# taxmyPHAGE
[](https://pypi.org/project/taxmyphage/)
[](https://opensource.org/licenses/MIT)
[](https://pypi.org/project/taxmyphage/)
[](https://anaconda.org/bioconda/taxmyphage)
[](https://pepy.tech/project/taxmyphage)
----------
Developed by [Andrew Millard](https://github.com/amillard) , [Thomas Sicheritz-Ponten](https://github.com/tsp-kucbd) and [Remi Denise](https://github.com/rdenise)
Script to assign taxonomy to a bacteriophage at the genus and species level. It will identify the most similar genomes in the set of currently classified ICTV genomes that are present in the VMR.
Read about the VMR [here](https://ictv.global/vmr). It will compare the query genome against these genomes and run a [VIRIDIC](https://doi.org/10.3390/v12111268)-**like analysis** on the closest relatives. Interpret the output of VIRIDIC-like analysis to determine if the phage falls within a current genus and or species. It does not run VIRIDIC, but utilises the same formula for comparison of genomes. The input is a single genome sequence. The remainder of the analysis is automated
----------
Designed for:
- Individual complete phage genomes
What it will do:
- Classify a dsDNA phage genomes at the Genus and or species level against ICTV genomes
- Tell you if your genome represents a new genus
- Use current ICTV cutoffs for Genera and Species
- accept multiple inputs at the same time
----------
What it wont do:
- Metagenomic samples
- Eukaryotic viruses
- RNA phages - it will give a result - not necessarily the correct one
- ssDNA phages - again a result but likely not accurate
- Classify a phage into a new family
- Compare against every single phage genome in Genbank. It is designed for classification , so compares against currently classified phages.
*A web version will be available soon.*
------
## QUICK start and test
```
mamba create -n taxmyphage -c conda-forge -c bioconda taxmyphage
mamba activate taxmyphage
# If databases not installed, install them
taxmyphage install
# Run taxmyphage
taxmyphage run -i test.fna -t 4
```
if you are on macosx with a M1/M2 chip, you will need to install the following packages first
```
CONDA_SUBDIR=osx-64 mamba create -n taxmyphage -c conda-forge -c bioconda taxmyphage
mamba activate taxmyphage
# If databases not installed, install them
taxmyphage install
# Run taxmyphage
taxmyphage run -i test.fna -t 4
```
This should check the required software is installed and give a warning if not. It will also download the required fasta database and MASH file for comparison. These will be installed in the cloned tax_myPHAGE directory. If you download manually then please move them into tax_myPHAGE directory.
Output of the test should have the following lines at the bottom
<img src="/img/example_result.png" width="70%" height="70%">
----------
## Requirements
It can be run on a standard laptop in a reasonable time.
| **Input Files** | **Description** | **Download Instructions** |
|---------------------------------|---------------------------------------------------------------------------------------------------------------------------|------------------------------------------------------------------------|
| `ICTV.msh` (MASH index) | Prebuilt MASH index of ICTV genomes. Download [here](https://millardlab-inphared.s3.climb.ac.uk/ICTV.msh) | Download: `wget https://millardlab-inphared.s3.climb.ac.uk/ICTV_2023.msh` |
| `Bacteriophage_genomes.fasta.gz` | Database of ICTV-classified genomes. Download [here](https://millardlab-inphared.s3.climb.ac.uk/Bacteriophage_genomes.fasta.gz). | - Download: `wget https://millardlab-inphared.s3.climb.ac.uk/Bacteriophage_genomes.fasta.gz`<br /> - Unzip: `gunzip Bacteriophage_genomes.fasta.gz`<br /> - Create blast db: `makeblastdb -in Bacteriophage_genomes.fasta -parse_seqids -dbtype nucl` |
| `VMR.xlsx` | Virus Metadata Resource (VMR). Download [here](https://ictv.global/vmr/current). | - Download: `wget https://ictv.global/vmr/current` |
------
## Install
> [!IMPORTANT]
> tax_myPHAGE requires [MASH](https://mash.readthedocs.io/en/latest/) >=2.3 and [BLAST](https://blast.ncbi.nlm.nih.gov/Blast.cgi?PAGE_TYPE=BlastDocs&DOC_TYPE=Download) >=2.14.0.
> You need to install mash and NCBI BLAST by yourself (except if you install macsyfinder via *conda/mamba*).
> The other dependencies are managed by the python package manager *pip*.
### Conda
```
mamba install -c conda-forge -c bioconda taxmyphage
```
if you are on macosx with a M1/M2 chip, you will need to install the following packages first
```
CONDA_SUBDIR=osx-64 mamba install -c conda-forge -c bioconda taxmyphage
```
Bioconda doesn't support osx-arm64 yet.
### Pypi
```
pip install taxmyphage
```
If you installing by pip, don't forget to install a working version of [MASH](https://mash.readthedocs.io/en/latest/) and [BLAST](https://blast.ncbi.nlm.nih.gov/Blast.cgi?PAGE_TYPE=BlastDocs&DOC_TYPE=Download)
### Source
Alternatively, a development version of `taxmyphage` can be install from github.
```
git clone https://github.com/amillard/tax_myPHAGE
```
either you can install the taxmyphage and its dependencies via pip
```
cd tax_myPHAGE
pip install -e .
taxmyphage -h
```
or you install following dependencies yourself
```
biopython >= 1.81
pandas >= 2.1.1
seaborn >= 0.13
wget >= 3.2
scipy >= 1.11.3
tqdm >= 4.66.1
openpyxl >= 3.1.2
networkx >= 3.1
icecream >= 2.1.3
```
and run it via
```
pip install -e --no-dependencies .
taxmyphage -h
```
or
```
tax_myPHAGE/taxmyphage/bin/taxmyphage.py -h
```
## Modules
### Install
Allows to install the databases before running the `Run` module.
```
taxmyphage install
```
#### Options
```
usage: taxmyphage install [-h] [-v] [-V] [-db FOLDER_PATH] [--makeblastdb MAKEBLASTDB]
optional arguments:
-h, --help show this help message and exit
-v, --verbose Show verbose output. (For debugging purposes)
-V, --version Show the version number and exit.
Databases options:
-db FOLDER_PATH, --db_folder FOLDER_PATH
Path to the database directory where the databases are stored. (Default is /Users/rdenise/Documents/Scripts/tax_myPHAGE/taxmyphage/database)
Install options:
--makeblastdb MAKEBLASTDB
Path to the blastn executable (default: makeblastdb)
```
----------
### Run
```
taxmyphage run -i input.fasta
```
#### Options
```
usage: taxmyphage run [-h] -i [FASTA_FILE ...] [[FASTA_FILE ...] ...] [-o OUTPUT] [-p PREFIX] [-t THREADS] [-d DIST] [--mash MASH] [--blastdbcmd BLASTDBCMD] [--blastn BLASTN] [--makeblastdb MAKEBLASTDB]
[--no-figures] [-v] [-V] [-db FOLDER_PATH]
optional arguments:
-h, --help show this help message and exit
-v, --verbose Show verbose output. (For debugging purposes)
-V, --version Show the version number and exit.
General options:
-i [FASTA_FILE ...] [[FASTA_FILE ...] ...], --input [FASTA_FILE ...] [[FASTA_FILE ...] ...]
Path to an input fasta file(s), or directory containing fasta files. The fasta file(s) could contain multiple phage genomes. They can be compressed (gzip). If a directory is given the
expected fasta extentions are ['fasta', 'fna', 'fsa', 'fa'] but can be gzipped. (Required)
-o OUTPUT, --output OUTPUT
Path to the output directory. (Default is current directory)
-p PREFIX, --prefix PREFIX
Will add the prefix to results and summary files that will store results of MASH and comparision to the VMR Data produced by ICTV combines both sets of this data into a single csv file.
Use this flag if you want to run multiple times and keep the results files without manual renaming of files. (Default no prefix)
-t THREADS, --threads THREADS
Maximum number of threads that will be used by BLASTn. (Default is 1)
MASH options:
-d DIST, --distance DIST
Will change the mash distance for the intial seraching for close relatives. We suggesting keeping at 0.2 If this results in the phage not being classified, then increasing to 0.3 might
result in an output that shows the phage is a new genus. We have found increasing above 0.2 does not place the query in any current genus, only provides the output files to demonstrate it
falls outside of current genera. (Default is 0.2)
--mash MASH Path to the MASH executable (default: mash)
--blastdbcmd BLASTDBCMD
Path to the blastn executable (default: blastdbcmd)
Similarity options:
--blastn BLASTN Path to the blastn executable (default: blastn)
--makeblastdb MAKEBLASTDB
Path to the blastn executable (default: makeblastdb)
--no-figures Use this option if you don't want to generate Figures. This will speed up the time it takes to run the script - but you get no Figures. (By default, Figures are generated)
Databases options:
-db FOLDER_PATH, --db_folder FOLDER_PATH
Path to the database directory where the databases are stored. (Default is /Users/rdenise/Documents/Scripts/tax_myPHAGE/taxmyphage/database)
```
#### Indicative run time
The time to classify a phage will depend on the number of hits and number of phages currently classified within a particular genus. The more species within a genus, the longer the time for classification. The numbers below are from running on a 16 core server. We have been running the process on a MAC book and Windows laptop in reasonable time periods.
| Genus | Number of genomes in Genera|Time(H:M:S)
| ------------- | ------------- |-------
|Cheoctovirus |96|00:07:44
|Tequatrovirus|83|00:26:19|
|Peduovirus |27|00:00:23|
|Warwickvirus|18|00:00:18|
|Pseudotevenvirus|9|0:01:15|
|Changmaivirus|2|0:00:17
|Stompvirus|1|0:00:16
#### Output files for the `Run` module
```
[output_folder] <- General output folder
├── Summary_taxonomy.tsv <- Summary of the analysis for all the genomes (summarises what was printed to screen)
└── Results_per_genome <- Folder containing the results for each genome
└── [genome query_id] <- Results output for the genome query_id
├── Output_of_taxonomy.tsv <- Output of the taxonomy classification
├── Summary_file.txt <- Summary of the analysis (summarises what was printed to screen)
├── heatmap.pdf <- Heatmap of the similarity to the closest relatives (pdf)
├── heatmap.png <- Heatmap of the similarity to the closest relatives (png)
├── heatmap.svg <- Heatmap of the similarity to the closest relatives (svg)
├── known_taxa.fa <- Fasta file of the closest relatives
├── mash.txt <- Output of the MASH analysis
├── query.fasta <- Input fasta file
├── similarities.tsv <- Similarities to the closest relatives
├── top_right_matrix.tsv <- Top right matrix of similarity to closest relatives (same as heatmap)
└── pmv <- VIRIDIC-like analysis
├── pmv_in.fa <- Input fasta file
├── pmv_in.fa.blastn_vs2_self.tab.gz <- Blastn output of the input fasta file against itself
├── pmv_in.fa.genus_species_clusters.tsv <- Clusters of the closest relatives
├── pmv_in.fa.ndb <- Blastn database of the closest relatives
├── pmv_in.fa.nhr
├── pmv_in.fa.nin
├── pmv_in.fa.njs
├── pmv_in.fa.not
├── pmv_in.fa.nsq
├── pmv_in.fa.ntf
└── pmv_in.fa.nto
```
##### Output files explained
- **Summary_taxonomy.tsv** - Summarises what was printed to screen for all the genomes
| Query sequence header | Realm | Kingdom | Phylum | Class | Order | Family | Subfamily | Genus | Species | Full classification | Message |
| ---- | ---- | ---- | ---- | ---- | ---- | ---- | ---- | ---- | ---- | ---- | ---- |
| MZ130489 | Duplodnaviria | Heunggongvirae | Uroviricota | Caudoviricetes | Crassvirales | Crevaviridae | Coarsevirinae | Junduvirus | Junduvirus communis | r__Duplodnaviria;k__Heunggongvirae;p__Uroviricota;c__Caudoviricetes;o__Crassvirales;f__Crevaviridae;sf__Coarsevirinae;g__Junduvirus;s__Junduvirus communis | Current ICTV taxonomy and VIRIDIC-algorithm output appear to be consistent at the genus level |
| newGenus_phage | Unknown | Unknown | Unknown | Unknown | Unknown | Unknown | Unknown | New_genus | New_genus new_species | r__Unknown;k__Unknown;p__Unknown;c__Unknown;o__Unknown;f__Unknown;sf_Unknown;g__New_genus;s__New_genus new_species | Query is a new genus and species. You could try running again with if you larger distance |
| test1 | Duplodnaviria | Heunggongvirae | Uroviricota | Caudoviricetes | Not Defined Yet | Not Defined Yet | Vequintavirinae | Certrevirus | Certrevirus name_your_species | r__Duplodnaviria;k__Heunggongvirae;p__Uroviricota;c__Caudoviricetes;o__;f__;g__Certrevirus;s__Certrevirus name_your_species | The number of expected genera is different from the predicted number of genus clusters. It will require more manual curation |
- **Summary_file.txt** - Summarises what was printed to screen
```
Query sequence header was:test1
Query sequence can be classified within a current genus and represents a new species, it is in:
Class:Caudoviricetes Family: Not Defined Yet Subfamily:Vequintavirinae Genus:Certrevirus Species:name_your_species
```
- **Output_of_taxonomy.csv** - Provides Cluster and Species numbers for you query phage, merged with data from the VMR for the closest relatives to you query
- ***.pdf, *.svg, *.png** - image files of top right matrix of similarity to closest currently classified phages
<img src="/img/heatmap.png" width="60%" height="60%">
----------
### Similarity
```
taxmyphage similarity -i input.fasta
```
#### Options
```
usage: taxmyphage similarity [-h] -i [FASTA_FILE ...] [[FASTA_FILE ...] ...] [-o OUTPUT] [-p PREFIX] [-t THREADS] [--reference REFERENCE] [--blastn BLASTN] [--makeblastdb MAKEBLASTDB] [--no-figures] [-v] [-V]
[-db FOLDER_PATH]
optional arguments:
-h, --help show this help message and exit
-v, --verbose Show verbose output. (For debugging purposes)
-V, --version Show the version number and exit.
General options:
-i [FASTA_FILE ...] [[FASTA_FILE ...] ...], --input [FASTA_FILE ...] [[FASTA_FILE ...] ...]
Path to an input fasta file(s), or directory containing fasta files. The fasta file(s) could contain multiple phage genomes. They can be compressed (gzip). If a directory is given the
expected fasta extentions are ['fasta', 'fna', 'fsa', 'fa'] but can be gzipped. (Required)
-o OUTPUT, --output OUTPUT
Path to the output directory. (Default is current directory)
-p PREFIX, --prefix PREFIX
Will add the prefix to results and summary files that will store results of MASH and comparision to the VMR Data produced by ICTV combines both sets of this data into a single csv file.
Use this flag if you want to run multiple times and keep the results files without manual renaming of files. (Default no prefix)
-t THREADS, --threads THREADS
Maximum number of threads that will be used by BLASTn. (Default is 1)
Comparison options:
--reference REFERENCE
Path to the reference database file. Input file will be used as query against it. If not provided, input will be compare against itself. If you use reference no figure is generated.
(Default is '')
Similarity options:
--blastn BLASTN Path to the blastn executable (default: blastn)
--makeblastdb MAKEBLASTDB
Path to the blastn executable (default: makeblastdb)
--no-figures Use this option if you don't want to generate Figures. This will speed up the time it takes to run the script - but you get no Figures. (By default, Figures are generated)
Databases options:
-db FOLDER_PATH, --db_folder FOLDER_PATH
Path to the database directory where the databases are stored. (Default is /Users/rdenise/Documents/Scripts/tax_myPHAGE/taxmyphage/database)
```
#### Output files for the `similarity` module
```
[output_folder] <- General output folder
├── heatmap.pdf <- Heatmap of the similarity to the closest relatives (pdf)
├── heatmap.png <- Heatmap of the similarity to the closest relatives (png)
├── heatmap.svg <- Heatmap of the similarity to the closest relatives (svg)
├── pmv.fasta <- Input fasta file
├── pmv.fasta.blastn_vs2_self.tab.gz <- Blastn output of the input fasta file against itself
├── pmv.fasta.genus_species_clusters.tsv <- Clusters of the closest relatives
├── pmv.fasta.ndb <- Blastn database of the closest relatives
├── pmv.fasta.nhr
├── pmv.fasta.nin
├── pmv.fasta.njs
├── pmv.fasta.not
├── pmv.fasta.nsq
├── pmv.fasta.ntf
├── pmv.fasta.nto
├── similarities.tsv <- Similarities to the closest relatives
└── top_right_matrix.tsv <- Top right matrix of similarity to closest relatives (same as heatmap)
```
##### Output files explained
- ***.pdf, *.svg, *.png** - image files of top right matrix of similarity to closest currently classified phages
<img src="/img/heatmap.png" width="60%" height="60%">
Raw data
{
"_id": null,
"home_page": "https://github.com/amillard/tax_myPHAGE",
"name": "taxmyphage",
"maintainer": "",
"docs_url": null,
"requires_python": ">=3.9,<3.13",
"maintainer_email": "",
"keywords": "Phage,Scientific/Engineering,Bio-Informatics,Taxonomy,Bacteriophage",
"author": "Andrew Millard",
"author_email": "adm39@leicester.ac.uk",
"download_url": "https://files.pythonhosted.org/packages/3b/12/2c52aa6551fcdee407fd7ad1a9259228ed39fbc32150b55ddc9cf9a48478/taxmyphage-0.2.9.tar.gz",
"platform": null,
"description": "# taxmyPHAGE\n\n[](https://pypi.org/project/taxmyphage/)\n[](https://opensource.org/licenses/MIT)\n[](https://pypi.org/project/taxmyphage/)\n[](https://anaconda.org/bioconda/taxmyphage)\n[](https://pepy.tech/project/taxmyphage)\n\n----------\n\nDeveloped by [Andrew Millard](https://github.com/amillard) , [Thomas Sicheritz-Ponten](https://github.com/tsp-kucbd) and [Remi Denise](https://github.com/rdenise)\n\nScript to assign taxonomy to a bacteriophage at the genus and species level. It will identify the most similar genomes in the set of currently classified ICTV genomes that are present in the VMR. \nRead about the VMR [here](https://ictv.global/vmr). It will compare the query genome against these genomes and run a [VIRIDIC](https://doi.org/10.3390/v12111268)-**like analysis** on the closest relatives. Interpret the output of VIRIDIC-like analysis to determine if the phage falls within a current genus and or species. It does not run VIRIDIC, but utilises the same formula for comparison of genomes. The input is a single genome sequence. The remainder of the analysis is automated \n\n----------\n\nDesigned for:\n\n- Individual complete phage genomes \n\nWhat it will do:\n\n- Classify a dsDNA phage genomes at the Genus and or species level against ICTV genomes \n- Tell you if your genome represents a new genus \n- Use current ICTV cutoffs for Genera and Species \n- accept multiple inputs at the same time\n\n----------\n\nWhat it wont do:\n \n- Metagenomic samples \n- Eukaryotic viruses\n- RNA phages - it will give a result - not necessarily the correct one \n- ssDNA phages - again a result but likely not accurate \n- Classify a phage into a new family \n- Compare against every single phage genome in Genbank. It is designed for classification , so compares against currently classified phages.\n\n\n*A web version will be available soon.*\n\n------\n\n## QUICK start and test\n\n```\nmamba create -n taxmyphage -c conda-forge -c bioconda taxmyphage\nmamba activate taxmyphage\n\n# If databases not installed, install them\ntaxmyphage install\n\n# Run taxmyphage\ntaxmyphage run -i test.fna -t 4\n```\n\nif you are on macosx with a M1/M2 chip, you will need to install the following packages first\n\n```\nCONDA_SUBDIR=osx-64 mamba create -n taxmyphage -c conda-forge -c bioconda taxmyphage\nmamba activate taxmyphage\n\n# If databases not installed, install them\ntaxmyphage install\n\n# Run taxmyphage\ntaxmyphage run -i test.fna -t 4\n```\n\nThis should check the required software is installed and give a warning if not. It will also download the required fasta database and MASH file for comparison. These will be installed in the cloned tax_myPHAGE directory. If you download manually then please move them into tax_myPHAGE directory.\n\n\nOutput of the test should have the following lines at the bottom \n\n<img src=\"/img/example_result.png\" width=\"70%\" height=\"70%\">\n\n\n----------\n\n## Requirements \n\nIt can be run on a standard laptop in a reasonable time. \n\n\n| **Input Files** | **Description** | **Download Instructions** |\n|---------------------------------|---------------------------------------------------------------------------------------------------------------------------|------------------------------------------------------------------------|\n| `ICTV.msh` (MASH index) | Prebuilt MASH index of ICTV genomes. Download [here](https://millardlab-inphared.s3.climb.ac.uk/ICTV.msh) | Download: `wget https://millardlab-inphared.s3.climb.ac.uk/ICTV_2023.msh` |\n| `Bacteriophage_genomes.fasta.gz` | Database of ICTV-classified genomes. Download [here](https://millardlab-inphared.s3.climb.ac.uk/Bacteriophage_genomes.fasta.gz). | - Download: `wget https://millardlab-inphared.s3.climb.ac.uk/Bacteriophage_genomes.fasta.gz`<br /> - Unzip: `gunzip Bacteriophage_genomes.fasta.gz`<br /> - Create blast db: `makeblastdb -in Bacteriophage_genomes.fasta -parse_seqids -dbtype nucl` |\n| `VMR.xlsx` | Virus Metadata Resource (VMR). Download [here](https://ictv.global/vmr/current). | - Download: `wget https://ictv.global/vmr/current` |\n\n\n------\n\n## Install \n\n> [!IMPORTANT] \n> tax_myPHAGE requires [MASH](https://mash.readthedocs.io/en/latest/) >=2.3 and [BLAST](https://blast.ncbi.nlm.nih.gov/Blast.cgi?PAGE_TYPE=BlastDocs&DOC_TYPE=Download) >=2.14.0. \n> You need to install mash and NCBI BLAST by yourself (except if you install macsyfinder via *conda/mamba*). \n> The other dependencies are managed by the python package manager *pip*. \n\n### Conda \n\n```\nmamba install -c conda-forge -c bioconda taxmyphage\n```\n\nif you are on macosx with a M1/M2 chip, you will need to install the following packages first\n\n```\nCONDA_SUBDIR=osx-64 mamba install -c conda-forge -c bioconda taxmyphage\n```\n\nBioconda doesn't support osx-arm64 yet.\n\n\n### Pypi\n\n```\npip install taxmyphage\n```\n\nIf you installing by pip, don't forget to install a working version of [MASH](https://mash.readthedocs.io/en/latest/) and [BLAST](https://blast.ncbi.nlm.nih.gov/Blast.cgi?PAGE_TYPE=BlastDocs&DOC_TYPE=Download)\n\n### Source\n\nAlternatively, a development version of `taxmyphage` can be install from github.\n\n```\ngit clone https://github.com/amillard/tax_myPHAGE\n```\n\neither you can install the taxmyphage and its dependencies via pip\n\n```\ncd tax_myPHAGE\npip install -e .\ntaxmyphage -h\n```\n\nor you install following dependencies yourself\n\n```\nbiopython >= 1.81\npandas >= 2.1.1\nseaborn >= 0.13\nwget >= 3.2\nscipy >= 1.11.3\ntqdm >= 4.66.1\nopenpyxl >= 3.1.2\nnetworkx >= 3.1\nicecream >= 2.1.3\n```\n\nand run it via\n\n```\npip install -e --no-dependencies .\ntaxmyphage -h\n```\n\nor\n\n```\ntax_myPHAGE/taxmyphage/bin/taxmyphage.py -h\n```\n\n\n## Modules\n\n### Install\n\nAllows to install the databases before running the `Run` module.\n\n```\ntaxmyphage install\n```\n\n#### Options \n\n```\nusage: taxmyphage install [-h] [-v] [-V] [-db FOLDER_PATH] [--makeblastdb MAKEBLASTDB]\n\noptional arguments:\n -h, --help show this help message and exit\n -v, --verbose Show verbose output. (For debugging purposes)\n -V, --version Show the version number and exit.\n\nDatabases options:\n -db FOLDER_PATH, --db_folder FOLDER_PATH\n Path to the database directory where the databases are stored. (Default is /Users/rdenise/Documents/Scripts/tax_myPHAGE/taxmyphage/database)\n\nInstall options:\n --makeblastdb MAKEBLASTDB\n Path to the blastn executable (default: makeblastdb)\n```\n----------\n### Run\n\n```\ntaxmyphage run -i input.fasta\n```\n\n#### Options \n\n```\nusage: taxmyphage run [-h] -i [FASTA_FILE ...] [[FASTA_FILE ...] ...] [-o OUTPUT] [-p PREFIX] [-t THREADS] [-d DIST] [--mash MASH] [--blastdbcmd BLASTDBCMD] [--blastn BLASTN] [--makeblastdb MAKEBLASTDB]\n [--no-figures] [-v] [-V] [-db FOLDER_PATH]\n\noptional arguments:\n -h, --help show this help message and exit\n -v, --verbose Show verbose output. (For debugging purposes)\n -V, --version Show the version number and exit.\n\nGeneral options:\n -i [FASTA_FILE ...] [[FASTA_FILE ...] ...], --input [FASTA_FILE ...] [[FASTA_FILE ...] ...]\n Path to an input fasta file(s), or directory containing fasta files. The fasta file(s) could contain multiple phage genomes. They can be compressed (gzip). If a directory is given the\n expected fasta extentions are ['fasta', 'fna', 'fsa', 'fa'] but can be gzipped. (Required)\n -o OUTPUT, --output OUTPUT\n Path to the output directory. (Default is current directory)\n -p PREFIX, --prefix PREFIX\n Will add the prefix to results and summary files that will store results of MASH and comparision to the VMR Data produced by ICTV combines both sets of this data into a single csv file.\n Use this flag if you want to run multiple times and keep the results files without manual renaming of files. (Default no prefix)\n -t THREADS, --threads THREADS\n Maximum number of threads that will be used by BLASTn. (Default is 1)\n\nMASH options:\n -d DIST, --distance DIST\n Will change the mash distance for the intial seraching for close relatives. We suggesting keeping at 0.2 If this results in the phage not being classified, then increasing to 0.3 might\n result in an output that shows the phage is a new genus. We have found increasing above 0.2 does not place the query in any current genus, only provides the output files to demonstrate it\n falls outside of current genera. (Default is 0.2)\n --mash MASH Path to the MASH executable (default: mash)\n --blastdbcmd BLASTDBCMD\n Path to the blastn executable (default: blastdbcmd)\n\nSimilarity options:\n --blastn BLASTN Path to the blastn executable (default: blastn)\n --makeblastdb MAKEBLASTDB\n Path to the blastn executable (default: makeblastdb)\n --no-figures Use this option if you don't want to generate Figures. This will speed up the time it takes to run the script - but you get no Figures. (By default, Figures are generated)\n\nDatabases options:\n -db FOLDER_PATH, --db_folder FOLDER_PATH\n Path to the database directory where the databases are stored. (Default is /Users/rdenise/Documents/Scripts/tax_myPHAGE/taxmyphage/database)\n```\n\n\n#### Indicative run time \n\nThe time to classify a phage will depend on the number of hits and number of phages currently classified within a particular genus. The more species within a genus, the longer the time for classification. The numbers below are from running on a 16 core server. We have been running the process on a MAC book and Windows laptop in reasonable time periods. \n\n\n\n| Genus | Number of genomes in Genera|Time(H:M:S)\n| ------------- | ------------- |-------\n|Cheoctovirus |96|00:07:44\n|Tequatrovirus|83|00:26:19|\n|Peduovirus |27|00:00:23|\n|Warwickvirus|18|00:00:18|\n|Pseudotevenvirus|9|0:01:15|\n|Changmaivirus|2|0:00:17\n|Stompvirus|1|0:00:16\n\n\n\n#### Output files for the `Run` module\n\n```\n[output_folder] <- General output folder\n\u251c\u2500\u2500 Summary_taxonomy.tsv <- Summary of the analysis for all the genomes (summarises what was printed to screen)\n\u2514\u2500\u2500 Results_per_genome <- Folder containing the results for each genome\n \u2514\u2500\u2500 [genome query_id] <- Results output for the genome query_id\n \u251c\u2500\u2500 Output_of_taxonomy.tsv <- Output of the taxonomy classification\n \u251c\u2500\u2500 Summary_file.txt <- Summary of the analysis (summarises what was printed to screen)\n \u251c\u2500\u2500 heatmap.pdf <- Heatmap of the similarity to the closest relatives (pdf)\n \u251c\u2500\u2500 heatmap.png <- Heatmap of the similarity to the closest relatives (png)\n \u251c\u2500\u2500 heatmap.svg <- Heatmap of the similarity to the closest relatives (svg)\n \u251c\u2500\u2500 known_taxa.fa <- Fasta file of the closest relatives\n \u251c\u2500\u2500 mash.txt <- Output of the MASH analysis\n \u251c\u2500\u2500 query.fasta <- Input fasta file\n \u251c\u2500\u2500 similarities.tsv <- Similarities to the closest relatives\n \u251c\u2500\u2500 top_right_matrix.tsv <- Top right matrix of similarity to closest relatives (same as heatmap)\n \u2514\u2500\u2500 pmv <- VIRIDIC-like analysis\n \u251c\u2500\u2500 pmv_in.fa <- Input fasta file\n \u251c\u2500\u2500 pmv_in.fa.blastn_vs2_self.tab.gz <- Blastn output of the input fasta file against itself\n \u251c\u2500\u2500 pmv_in.fa.genus_species_clusters.tsv <- Clusters of the closest relatives\n \u251c\u2500\u2500 pmv_in.fa.ndb <- Blastn database of the closest relatives\n \u251c\u2500\u2500 pmv_in.fa.nhr\n \u251c\u2500\u2500 pmv_in.fa.nin\n \u251c\u2500\u2500 pmv_in.fa.njs\n \u251c\u2500\u2500 pmv_in.fa.not\n \u251c\u2500\u2500 pmv_in.fa.nsq\n \u251c\u2500\u2500 pmv_in.fa.ntf\n \u2514\u2500\u2500 pmv_in.fa.nto\n```\n\n##### Output files explained\n\n- **Summary_taxonomy.tsv** - Summarises what was printed to screen for all the genomes\n\n| Query sequence header | Realm | Kingdom | Phylum | Class | Order | Family | Subfamily | Genus | Species | Full classification | Message |\n| ---- | ---- | ---- | ---- | ---- | ---- | ---- | ---- | ---- | ---- | ---- | ---- |\n| MZ130489 | Duplodnaviria | Heunggongvirae | Uroviricota | Caudoviricetes | Crassvirales | Crevaviridae | Coarsevirinae | Junduvirus | Junduvirus communis | r__Duplodnaviria;k__Heunggongvirae;p__Uroviricota;c__Caudoviricetes;o__Crassvirales;f__Crevaviridae;sf__Coarsevirinae;g__Junduvirus;s__Junduvirus communis | Current ICTV taxonomy and VIRIDIC-algorithm output appear to be consistent at the genus level |\n| newGenus_phage | Unknown | Unknown | Unknown | Unknown | Unknown | Unknown | Unknown | New_genus | New_genus new_species | r__Unknown;k__Unknown;p__Unknown;c__Unknown;o__Unknown;f__Unknown;sf_Unknown;g__New_genus;s__New_genus new_species | Query is a new genus and species. You could try running again with if you larger distance |\n| test1 | Duplodnaviria | Heunggongvirae | Uroviricota | Caudoviricetes | Not Defined Yet | Not Defined Yet | Vequintavirinae | Certrevirus | Certrevirus name_your_species | r__Duplodnaviria;k__Heunggongvirae;p__Uroviricota;c__Caudoviricetes;o__;f__;g__Certrevirus;s__Certrevirus name_your_species | The number of expected genera is different from the predicted number of genus clusters. It will require more manual curation |\n\n- **Summary_file.txt** - Summarises what was printed to screen \n\n```\nQuery sequence header was:test1 \n \n \nQuery sequence can be classified within a current genus and represents a new species, it is in:\n \nClass:Caudoviricetes Family: Not Defined Yet Subfamily:Vequintavirinae Genus:Certrevirus Species:name_your_species\n```\n\n- **Output_of_taxonomy.csv** - Provides Cluster and Species numbers for you query phage, merged with data from the VMR for the closest relatives to you query\n\n- ***.pdf, *.svg, *.png** - image files of top right matrix of similarity to closest currently classified phages \n\n<img src=\"/img/heatmap.png\" width=\"60%\" height=\"60%\">\n\n----------\n### Similarity\n\n```\ntaxmyphage similarity -i input.fasta\n```\n\n#### Options \n\n```\nusage: taxmyphage similarity [-h] -i [FASTA_FILE ...] [[FASTA_FILE ...] ...] [-o OUTPUT] [-p PREFIX] [-t THREADS] [--reference REFERENCE] [--blastn BLASTN] [--makeblastdb MAKEBLASTDB] [--no-figures] [-v] [-V]\n [-db FOLDER_PATH]\n\noptional arguments:\n -h, --help show this help message and exit\n -v, --verbose Show verbose output. (For debugging purposes)\n -V, --version Show the version number and exit.\n\nGeneral options:\n -i [FASTA_FILE ...] [[FASTA_FILE ...] ...], --input [FASTA_FILE ...] [[FASTA_FILE ...] ...]\n Path to an input fasta file(s), or directory containing fasta files. The fasta file(s) could contain multiple phage genomes. They can be compressed (gzip). If a directory is given the\n expected fasta extentions are ['fasta', 'fna', 'fsa', 'fa'] but can be gzipped. (Required)\n -o OUTPUT, --output OUTPUT\n Path to the output directory. (Default is current directory)\n -p PREFIX, --prefix PREFIX\n Will add the prefix to results and summary files that will store results of MASH and comparision to the VMR Data produced by ICTV combines both sets of this data into a single csv file.\n Use this flag if you want to run multiple times and keep the results files without manual renaming of files. (Default no prefix)\n -t THREADS, --threads THREADS\n Maximum number of threads that will be used by BLASTn. (Default is 1)\n\nComparison options:\n --reference REFERENCE\n Path to the reference database file. Input file will be used as query against it. If not provided, input will be compare against itself. If you use reference no figure is generated.\n (Default is '')\n\nSimilarity options:\n --blastn BLASTN Path to the blastn executable (default: blastn)\n --makeblastdb MAKEBLASTDB\n Path to the blastn executable (default: makeblastdb)\n --no-figures Use this option if you don't want to generate Figures. This will speed up the time it takes to run the script - but you get no Figures. (By default, Figures are generated)\n\nDatabases options:\n -db FOLDER_PATH, --db_folder FOLDER_PATH\n Path to the database directory where the databases are stored. (Default is /Users/rdenise/Documents/Scripts/tax_myPHAGE/taxmyphage/database)\n```\n\n#### Output files for the `similarity` module\n\n```\n[output_folder] <- General output folder\n\u251c\u2500\u2500 heatmap.pdf <- Heatmap of the similarity to the closest relatives (pdf)\n\u251c\u2500\u2500 heatmap.png <- Heatmap of the similarity to the closest relatives (png)\n\u251c\u2500\u2500 heatmap.svg <- Heatmap of the similarity to the closest relatives (svg)\n\u251c\u2500\u2500 pmv.fasta <- Input fasta file\n\u251c\u2500\u2500 pmv.fasta.blastn_vs2_self.tab.gz <- Blastn output of the input fasta file against itself\n\u251c\u2500\u2500 pmv.fasta.genus_species_clusters.tsv <- Clusters of the closest relatives\n\u251c\u2500\u2500 pmv.fasta.ndb <- Blastn database of the closest relatives\n\u251c\u2500\u2500 pmv.fasta.nhr\n\u251c\u2500\u2500 pmv.fasta.nin\n\u251c\u2500\u2500 pmv.fasta.njs\n\u251c\u2500\u2500 pmv.fasta.not\n\u251c\u2500\u2500 pmv.fasta.nsq\n\u251c\u2500\u2500 pmv.fasta.ntf\n\u251c\u2500\u2500 pmv.fasta.nto\n\u251c\u2500\u2500 similarities.tsv <- Similarities to the closest relatives\n\u2514\u2500\u2500 top_right_matrix.tsv <- Top right matrix of similarity to closest relatives (same as heatmap)\n```\n\n##### Output files explained\n\n- ***.pdf, *.svg, *.png** - image files of top right matrix of similarity to closest currently classified phages \n\n<img src=\"/img/heatmap.png\" width=\"60%\" height=\"60%\">\n",
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