9,4.033664950188261,0.5050385978575492,3492.16
+```
+
+### β-diversity output
+
+`beta_div_bray.csv` calculated from 7 kraken2 reports of metagenomic samples using `KrakenParser`:
+
+```
+,X1,X2,...,X8,X9
+X1,0.0,0.398,...,0.61,0.353
+X2,0.398,0.0,...,0.723,0.388
+...
+X8,0.61,0.723,...,0.0,0.665
+X9,0.353,0.388,...,0.665,0.0
+```
+
+`beta_div_jaccard.csv` calculated from 7 kraken2 reports of metagenomic samples using `KrakenParser`:
+
+```
+,X1,X2,...,X8,X9
+X1,0.0,0.7073170731707317,...,0.8223938223938224,0.7232472324723247
+X2,0.7073170731707317,0.0,...,0.835016835016835,0.7352941176470589
+...
+X8,0.8223938223938224,0.835016835016835,...,0.0,0.8066914498141264
+X9,0.7232472324723247,0.7352941176470589,...,0.8066914498141264,0.0
+```
+
+### Visualization examples gallery
+
+|[Stacked Barplot](https://github.com/PopovIILab/KrakenParser/wiki/Stacked-Barplot-API)|[Streamgraph](https://github.com/PopovIILab/KrakenParser/wiki/Streamgraph-API)|
+|-------|-------|
+|![kpstbar](https://github.com/user-attachments/assets/916b0164-28be-4f49-9634-707408487b85)|![kpstream](https://github.com/user-attachments/assets/5c6d930c-e85f-4e2e-9dbf-8caefca49a76)|
+
+[Stacked Barplot + Streamgraph](https://github.com/PopovIILab/KrakenParser/wiki/Combined-Stacked-Barplot-&-Streamgraph)|[Clustermap](https://github.com/PopovIILab/KrakenParser/wiki/Clustermap)|
+|-------|-------|
+|![combined_white](https://github.com/user-attachments/assets/58acea93-f079-46fd-ac4b-d2ac83098c59)|![kpclust](https://github.com/user-attachments/assets/98a4d540-7c43-4802-8f77-277a5637a7a1)|
+
+## Quick Start (Full Pipeline)
+To run the full pipeline, use the following command:
+```bash
+KrakenParser --complete -i data/kreports
+#Having troubles? Run KrakenParser --complete -h
+```
+This will:
+1. Convert Kraken2 reports to MPA format
+2. Combine MPA files into a single file
+3. Extract taxonomic levels into separate text files
+4. Process extracted text files
+5. Convert them into CSV format
+6. Calculate relative abundance
+7. Calculate α & β-diversities
+
+### **Input Requirements**
+- The Kraken2 reports must be inside a **subdirectory** (e.g., `data/kreports`).
+- The script automatically creates output directories and processes the data.
+
+## Installation
+
+```
+pip install krakenparser
+```
+
+## Using Individual Modules
+You can also run each step manually if needed.
+
+### **Step 1: Convert Kraken2 Reports to MPA Format**
+```bash
+KrakenParser --kreport2mpa -i data/kreports -o data/mpa
+#Having troubles? Run KrakenParser --kreport2mpa -h
+```
+This script converts Kraken2 `.kreport` files into **MPA format** using KrakenTools.
+
+### **Step 2: Combine MPA Files**
+```bash
+KrakenParser --combine_mpa -i data/mpa/* -o data/COMBINED.txt
+#Having troubles? Run KrakenParser --combine_mpa -h
+```
+This merges multiple MPA files into a single combined file.
+
+### **Step 3: Extract Taxonomic Levels**
+```bash
+KrakenParser --deconstruct -i data/COMBINED.txt -o data/counts
+#Having troubles? Run KrakenParser --deconstruct -h
+```
+
+If user wants to inspect **Viruses** domain separately:
+```bash
+KrakenParser --deconstruct_viruses -i data/COMBINED.txt -o data/counts_viruses
+#Having troubles? Run KrakenParser --deconstruct_viruses -h
+```
+
+This step extracts only species-level data (excluding human reads).
+
+### **Step 4: Process Extracted Taxonomic Data**
+```bash
+KrakenParser --process -i data/COMBINED.txt -o data/counts/txt/counts_phylum.txt
+#Having troubles? Run KrakenParser --process -h
+```
+
+Repeat on other 5 taxonomical levels (class, order, family, genus, species) or wrap up `KrakenParser --process` to a loop!
+
+This script cleans up taxonomic names (removes prefixes, replaces underscores with spaces).
+
+### **Step 5: Convert TXT to CSV**
+```bash
+KrakenParser --txt2csv -i data/counts/txt/counts_phylum.txt -o data/counts/csv/counts_phylum.csv
+#Having troubles? Run KrakenParser --txt2csv -h
+```
+Repeat on other 5 taxonomical levels (class, order, family, genus, species) or wrap up `KrakenParser --txt2csv` to a loop!
+
+This converts the processed text files into structured CSV format.
+
+### **Step 6: Calculate relative abundance**
+```bash
+KrakenParser --relabund -i data/counts/csv/counts_phylum.csv -o data/counts/csv_relabund/counts_phylum.csv
+#Having troubles? Run KrakenParser --relabund -h
+```
+Repeat on other 5 taxonomical levels (class, order, family, genus, species) or wrap up `KrakenParser --relabund` to a loop!
+
+This calculates relative abundance and saves as CSV format.
+
+If user wants to group low abundant taxa in "Other" group:
+```bash
+KrakenParser --relabund -i data/counts/csv/counts_phylum.csv -o data/counts/csv_relabund/counts_phylum.csv --other 3.5
+#Having troubles? Run KrakenParser --relabund -h
+```
+
+This will group all the taxa that have abundance <3.5 into "Other <3.5%" group. Other parameters are welcome!
+
+### **Step 7: Calculate α & β-diversities**
+```bash
+KrakenParser --diversity -i data/counts/csv/counts_species.csv -o data/diversity
+#Having troubles? Run KrakenParser --diversity -h
+```
+
+This calculates α & β-diversities and saves them as CSV format to directory provided in the output.
+
+If user wants to use another depth for β-diversity calculations:
+```bash
+KrakenParser --diversity -i data/counts/csv/counts_species.csv -o data/diversity --depth 750
+#Having troubles? Run KrakenParser --diversity -h
+```
+
+Other parameters are welcome!
+
+## Arguments Breakdown
+### **KrakenParser** (Main Pipeline)
+- Automates the entire workflow.
+- Takes **one argument**: the path to Kraken2 reports (`data/kreports`).
+- Runs all the scripts in sequence.
+
+### **--kreport2mpa** (Step 1)
+- Converts Kraken2 reports to MPA format.
+- Uses `KrakenTools/kreport2mpa.py`.
+
+### **--combine_mpa** (Step 2)
+- Combines multiple MPA files into one.
+- Uses `KrakenTools/combine_mpa.py`.
+
+### **--deconstruct** & **--deconstruct_viruses** (Step 3)
+- Extracts **phylum, class, order, family, genus, species** into separate text files.
+- Removes human-related reads (**--deconstruct** only).
+
+### **--process** (Step 4)
+- Cleans and formats extracted taxonomic data.
+- Removes prefixes (`s__`, `g__`, etc.), replaces underscores with spaces.
+
+### **--txt2csv** (Step 5)
+- Converts cleaned text files to CSV.
+- Transposes data so that sample names become rows.
+
+### **--relabund** (Step 6)
+- Calculates relative abundance based on total abundance CSV.
+- Optionally can group low abundant taxa.
+
+### **--diversity** (Step 7)
+- Calculates α & β-diversities based on total species abundance CSV.
+- Shannon, Pielou & Chao1 indices for α-diversity
+- Bray-Curtis & Jaccard indices for β-diversity
+- Uses 1000 depth for β-diversity as default (can be adjusted with -d)
+
+## Example Output Structure
+After running the full pipeline, the output directory will look like this:
+```
+data/
+├─ kreports/               # Input Kraken2 reports
+├─ mpa/                    # Converted MPA files
+├─ COMBINED.txt            # Merged MPA file
+├─ counts/
+│  ├─ txt/                 # Extracted taxonomic levels in TXT
+│  │  ├─ counts_species.txt
+│  │  ├─ counts_genus.txt
+│  │  ├─ counts_family.txt
+│  │  ├─ ...
+│  └─ csv/                 # Total abundance CSV output
+│  │  ├─ counts_species.csv
+│  │  ├─ counts_genus.csv
+│  │  ├─ counts_family.csv
+│  │  ├─ ...
+├─ rel_abund/              # Relative abundance CSV output
+│  ├─ ra_species.csv
+│  ├─ ra_genus.csv
+│  ├─ ra_family.csv
+│  ├─ ...
+└─ diversity/
+   ├─ alpha_div.csv
+   ├─ beta_div_bray.csv
+   └─ beta_div_jaccard.csv
+```
+
+## Conclusion
+KrakenParser provides a **simple and automated** way to convert Kraken2 reports into usable CSV files for downstream analysis. You can run the **full pipeline** with a single command or use **individual scripts** as needed.
+
+For any issues or feature requests, feel free to open an issue on GitHub!
+
+🚀 Happy analyzing!

krakenparser-0.6.0/KrakenParser.egg-info/SOURCES.txt

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+LICENSE
+MANIFEST.in
+README_PyPI.md
+requirements.txt
+setup.py
+KrakenParser.egg-info/PKG-INFO
+KrakenParser.egg-info/SOURCES.txt
+KrakenParser.egg-info/dependency_links.txt
+KrakenParser.egg-info/entry_points.txt
+KrakenParser.egg-info/requires.txt
+KrakenParser.egg-info/top_level.txt
+krakenparser/__init__.py
+krakenparser/convert2csv.py
+krakenparser/decombine.sh
+krakenparser/decombine_viruses.sh
+krakenparser/diversity.py
+krakenparser/kraken2csv.sh
+krakenparser/krakenparser.py
+krakenparser/processing_script.py
+krakenparser/relabund.py
+krakenparser/run_kreport2mpa.sh
+krakenparser/version.py
+krakenparser.egg-info/PKG-INFO
+krakenparser.egg-info/SOURCES.txt
+krakenparser.egg-info/dependency_links.txt
+krakenparser.egg-info/entry_points.txt
+krakenparser.egg-info/requires.txt
+krakenparser.egg-info/top_level.txt
+krakenparser/kpplot/__init__.py
+krakenparser/kpplot/base.py
+krakenparser/kpplot/clustermap.py
+krakenparser/kpplot/stackedbar.py
+krakenparser/kpplot/streamgraph.py
+tests/test_full_pipeline.py

krakenparser-0.6.0/KrakenParser.egg-info/dependency_links.txt

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+

krakenparser-0.6.0/KrakenParser.egg-info/entry_points.txt

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+[console_scripts]
+KrakenParser = krakenparser:krakenparser.main

krakenparser-0.6.0/KrakenParser.egg-info/requires.txt

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+pandas==2.2.3
+matplotlib==3.10.0
+numpy==2.2.0
+pandas==2.2.3
+plotly==5.24.1
+seaborn==0.13.2
+scipy==1.14.1
+scikit-bio==0.6.3

krakenparser-0.6.0/KrakenParser.egg-info/top_level.txt

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+krakenparser

krakenparser-0.6.0/LICENSE

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+MIT License
+
+Copyright (c) 2025 Ilia Popov
+
+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.

krakenparser-0.6.0/MANIFEST.in

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+include LICENSE
+include README_PyPI.md
+include requirements.txt
+exclude demo_data/*
+exclude imgs/*.png
+exclude imgs/Layout/*
+exclude __pycache__
+exclude README.md
+exclude .pypirc
+exclude CITATION.cff
+exclude TESTS
+exclude miscellaneous