rdrpcatch 0.0.6__tar.gz → 0.0.8__tar.gz

{rdrpcatch-0.0.6 → rdrpcatch-0.0.8}/.idea/workspace.xml

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{rdrpcatch-0.0.6 → rdrpcatch-0.0.8}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: rdrpcatch
-Version: 0.0.6
+Version: 0.0.8
 Dynamic: Summary
 Project-URL: Home, https://github.com/dimitris-karapliafis/RdRpCATCH
 Project-URL: Source, https://github.com/dimitris-karapliafis/RdRpCATCH
@@ -34,18 +34,31 @@ library to perform pHMM searches.  In addition, the tool scans each sequence (aa
 In addition, RdRpCATCH provides information about the number of profiles
 that were positive for each sequence across all pHMM databases, and taxonomic information based on the MMseqs2 easy-taxonomy and search modules against a custom RefSeq Riboviria database.
 
+### Version 0.0.7 -> 0.0.8 Changelog
+- Added support for custom pHMM databases. See the [Setting up custom pHMM databases](#setting-up-custom-phmm-databases) section for more information.
+- All specified flags use '-' instead of '_' (e.g. `--db-dir` instead of `--db_dir`). 
+- Fixed issue with specifying the Lucaprot_HMM and Zayed_HMM databases in the `--db-options` argument.
+- Command `rdrpcatch download` renamed as `rdrpcatch databases` for clarity, as it now supports adding custom pHMM
+databases to the RdRpCATCH databases. This is facilitated by the `--add-custom-db` argument.
+- Added none option to the `--db-options` argument to search only against custom databases.
+
+
+
 ** The tool has been modified to use [rolypoly](https://code.jgi.doe.gov/UNeri/rolypoly) code/approaches **
 
-![rdrpcatch_flowchart_v0.png](images%2Frdrpcatch_flowchart_v0.png)
+
+
+![rdrpcatch_flowchart_v0.png](images%2Frdrpcatch_illustration.png)
 
 ### Supported databases
 - NeoRdRp <sup>1</sup> : 1182 pHMMs 
 - NeoRdRp2 <sup>2</sup>: 19394 pHMMs  
 - RVMT <sup>3</sup>: 710 pHMMs  
 - RdRp-Scan <sup>4</sup> : 68 pHMMs
-- TSA_Oleandrite_fam <sup>5</sup>: 77 pHMMs 
-- TSA_Oleandrite_gen <sup>6</sup> : 341 pHMMs
-- LucaProt_pHMM<sup>7 </sup> : 754 pHMMs 
+- TSA_Olendraite_fam <sup>5</sup>: 77 pHMMs 
+- TSA_Olendraite_gen <sup>6</sup> : 341 pHMMs
+- LucaProt_HMM<sup>7 </sup> : 754 pHMMs
+- Zayed_HMM<sup>8 </sup> : 2489 pHMMs
 
 1. Sakaguchi, S. et al. (2022) 'NeoRdRp: A comprehensive dataset for identifying RNA-dependent RNA polymerases of various RNA viruses from metatranscriptomic data', *Microbes and Environments*, 37(3). [doi:10.1264/jsme2.me22001](https://doi.org/10.1264/jsme2.me22001)
 2. Sakaguchi, S., Nakano, T. and Nakagawa, S. (2024) 'Neordrp2 with improved seed data, annotations, and scoring', *Frontiers in Virology*, 4. [doi:10.3389/fviro.2024.1378695](https://doi.org/10.3389/fviro.2024.1378695)
@@ -53,7 +66,9 @@ that were positive for each sequence across all pHMM databases, and taxonomic in
 4. Charon, J. et al. (2022) 'RDRP-Scan: A bioinformatic resource to identify and annotate divergent RNA viruses in metagenomic sequence data', *Virus Evolution*, 8(2). [doi:10.1093/ve/veac082](https://doi.org/10.1093/ve/veac082)
 5. Olendraite, I., Brown, K. and Firth, A.E. (2023) 'Identification of RNA virus–derived rdrp sequences in publicly available transcriptomic data sets', *Molecular Biology and Evolution*, 40(4). [doi:10.1093/molbev/msad060](https://doi.org/10.1093/molbev/msad060)
 6. Olendraite, I. (2021) 'Mining diverse and novel RNA viruses in transcriptomic datasets', Apollo. Available at: [https://www.repository.cam.ac.uk/items/1fabebd2-429b-45c9-b6eb-41d27d0a90c2](https://www.repository.cam.ac.uk/items/1fabebd2-429b-45c9-b6eb-41d27d0a90c2)
-7. Hou, X. et al. (2024) 'Using artificial intelligence to document the hidden RNA virosphere', *Cell*, 187(24). [doi:10.1016/j.cell.2024.09.027](https://doi.org/10.1016/j.cell.2024.09.027)
+7. Hou, X. and He, Y. et al. (2024) 'Using artificial intelligence to document the hidden RNA virosphere', *Cell*, 187(24). [doi:10.1016/j.cell.2024.09.027](https://doi.org/10.1016/j.cell.2024.09.027)
+8. Zayed, A. A., et al. (2022)  'Cryptic and abundant marine viruses at the evolutionary origins of Earth’s RNA virome.' *Science*, 376(6589), 156–162. [doi:10.1126/science.abm5847](https://doi.org/10.1126/science.abm5847)
+
 
 
 ## Installation
@@ -94,13 +109,16 @@ Activate the environment and download the RdRpCATCH databases:
 
 ```bash 
 conda activate rdrpcatch
-rdrpcatch download --destination_dir path/to/store/databases
+rdrpcatch databases --destination_dir path/to/store/databases
 ```
 
 * Note 1: The databases are large files and may take some time to download (~ 3 GB).
 * Note 2: The databases are stored in the specified directory, and the path is required to run RdRpCATCH.
 * Note 3: If you encounter an SSL error while downloading, please try again. The error seems to appear sporadically during testing, and a simple re-initiation of the downloading process seems to fix it. 
 
+
+
+
 ## Usage
 RdRpCATCH can be used as a CLI tool as follows:
 
@@ -109,20 +127,58 @@ RdRpCATCH can be used as a CLI tool as follows:
 # conda activate rdrpcatch
 
 # scan the input fasta file with the selected databases
-rdrpcatch scan -i path/to/input.fasta -o path/to/output_dir -db_dir path/to/database
+rdrpcatch scan -i path/to/input.fasta -o path/to/output_dir -db-dir path/to/database
 ```
-### input: 
+
+## Input description
 The input file can be one or more nucleotide or protein sequences in multi-fasta format. 
 The output directory is where the results will be stored. We recommend specifying the type of the sequence in the command line,
 An optional argument `--seq_type` (nuc or prot) can be used to specify if the input fasta file sequences are nucleotide or amino acid.
 
+
+## Setting up custom pHMM databases
+It is possible to use custom pHMM databases with RdRpCATCH. As a prerequisite, you need to install the RdRpCATCH 
+databases using the `rdrpcatch databases` command as described above, to a directory of your choice.
+
+The custom databases should be formatted as follows:
+
+- First create a directory and give it a descriptive name, e.g. `my_custom_rdrp_database`. Important: The name should not contain  comma `,` characters.
+- Inside the directory put your custom pHMM HMMER pressed database. You can use the `hmmpress` command of HMMER to create the pressed database from your custom HMM file. This creates a set of files with the same name as the original HMM file, but with different extensions (e.g. `.h3f`, `.h3i`, `.h3m`, `.h3p`).  The directory should contain all these files. Please refer to the HMMER manual for more information on how to create a pressed database from an HMM file. (http://eddylab.org/software/hmmer/Userguide.pdf) 
+- Next you can add the directory to the custom databases that are readable by RdRpCATCH. This can be done by using the rdrpcatch databases command as follows:
+
+```bash
+rdrpcatch databases --add-custom-db path/to/my_custom_rdrp_database --destination-dir path/that/contains/rdrpcatch/databases
+```
+
+- This will add the custom database to the list of databases that can be used with RdRpCATCH.
+- The custom database can then be used with the `rdrpcatch scan` command by specifying the `--custom-dbs` argument as follows:
+- 
+```bash
+rdrpcatch scan -i path/to/input.fasta -o path/to/output_dir -db_dir path/to/database --custom-dbs custom_database_name
+```
+
+- The `custom_database_name` should be the name of the directory that contains the custom pHMM files, without the path.
+- For example, if the custom database is stored in `path/to/my_custom_rdrp_database`, you would use `--custom-dbs my_custom_rdrp_database` in the command line.
+- You can add multiple custom databases by installing them in the same way and specifying them  by separating them with commas, e.g. `--custom-dbs my_custom_rdrp_database,another_custom_database`.
+- The custom databases can be used in combination with the pre-compiled databases provided by RdRpCATCH. To do this, you can specify the `--db_options` argument with the names of the pre-compiled databases you want to use, and specify the custom databases with the `--custom-dbs` argument.
+- For example, if you want to use the NeoRdRp and RVMT databases along with your custom database, you would use the following command:
+
+```bash
+rdrpcatch scan -i path/to/input.fasta -o path/to/output_dir -db_dir path/to/database --db_options NeoRdRp,RVMT --custom-dbs my_custom_rdrp_database
+```
+
+- Note: By default, RdRpCATCH will search against all pre-compiled databases if no `--db_options` argument is specified. If you want to use only the custom databases, you can specify `--db_options none` to avoid searching against the pre-compiled databases.
+
+
+
+
 ## Commands
 The following two commands are available in RdRpCATCH:  
 * [`rdrpcatch scan`](#rdrpcatch-scan)  
-* [`rdrpcatch download`](#rdrpcatch-download)
+* [`rdrpcatch databases`](#rdrpcatch-download)
 
-### rdrpcatch download:
-Command to download pre-compiled databases from Zenodo. If the databases are already downloaded in the specified directory
+### rdrpcatch databases:
+Command to download pre-compiled databases from Zenodo and to set up custom databases. If the databases are already downloaded in the specified directory
 , the command will check for updates and download the latest version if available.
 
 | Argument | Short Flag | Type | Description                                                 |
@@ -130,28 +186,30 @@ Command to download pre-compiled databases from Zenodo. If the databases are alr
 | `--destination_dir` | `-dest` | PATH | Path to the directory to download HMM databases. [required] |
 | `--concept-doi` | `` | TEXT | Zenodo Concept DOI for database repository                  |
 | `--help` | `` |  | Show help message and exit                                  |
+| `--add-custom-db` | `` | PATH | Path to the directory containing custom pHMM files to add to the RdRpCATCH databases. |
+
 ### rdrpcatch scan:
 Search a given input using selected RdRp databases.  
 
-| Argument | Short Flag | Type | Description |
-|----------|------------|------|-------------|
-| `--input` | `-i` | FILE | Path to the input FASTA file. [required] |
-| `--output` | `-o` | DIRECTORY | Path to the output directory. [required] |
-| `--db_dir` | `-db_dir` | PATH | Path to the directory containing RdRpCATCH databases. [required] |
-| `--db_options` | `-dbs` | TEXT | Comma-separated list of databases to search against. Valid options: RVMT, NeoRdRp, NeoRdRp.2.1, TSA_Olendraite_fam, TSA_Olendraite_gen, RDRP-scan, Lucaprot, all |
-| `--custom-dbs` | | PATH | Path to directory containing custom MSAs/pHMM files to use as additional databases |
-| `--seq_type` | `-seq_type` | TEXT | Type of sequence to search against: (prot,nuc) Default: unknown |
-| `--verbose` | `-v` | FLAG | Print verbose output. |
-| `--evalue` | `-e` | FLOAT | E-value threshold for HMMsearch. (default: 1e-5) |
-| `--incevalue` | `-incE` | FLOAT | Inclusion E-value threshold for HMMsearch. (default: 1e-5) |
-| `--domevalue` | `-domE` | FLOAT | Domain E-value threshold for HMMsearch. (default: 1e-5) |
-| `--incdomevalue` | `-incdomE` | FLOAT | Inclusion domain E-value threshold for HMMsearch. (default: 1e-5) |
-| `--zvalue` | `-z` | INTEGER | Number of sequences to search against. (default: 1000000) |
-| `--cpus` | `-cpus` | INTEGER | Number of CPUs to use for HMMsearch. (default: 1) |
-| `--length_thr` | `-length_thr` | INTEGER | Minimum length threshold for seqkit seq. (default: 400) |
-| `--gen_code` | `-gen_code` | INTEGER | Genetic code to use for translation. (default: 1) |
-| `--bundle` | `-bundle` |  |  Bundle the output files into a single archive. (default: False) |
-| `--keep_tmp` | `-keep_tmp` |  | Keep the temporary files generated during the analysis. (default: False) |
+| Argument         | Short Flag    | Type | Description                                                                                                                                                                                  |
+|------------------|---------------|------|----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|
+| `--input`        | `-i`          | FILE | Path to the input FASTA file. [required]                                                                                                                                                     |
+| `--output`       | `-o`          | DIRECTORY | Path to the output directory. [required]                                                                                                                                                     |
+| `--db-dir`       | `-db-dir`     | PATH | Path to the directory containing RdRpCATCH databases. [required]                                                                                                                             |
+| `--db-options`   | `-dbs`        | TEXT | Comma-separated list of pre-installed databases to search against. Valid options: RVMT, NeoRdRp, NeoRdRp.2.1, TSA_Olendraite_fam, TSA_Olendraite_gen, RDRP-scan, Lucaprot_HMM,Zayed_HMM, all |
+| `--custom-dbs`   |               | PATH | Comma-separated list of custom databases to search against. Valid options: names of the directories that the custom databases are stored in.                                                 |
+| `--seq-type`     | `-seq-type`   | TEXT | Type of sequence to search against: (prot,nuc) Default: unknown                                                                                                                              |
+| `--verbose`      | `-v`          | FLAG | Print verbose output.                                                                                                                                                                        |
+| `--evalue`       | `-e`          | FLOAT | E-value threshold for HMMsearch. (default: 1e-5)                                                                                                                                             |
+| `--incevalue`    | `-incE`       | FLOAT | Inclusion E-value threshold for HMMsearch. (default: 1e-5)                                                                                                                                   |
+| `--domevalue`    | `-domE`       | FLOAT | Domain E-value threshold for HMMsearch. (default: 1e-5)                                                                                                                                      |
+| `--incdomevalue` | `-incdomE`    | FLOAT | Inclusion domain E-value threshold for HMMsearch. (default: 1e-5)                                                                                                                            |
+| `--zvalue`       | `-z`          | INTEGER | Number of sequences to search against. (default: 1000000)                                                                                                                                    |
+| `--cpus`         | `-cpus`       | INTEGER | Number of CPUs to use for HMMsearch. (default: 1)                                                                                                                                            |
+| `--length-thr`   | `-length-thr` | INTEGER | Minimum length threshold for seqkit seq. (default: 400)                                                                                                                                      |
+| `--gen-code`     | `-gen-code`   | INTEGER | Genetic code to use for translation. (default: 1)                                                                                                                                            |
+| `--bundle`       | `-bundle`     |  | Bundle the output files into a single archive. (default: False)                                                                                                                              |
+| `--keep-tmp`     | `-keep-tmp`   |  | Keep the temporary files generated during the analysis. (default: False)                                                                                                                     |
 
 
 

{rdrpcatch-0.0.6 → rdrpcatch-0.0.8}/README.md

@@ -12,18 +12,31 @@ library to perform pHMM searches.  In addition, the tool scans each sequence (aa
 In addition, RdRpCATCH provides information about the number of profiles
 that were positive for each sequence across all pHMM databases, and taxonomic information based on the MMseqs2 easy-taxonomy and search modules against a custom RefSeq Riboviria database.
 
+### Version 0.0.7 -> 0.0.8 Changelog
+- Added support for custom pHMM databases. See the [Setting up custom pHMM databases](#setting-up-custom-phmm-databases) section for more information.
+- All specified flags use '-' instead of '_' (e.g. `--db-dir` instead of `--db_dir`). 
+- Fixed issue with specifying the Lucaprot_HMM and Zayed_HMM databases in the `--db-options` argument.
+- Command `rdrpcatch download` renamed as `rdrpcatch databases` for clarity, as it now supports adding custom pHMM
+databases to the RdRpCATCH databases. This is facilitated by the `--add-custom-db` argument.
+- Added none option to the `--db-options` argument to search only against custom databases.
+
+
+
 ** The tool has been modified to use [rolypoly](https://code.jgi.doe.gov/UNeri/rolypoly) code/approaches **
 
-![rdrpcatch_flowchart_v0.png](images%2Frdrpcatch_flowchart_v0.png)
+
+
+![rdrpcatch_flowchart_v0.png](images%2Frdrpcatch_illustration.png)
 
 ### Supported databases
 - NeoRdRp <sup>1</sup> : 1182 pHMMs 
 - NeoRdRp2 <sup>2</sup>: 19394 pHMMs  
 - RVMT <sup>3</sup>: 710 pHMMs  
 - RdRp-Scan <sup>4</sup> : 68 pHMMs
-- TSA_Oleandrite_fam <sup>5</sup>: 77 pHMMs 
-- TSA_Oleandrite_gen <sup>6</sup> : 341 pHMMs
-- LucaProt_pHMM<sup>7 </sup> : 754 pHMMs 
+- TSA_Olendraite_fam <sup>5</sup>: 77 pHMMs 
+- TSA_Olendraite_gen <sup>6</sup> : 341 pHMMs
+- LucaProt_HMM<sup>7 </sup> : 754 pHMMs
+- Zayed_HMM<sup>8 </sup> : 2489 pHMMs
 
 1. Sakaguchi, S. et al. (2022) 'NeoRdRp: A comprehensive dataset for identifying RNA-dependent RNA polymerases of various RNA viruses from metatranscriptomic data', *Microbes and Environments*, 37(3). [doi:10.1264/jsme2.me22001](https://doi.org/10.1264/jsme2.me22001)
 2. Sakaguchi, S., Nakano, T. and Nakagawa, S. (2024) 'Neordrp2 with improved seed data, annotations, and scoring', *Frontiers in Virology*, 4. [doi:10.3389/fviro.2024.1378695](https://doi.org/10.3389/fviro.2024.1378695)
@@ -31,7 +44,9 @@ that were positive for each sequence across all pHMM databases, and taxonomic in
 4. Charon, J. et al. (2022) 'RDRP-Scan: A bioinformatic resource to identify and annotate divergent RNA viruses in metagenomic sequence data', *Virus Evolution*, 8(2). [doi:10.1093/ve/veac082](https://doi.org/10.1093/ve/veac082)
 5. Olendraite, I., Brown, K. and Firth, A.E. (2023) 'Identification of RNA virus–derived rdrp sequences in publicly available transcriptomic data sets', *Molecular Biology and Evolution*, 40(4). [doi:10.1093/molbev/msad060](https://doi.org/10.1093/molbev/msad060)
 6. Olendraite, I. (2021) 'Mining diverse and novel RNA viruses in transcriptomic datasets', Apollo. Available at: [https://www.repository.cam.ac.uk/items/1fabebd2-429b-45c9-b6eb-41d27d0a90c2](https://www.repository.cam.ac.uk/items/1fabebd2-429b-45c9-b6eb-41d27d0a90c2)
-7. Hou, X. et al. (2024) 'Using artificial intelligence to document the hidden RNA virosphere', *Cell*, 187(24). [doi:10.1016/j.cell.2024.09.027](https://doi.org/10.1016/j.cell.2024.09.027)
+7. Hou, X. and He, Y. et al. (2024) 'Using artificial intelligence to document the hidden RNA virosphere', *Cell*, 187(24). [doi:10.1016/j.cell.2024.09.027](https://doi.org/10.1016/j.cell.2024.09.027)
+8. Zayed, A. A., et al. (2022)  'Cryptic and abundant marine viruses at the evolutionary origins of Earth’s RNA virome.' *Science*, 376(6589), 156–162. [doi:10.1126/science.abm5847](https://doi.org/10.1126/science.abm5847)
+
 
 
 ## Installation
@@ -72,13 +87,16 @@ Activate the environment and download the RdRpCATCH databases:
 
 ```bash 
 conda activate rdrpcatch
-rdrpcatch download --destination_dir path/to/store/databases
+rdrpcatch databases --destination_dir path/to/store/databases
 ```
 
 * Note 1: The databases are large files and may take some time to download (~ 3 GB).
 * Note 2: The databases are stored in the specified directory, and the path is required to run RdRpCATCH.
 * Note 3: If you encounter an SSL error while downloading, please try again. The error seems to appear sporadically during testing, and a simple re-initiation of the downloading process seems to fix it. 
 
+
+
+
 ## Usage
 RdRpCATCH can be used as a CLI tool as follows:
 
@@ -87,20 +105,58 @@ RdRpCATCH can be used as a CLI tool as follows:
 # conda activate rdrpcatch
 
 # scan the input fasta file with the selected databases
-rdrpcatch scan -i path/to/input.fasta -o path/to/output_dir -db_dir path/to/database
+rdrpcatch scan -i path/to/input.fasta -o path/to/output_dir -db-dir path/to/database
 ```
-### input: 
+
+## Input description
 The input file can be one or more nucleotide or protein sequences in multi-fasta format. 
 The output directory is where the results will be stored. We recommend specifying the type of the sequence in the command line,
 An optional argument `--seq_type` (nuc or prot) can be used to specify if the input fasta file sequences are nucleotide or amino acid.
 
+
+## Setting up custom pHMM databases
+It is possible to use custom pHMM databases with RdRpCATCH. As a prerequisite, you need to install the RdRpCATCH 
+databases using the `rdrpcatch databases` command as described above, to a directory of your choice.
+
+The custom databases should be formatted as follows:
+
+- First create a directory and give it a descriptive name, e.g. `my_custom_rdrp_database`. Important: The name should not contain  comma `,` characters.
+- Inside the directory put your custom pHMM HMMER pressed database. You can use the `hmmpress` command of HMMER to create the pressed database from your custom HMM file. This creates a set of files with the same name as the original HMM file, but with different extensions (e.g. `.h3f`, `.h3i`, `.h3m`, `.h3p`).  The directory should contain all these files. Please refer to the HMMER manual for more information on how to create a pressed database from an HMM file. (http://eddylab.org/software/hmmer/Userguide.pdf) 
+- Next you can add the directory to the custom databases that are readable by RdRpCATCH. This can be done by using the rdrpcatch databases command as follows:
+
+```bash
+rdrpcatch databases --add-custom-db path/to/my_custom_rdrp_database --destination-dir path/that/contains/rdrpcatch/databases
+```
+
+- This will add the custom database to the list of databases that can be used with RdRpCATCH.
+- The custom database can then be used with the `rdrpcatch scan` command by specifying the `--custom-dbs` argument as follows:
+- 
+```bash
+rdrpcatch scan -i path/to/input.fasta -o path/to/output_dir -db_dir path/to/database --custom-dbs custom_database_name
+```
+
+- The `custom_database_name` should be the name of the directory that contains the custom pHMM files, without the path.
+- For example, if the custom database is stored in `path/to/my_custom_rdrp_database`, you would use `--custom-dbs my_custom_rdrp_database` in the command line.
+- You can add multiple custom databases by installing them in the same way and specifying them  by separating them with commas, e.g. `--custom-dbs my_custom_rdrp_database,another_custom_database`.
+- The custom databases can be used in combination with the pre-compiled databases provided by RdRpCATCH. To do this, you can specify the `--db_options` argument with the names of the pre-compiled databases you want to use, and specify the custom databases with the `--custom-dbs` argument.
+- For example, if you want to use the NeoRdRp and RVMT databases along with your custom database, you would use the following command:
+
+```bash
+rdrpcatch scan -i path/to/input.fasta -o path/to/output_dir -db_dir path/to/database --db_options NeoRdRp,RVMT --custom-dbs my_custom_rdrp_database
+```
+
+- Note: By default, RdRpCATCH will search against all pre-compiled databases if no `--db_options` argument is specified. If you want to use only the custom databases, you can specify `--db_options none` to avoid searching against the pre-compiled databases.
+
+
+
+
 ## Commands
 The following two commands are available in RdRpCATCH:  
 * [`rdrpcatch scan`](#rdrpcatch-scan)  
-* [`rdrpcatch download`](#rdrpcatch-download)
+* [`rdrpcatch databases`](#rdrpcatch-download)
 
-### rdrpcatch download:
-Command to download pre-compiled databases from Zenodo. If the databases are already downloaded in the specified directory
+### rdrpcatch databases:
+Command to download pre-compiled databases from Zenodo and to set up custom databases. If the databases are already downloaded in the specified directory
 , the command will check for updates and download the latest version if available.
 
 | Argument | Short Flag | Type | Description                                                 |
@@ -108,28 +164,30 @@ Command to download pre-compiled databases from Zenodo. If the databases are alr
 | `--destination_dir` | `-dest` | PATH | Path to the directory to download HMM databases. [required] |
 | `--concept-doi` | `` | TEXT | Zenodo Concept DOI for database repository                  |
 | `--help` | `` |  | Show help message and exit                                  |
+| `--add-custom-db` | `` | PATH | Path to the directory containing custom pHMM files to add to the RdRpCATCH databases. |
+
 ### rdrpcatch scan:
 Search a given input using selected RdRp databases.  
 
-| Argument | Short Flag | Type | Description |
-|----------|------------|------|-------------|
-| `--input` | `-i` | FILE | Path to the input FASTA file. [required] |
-| `--output` | `-o` | DIRECTORY | Path to the output directory. [required] |
-| `--db_dir` | `-db_dir` | PATH | Path to the directory containing RdRpCATCH databases. [required] |
-| `--db_options` | `-dbs` | TEXT | Comma-separated list of databases to search against. Valid options: RVMT, NeoRdRp, NeoRdRp.2.1, TSA_Olendraite_fam, TSA_Olendraite_gen, RDRP-scan, Lucaprot, all |
-| `--custom-dbs` | | PATH | Path to directory containing custom MSAs/pHMM files to use as additional databases |
-| `--seq_type` | `-seq_type` | TEXT | Type of sequence to search against: (prot,nuc) Default: unknown |
-| `--verbose` | `-v` | FLAG | Print verbose output. |
-| `--evalue` | `-e` | FLOAT | E-value threshold for HMMsearch. (default: 1e-5) |
-| `--incevalue` | `-incE` | FLOAT | Inclusion E-value threshold for HMMsearch. (default: 1e-5) |
-| `--domevalue` | `-domE` | FLOAT | Domain E-value threshold for HMMsearch. (default: 1e-5) |
-| `--incdomevalue` | `-incdomE` | FLOAT | Inclusion domain E-value threshold for HMMsearch. (default: 1e-5) |
-| `--zvalue` | `-z` | INTEGER | Number of sequences to search against. (default: 1000000) |
-| `--cpus` | `-cpus` | INTEGER | Number of CPUs to use for HMMsearch. (default: 1) |
-| `--length_thr` | `-length_thr` | INTEGER | Minimum length threshold for seqkit seq. (default: 400) |
-| `--gen_code` | `-gen_code` | INTEGER | Genetic code to use for translation. (default: 1) |
-| `--bundle` | `-bundle` |  |  Bundle the output files into a single archive. (default: False) |
-| `--keep_tmp` | `-keep_tmp` |  | Keep the temporary files generated during the analysis. (default: False) |
+| Argument         | Short Flag    | Type | Description                                                                                                                                                                                  |
+|------------------|---------------|------|----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|
+| `--input`        | `-i`          | FILE | Path to the input FASTA file. [required]                                                                                                                                                     |
+| `--output`       | `-o`          | DIRECTORY | Path to the output directory. [required]                                                                                                                                                     |
+| `--db-dir`       | `-db-dir`     | PATH | Path to the directory containing RdRpCATCH databases. [required]                                                                                                                             |
+| `--db-options`   | `-dbs`        | TEXT | Comma-separated list of pre-installed databases to search against. Valid options: RVMT, NeoRdRp, NeoRdRp.2.1, TSA_Olendraite_fam, TSA_Olendraite_gen, RDRP-scan, Lucaprot_HMM,Zayed_HMM, all |
+| `--custom-dbs`   |               | PATH | Comma-separated list of custom databases to search against. Valid options: names of the directories that the custom databases are stored in.                                                 |
+| `--seq-type`     | `-seq-type`   | TEXT | Type of sequence to search against: (prot,nuc) Default: unknown                                                                                                                              |
+| `--verbose`      | `-v`          | FLAG | Print verbose output.                                                                                                                                                                        |
+| `--evalue`       | `-e`          | FLOAT | E-value threshold for HMMsearch. (default: 1e-5)                                                                                                                                             |
+| `--incevalue`    | `-incE`       | FLOAT | Inclusion E-value threshold for HMMsearch. (default: 1e-5)                                                                                                                                   |
+| `--domevalue`    | `-domE`       | FLOAT | Domain E-value threshold for HMMsearch. (default: 1e-5)                                                                                                                                      |
+| `--incdomevalue` | `-incdomE`    | FLOAT | Inclusion domain E-value threshold for HMMsearch. (default: 1e-5)                                                                                                                            |
+| `--zvalue`       | `-z`          | INTEGER | Number of sequences to search against. (default: 1000000)                                                                                                                                    |
+| `--cpus`         | `-cpus`       | INTEGER | Number of CPUs to use for HMMsearch. (default: 1)                                                                                                                                            |
+| `--length-thr`   | `-length-thr` | INTEGER | Minimum length threshold for seqkit seq. (default: 400)                                                                                                                                      |
+| `--gen-code`     | `-gen-code`   | INTEGER | Genetic code to use for translation. (default: 1)                                                                                                                                            |
+| `--bundle`       | `-bundle`     |  | Bundle the output files into a single archive. (default: False)                                                                                                                              |
+| `--keep-tmp`     | `-keep-tmp`   |  | Keep the temporary files generated during the analysis. (default: False)                                                                                                                     |
 
 
 

{rdrpcatch-0.0.6 → rdrpcatch-0.0.8}/pyproject.toml

@@ -4,7 +4,7 @@ build-backend = "hatchling.build"
 
 [project]
 name = "rdrpcatch"
-version = "0.0.6"
+version = "0.0.8"
 authors = [
     {name = "Dimitris Karapliafis", email = "dimitris.karapliafis@wur.nl"},
     {name = "Uri Neri", email = "uneri@lbl.gov"},

{rdrpcatch-0.0.6 → rdrpcatch-0.0.8}/rdrpcatch/cli/args.py

@@ -26,7 +26,7 @@ def parse_comma_separated_options(ctx, param, value):
         return ['all']
 
     allowed_choices = ['RVMT', 'NeoRdRp', 'NeoRdRp.2.1', 'TSA_Olendraite_fam', 'TSA_Olendraite_gen', 'RDRP-scan',
-                       'Lucaprot', 'all']
+                       'Lucaprot_HMM', 'Zayed_HMM', 'all', 'none']
     lower_choices = [choice.lower() for choice in allowed_choices]
     options = value.split(',')
     lower_options = [option.lower() for option in options]
@@ -66,17 +66,16 @@ def cli():
 @click.option("-o", "--output",
               help="Path to the output directory.",
               type=click.Path(exists=False, file_okay=False, writable=True, path_type=Path), required=True)
-@click.option("-db_dir", "--db_dir",
+@click.option("-db-dir", "--db-dir",
               help="Path to the directory containing RdRpCATCH databases.",
               type=click.Path(exists=True, dir_okay=True, readable=True, path_type=Path),required=True)
-@click.option("-dbs", "--db_options",
+@click.option("-dbs", "--db-options",
               callback=parse_comma_separated_options,
               default="all",
               help="Comma-separated list of databases to search against. Valid options: RVMT, NeoRdRp, NeoRdRp.2.1,"
-                   " TSA_Olendraite_fam, TSA_Olendraite_gen, RDRP-scan,Lucaprot, all")
+                   " TSA_Olendraite_fam, TSA_Olendraite_gen, RDRP-scan,Lucaprot_HMM, Zayed_HMM, all, none. ")
 @click.option("--custom-dbs",
-              help="Path to directory containing custom MSAs/pHMM files to use as additional databases",
-              type=click.Path(exists=True, path_type=Path))
+              help="Path to directory containing custom MSAs/pHMM files to use as additional databases")
 @click.option("-seq_type", "--seq_type",
               type=click.STRING,
               default=None,
@@ -112,7 +111,7 @@ def cli():
               type=click.INT,
               default=400,
               help="Minimum length threshold for seqkit seq. (default: 400)")
-@click.option('-gen_code', '--gen_code',
+@click.option('-gen-code', '--gen_code',
               type=click.INT,
               default=1,
               help='Genetic code to use for translation. (default: 1) Possible genetic codes (supported by seqkit translate) : 1: The Standard Code, '
@@ -143,7 +142,7 @@ def cli():
               is_flag=True,
               default=False,
               help="Bundle the output files into a single archive. (default: False)")
-@click.option('-keep_tmp', '--keep_tmp',
+@click.option('-keep-tmp', '--keep_tmp',
               is_flag=True,
               default=False,
               help="Keep temporary files (Expert users) (default: False)")
@@ -164,7 +163,7 @@ def scan(ctx, input, output, db_options, db_dir, custom_dbs, seq_type, verbose,
 
     table.add_row("Input File", str(input))
     table.add_row("Output Directory", str(output))
-    table.add_row("Databases", ", ".join(db_options))
+    table.add_row("Supported databases", ", ".join(db_options))
     table.add_row("Database Directory", str(db_dir))
     if custom_dbs:
         table.add_row("Custom Databases", str(custom_dbs))
@@ -184,24 +183,13 @@ def scan(ctx, input, output, db_options, db_dir, custom_dbs, seq_type, verbose,
 
     console.print(Panel(table, title="Scan Configuration"))
 
-    # Add custom databases if provided
-    if custom_dbs:
-        db = db_fetcher(db_dir)
-        if os.path.isfile(custom_dbs):
-            db.add_custom_db(custom_dbs)
-        else:
-            for item in os.listdir(custom_dbs):
-                item_path = os.path.join(custom_dbs, item)
-                if os.path.isfile(item_path) and item_path.endswith(('.hmm', '.h3m', '.msa', '.sto', '.fasta', '.fa')):
-                    db.add_custom_db(item_path)
-                elif os.path.isdir(item_path):
-                    db.add_custom_db(item_path, item)
 
     run_scan(
         input_file=input,
         output_dir=output,
         db_options=db_options,
         db_dir=db_dir,
+        custom_dbs=custom_dbs,
         seq_type=seq_type,
         verbose=verbose,
         e=evalue,
@@ -217,29 +205,6 @@ def scan(ctx, input, output, db_options, db_dir, custom_dbs, seq_type, verbose,
         overwrite=overwrite
     )
 
-# @cli.command("download", help="Download RdRpCATCH databases.")
-# @click.option("--destination_dir", "-dest",
-#               help="Path to the directory to download HMM databases.",
-#               type=click.Path(exists=False, file_okay=False, writable=True, path_type=Path), required=True)
-# @click.option("--check-updates", "-u",
-#               is_flag=True,
-#               help="Check for database updates")
-# @click.pass_context
-# def download(ctx, destination_dir, check_updates):
-#     """Download RdRpCATCH databases."""
-#
-#     # if check_updates:
-#     #     db = db_fetcher(destination_dir)
-#     #     version_info = db.check_db_updates()
-#     #     if version_info:
-#     #         console.print("Current database versions:")
-#     #         for db_name, info in version_info.items():
-#     #             console.print(f"- {db_name}: {info}")
-#     #     else:
-#     #         console.print("No version information available")
-#     #     return
-#
-#     run_download(destination_dir)
 #
 # # @cli.command("gui", help="Launch the GUI.")
 # # @click.pass_context
@@ -251,17 +216,41 @@ def scan(ctx, input, output, db_options, db_dir, custom_dbs, seq_type, verbose,
 
 
 
-@cli.command("download", help="Download &  update RdRpCATCH databases. If databases are already installed in the "
+@cli.command("databases", help="Download &  update RdRpCATCH databases. If databases are already installed in the "
                               "specified directory,"
                               " it will check for updates and download the latest version if available.")
-@click.option("--destination_dir", "-dest",
+@click.option("--destination-dir", "-dest",
               help="Path to directory to download databases",
               type=click.Path(path_type=Path, file_okay=False, writable=True),
               required=True)
 @click.option("--concept-doi", default="10.5281/zenodo.14358348",
               help="Zenodo Concept DOI for database repository")
-def download(destination_dir: Path, concept_doi: str):
+@click.option("--add-custom-db", "-cdb",
+              help="Path to a custom, pressed pHMM database directory. This only works"
+                   "if the supported  databases have already been downloaded."
+                   " Please point to the directory the databases are stored ('rdrpcatch_dbs') using"
+                   "the '--destination-dir' flag."
+
+    , type = click.Path(exists=True, dir_okay=True, readable=True, path_type=Path))
+
+def databases(destination_dir: Path, concept_doi: str, add_custom_db: Path | None = None):
     """Handle database download/update workflow"""
+
+    if add_custom_db:
+        if not destination_dir.exists():
+            console.print("[red]× Destination directory does not exist![/red]")
+            raise click.Abort()
+        if not destination_dir.is_dir():
+            console.print("[red]× Destination path is not a directory![/red]")
+            raise click.Abort()
+
+        db = db_fetcher(destination_dir)
+        db.add_custom_db(add_custom_db)
+
+        console.print(f"[green]✓ Custom database added successfully to {destination_dir}[/green]")
+
+
+
     downloader = ZenodoDownloader(concept_doi, destination_dir)
 
     try:

{rdrpcatch-0.0.6 → rdrpcatch-0.0.8}/rdrpcatch/rdrpcatch_scripts/fetch_dbs.py

@@ -49,20 +49,23 @@ class db_fetcher:
 
         # Copy the database file
         if os.path.isfile(db_path):
-            shutil.copy2(db_path, target_path)
+            raise ValueError("Custom database must be a directory, not a file. Name the directory as the database name,"
+                             "and include a pressed HMMER HMM database inside. For directions, see the README.md file.")
+
         elif os.path.isdir(db_path):
             if os.path.exists(target_path):
                 shutil.rmtree(target_path)
             shutil.copytree(db_path, target_path)
 
-        # Update version info
-        version_info = self._get_db_version()
-        version_info.setdefault('custom_dbs', {})
-        version_info['custom_dbs'][db_name] = {
-            'added': datetime.datetime.now().isoformat(),
-            'path': target_path
-        }
-        self._save_db_version(version_info)
+        # For now, we stop saving the version info, cause it messes up with the download module.
+        # # Update version info
+        # version_info = self._get_db_version()
+        # version_info.setdefault('custom_dbs', {})
+        # version_info['custom_dbs'][db_name] = {
+        #     'added': datetime.datetime.now().isoformat(),
+        #     'path': target_path
+        # }
+        # self._save_db_version(version_info)
 
     def _resolve_rdrpcatch_path(self):
         """Automatically detect correct database path structure"""
@@ -93,6 +96,7 @@ class db_fetcher:
 
         # First check custom databases
         if os.path.exists(self.custom_db_dir):
+
             custom_path = os.path.join(self.custom_db_dir, db_name)
             if os.path.exists(custom_path):
                 if os.path.isfile(custom_path) and custom_path.endswith(('.h3m', '.hmm')):

{rdrpcatch-0.0.6 → rdrpcatch-0.0.8}/rdrpcatch/rdrpcatch_wrapper.py

@@ -53,7 +53,7 @@ def bundle_results(output_dir, prefix):
     
     return archive_path
 
-def run_scan(input_file, output_dir, db_options, db_dir, seq_type, verbose, e,incdomE,domE,incE,z, cpus, length_thr, gen_code, bundle, keep_tmp, overwrite):
+def run_scan(input_file, output_dir, db_options, db_dir, custom_dbs,  seq_type, verbose, e,incdomE,domE,incE,z, cpus, length_thr, gen_code, bundle, keep_tmp, overwrite):
     """
     Run RdRpCATCH scan.
 
@@ -127,7 +127,8 @@ def run_scan(input_file, output_dir, db_options, db_dir, seq_type, verbose, e,in
 
     logger.silent_log(f"Input File: {input_file}")
     logger.silent_log(f"Output Directory: {output_dir}")
-    logger.silent_log(f"Databases: {db_options}")
+    logger.silent_log(f"Supported Databases: {db_options}")
+    logger.silent_log(f"Custom Databases: {custom_dbs}")
     logger.silent_log(f"Database Directory: {db_dir}")
     logger.silent_log(f"Sequence Type: {seq_type}")
     logger.silent_log(f"Verbose Mode: {'ON' if verbose else 'OFF'}")
@@ -170,7 +171,7 @@ def run_scan(input_file, output_dir, db_options, db_dir, seq_type, verbose, e,in
 
     logger.loud_log("Fetching HMM databases...")
 
-    ## Fetch HMM databases- RVMT, NeoRdRp, NeoRdRp.2.1, TSA_Olendraite, RDRP-scan, Lucaprot
+    ## Fetch HMM databases- RVMT, NeoRdRp, NeoRdRp.2.1, TSA_Olendraite, RDRP-scan, Lucaprot_HMM,Zayed_HMM
     rvmt_hmm_db = fetch_dbs.db_fetcher(db_dir).fetch_hmm_db_path("RVMT")
     if verbose:
         logger.loud_log(f"RVMT HMM database fetched from: {rvmt_hmm_db}")
@@ -202,20 +203,32 @@ def run_scan(input_file, output_dir, db_options, db_dir, seq_type, verbose, e,in
         logger.loud_log(f"RDRP-scan HMM database fetched from: {rdrpscan_hmm_db}")
     else:
         logger.silent_log(f"RDRP-scan HMM database fetched from: {rdrpscan_hmm_db}")
-    lucaprot_hmm_db = fetch_dbs.db_fetcher(db_dir).fetch_hmm_db_path("Lucaprot")
+    lucaprot_hmm_db = fetch_dbs.db_fetcher(db_dir).fetch_hmm_db_path("Lucaprot_HMM")
     if verbose:
         logger.loud_log(f"Lucaprot HMM database fetched from: {lucaprot_hmm_db}")
     else:
         logger.silent_log(f"Lucaprot HMM database fetched from: {lucaprot_hmm_db}")
+    zayed_hmm_db = fetch_dbs.db_fetcher(db_dir).fetch_hmm_db_path("Zayed_HMM")
+    if verbose:
+        logger.loud_log(f"Zayed HMM database fetched from: {zayed_hmm_db}")
+    else:
+        logger.silent_log(f"Zayed HMM database fetched from: {zayed_hmm_db}")
 
     db_name_list = []
     db_path_list = []
 
     ## Set up HMM databases
     if db_options == ['all']:
-        db_name_list = ["RVMT", "NeoRdRp", "NeoRdRp.2.1", "TSA_Olendraite_fam","TSA_Olendraite_gen", "RDRP-scan", "Lucaprot"]
-        db_path_list = [rvmt_hmm_db, neordrp_hmm_db, neordrp_2_hmm_db, tsa_olen_fam_hmm_db,tsa_olen_gen_hmm_db, rdrpscan_hmm_db, lucaprot_hmm_db]
-
+        db_name_list = ["RVMT", "NeoRdRp", "NeoRdRp.2.1", "TSA_Olendraite_fam","TSA_Olendraite_gen", "RDRP-scan", "Lucaprot_HMM", "Zayed_HMM"]
+        db_path_list = [rvmt_hmm_db, neordrp_hmm_db, neordrp_2_hmm_db, tsa_olen_fam_hmm_db,tsa_olen_gen_hmm_db, rdrpscan_hmm_db, lucaprot_hmm_db, zayed_hmm_db]
+    elif db_options == ['none'] and not custom_dbs:
+        raise Exception("No databases selected. Please select at least one database or provide custom databases.")
+    elif db_options == ['none'] and custom_dbs:
+        logger.loud_log("No supported databases selected, but custom databases provided. Using only custom databases.")
+        if not os.path.exists(os.path.join(db_dir, "custom_dbs")):
+            raise Exception(f"Custom databases directory not found: {os.path.join(db_dir, 'custom_dbs')}. Please"
+                            f" use rdrpcatch databases to create a valid custom database as described in the "
+                            f"documentation.")
     else:
         for db in db_options:
             if db == "RVMT".lower():
@@ -236,15 +249,42 @@ def run_scan(input_file, output_dir, db_options, db_dir, seq_type, verbose, e,in
             elif db == "RDRP-scan".lower():
                 db_name_list.append("RDRP-scan")
                 db_path_list.append(rdrpscan_hmm_db)
-            elif db == "Lucaprot".lower():
-                db_name_list.append("Lucaprot")
+            elif db == "Lucaprot_HMM".lower():
+                db_name_list.append("Lucaprot_HMM")
                 db_path_list.append(lucaprot_hmm_db)
+            elif db == "Zayed_HMM".lower():
+                db_name_list.append("Zayed_HMM")
+                db_path_list.append(zayed_hmm_db)
             else:
                 raise Exception(f"Invalid database option: {db}")
 
-    # Fetch mmseqs database
+    ## Check if custom databases are provided
+    if custom_dbs:
 
+        if not os.path.exists(os.path.join(db_dir, "custom_dbs")):
+            raise Exception(f"Custom databases directory not found: {os.path.join(db_dir, 'custom_dbs')}. Please"
+                            f" use rdrpcatch databases to create a valid custom database as described in the "
+                            f"documentation.")
+
+        custom_db_names = custom_dbs.split(',')
+        for custom_db in custom_db_names:
+            if verbose:
+                logger.loud_log(f"Fetching custom database: {custom_db}")
+            else:
+                logger.silent_log(f"Fetching custom database: {custom_db}")
 
+            custom_db = custom_db.strip()
+            custom_db_path = fetch_dbs.db_fetcher(db_dir).fetch_hmm_db_path(custom_db)
+            db_name_list.append(custom_db)
+            db_path_list.append(custom_db_path)
+
+            if verbose:
+                logger.loud_log(f"Custom database {custom_db} fetched from: {custom_db_path}")
+            else:
+                logger.silent_log(f"Custom database {custom_db} fetched from: {custom_db_path}")
+
+
+    # Fetch mmseqs database
     logger.loud_log("Fetching Mmseqs2 databases...")
 
     mmseqs_db_path = fetch_dbs.db_fetcher(db_dir).fetch_mmseqs_db_path("mmseqs_refseq_riboviria_20250211")
@@ -382,7 +422,8 @@ def run_scan(input_file, output_dir, db_options, db_dir, seq_type, verbose, e,in
 
         # Check if the combined dataframe is empty
         if combined_df.is_empty():
-            logger.loud_log("No hits found by RdRpCATCH. Exiting.")
+            db_name_string = ', '.join(db_name_list)
+            logger.loud_log(f"No hits found by RdRpCATCH for databases {db_name_string}. Exiting.")
             return None
 
         # Generate upset plot
@@ -549,7 +590,8 @@ def run_scan(input_file, output_dir, db_options, db_dir, seq_type, verbose, e,in
 
         # Check if the combined dataframe is empty
         if combined_df.is_empty():
-            logger.loud_log("No hits found by RdRpCATCH. Exiting.")
+            db_name_string = ', '.join(db_name_list)
+            logger.loud_log(f"No hits found by RdRpCATCH for databases {db_name_string}. Exiting.")
             return None
 
         # Generate upset plot