rolypoly-tk 0.7.2__tar.gz → 0.7.4__tar.gz

{rolypoly_tk-0.7.2 → rolypoly_tk-0.7.4}/PKG-INFO

@@ -1,9 +1,9 @@
 Metadata-Version: 2.4
 Name: rolypoly_tk
-Version: 0.7.2
+Version: 0.7.4
 Summary: RNA virus analysis toolkit
 Project-URL: Source, https://github.com/UriNeri/rolypoly
-Project-URL: Documentation, https://pages.jgi.doe.gov/rolypoly/docs/
+Project-URL: Documentation, https://urineri.github.io/rolypoly/
 Project-URL: pypi, https://pypi.org/project/rolypoly-tk/
 Author: Lander De Coninck
 Author-email: Uri Neri <uneri@lbl.gov>, Dimitris Karapliafis <dimitris.karapliafis@atwur.nl>, Brian Bushnell <bbushnell@lbl.gov>, Frederik Schulz <fschulz@lbl.gov>, Antonio Camargo <antoniop.camargo@lbl.gov>, Andrei Stecca Steindorff <andreiss@jgi.doe.gov>, Clement Coclet <cclement@jgi.doe.gov>, David Parker <dparker@carnegiescience.edu>, Simon Roux <sroux@lbl.gov>
@@ -682,7 +682,7 @@ License:                     GNU GENERAL PUBLIC LICENSE
         Public License instead of this License.  But first, please read
         <https://www.gnu.org/licenses/why-not-lgpl.html>.
 License-File: LICENSE
-Requires-Python: >=3.10
+Requires-Python: <3.14,>=3.10
 Requires-Dist: bbmapy<0.0.58,>=0.0.56
 Requires-Dist: genomicranges<0.8,>=0.7.3
 Requires-Dist: intervaltree<4,>=3.1.0
@@ -708,16 +708,18 @@ Requires-Dist: viennarna<3,>=2.7.0
 Requires-Dist: xxhash<4,>=3.6.0
 Description-Content-Type: text/markdown
 
-![RolyPoly Logo](https://code.jgi.doe.gov/rolypoly/docs/-/raw/main/docs/rolypoly_logo.png?ref_type=heads)
+![RolyPoly Logo](https://raw.githubusercontent.com/UriNeri/rolypoly/main/docs/rolypoly_logo.png)
 
 # RolyPoly
 
+[![PyPI version](https://img.shields.io/pypi/v/rolypoly-tk.svg?cacheSeconds=300)](https://pypi.org/project/rolypoly-tk/) [![Python versions](https://img.shields.io/pypi/pyversions/rolypoly-tk.svg?cacheSeconds=300)](https://pypi.org/project/rolypoly-tk/) [![PyPI Downloads](https://static.pepy.tech/personalized-badge/rolypoly-tk?period=monthly&units=INTERNATIONAL_SYSTEM&left_color=BLACK&right_color=GREEN&left_text=Downloads+%28month%29)](https://pepy.tech/projects/rolypoly-tk) [![License](https://img.shields.io/github/license/UriNeri/rolypoly.svg)](LICENSE) [![Docs](https://img.shields.io/badge/docs-urineri.github.io%2Frolypoly-blue)](https://urineri.github.io/rolypoly/)
+
 RolyPoly is an RNA virus analysis toolkit, meant to be a "swiss-army knife" for RNA virus discovery and characterization by including a variety of commands, wrappers, parsers, automations, and some "quality of life" features for any many of a virus investigation process (from raw read processing to genome annotation). While it includes an "end-2-end" command that employs an entire pipeline, the main goals of rolypoly are:
 - Help non-computational researchers take a deep dive into their data without compromising on using tools that are non-techie friendly.  
 - Help (software) developers of virus analysis pipeline "plug" holes missing from their framework, by using specific RolyPoly commands to add features to their existing code base.
 
 ## Note - Rolypoly is still under development (contributions welcome!)
-RolyPoly is an open, still in progress project - I aim to summarise the main functionality into a manuscript ~early 2026. Pull requests and contributions are welcome and will be considered (see [CONTRIBUTING.md](CONTRIBUTING.md)).  
+RolyPoly is an open, still in progress project - I aim to summarise the main functionality into a manuscript ~mid 2026. Pull requests and contributions are welcome and will be considered (see [CONTRIBUTING.md](CONTRIBUTING.md)).  
 This also means that there are bugs, verbose logging even for non debug mode, and some place holders and TODOs here and there.
 
 ## Installation
@@ -726,23 +728,27 @@ This also means that there are bugs, verbose logging even for non debug mode, an
 **Recommended for most users** who want a "just works" solution and primarily intend to use rolypoly as a CLI tool in an independent environment.
 
 We hope to have rolypoly available from bioconda in the near future.  
-In the meantime, it can be installed with the [`quick_setup.sh`](https://code.jgi.doe.gov/rolypoly/rolypoly/-/raw/main/src/setup/quick_setup.sh) script, which will also fetch the pre-generated data rolypoly requires.
+In the meantime, it can be installed with the [`quick_setup.sh`](https://raw.githubusercontent.com/UriNeri/rolypoly/main/src/setup/quick_setup.sh) script, which is Conda/Mamba-based (uses `mamba` or `micromamba`) and also fetches the pre-generated data rolypoly requires.
 
 ```bash
-curl -O https://code.jgi.doe.gov/rolypoly/rolypoly/-/raw/main/src/setup/quick_setup.sh && \
+curl -O https://raw.githubusercontent.com/UriNeri/rolypoly/main/src/setup/quick_setup.sh && \
 bash quick_setup.sh 
 ```
 
 #### Quick Setup - Additional Options
-You can specify custom paths for the code, databases, and conda environment location:
+You can specify custom paths for the code, databases, and Conda/Mamba environment location (this is also how you "name" the environment by choosing its path):
 ```bash
 bash quick_setup.sh /path/to/conda/env /path/to/install/rolypoly_code /path/to/store/databases /path/to/logfile
 ```
+Example with an explicit environment path:
+```bash
+bash quick_setup.sh "$HOME/mamba_envs/rolypoly"
+```
 By default if no positional arguments are supplied, rolypoly is installed into the session current folder (path the quick_setup.sh is called from):   
 - database in `./rolypoly/data/`  
 - code in `./rolypoly/code/ `  
 - conda environment in `./rolypoly/env/`  
-- log file in `./RolyPoly_quick_setup.log`   
+- log file in `./rolypoly/RolyPoly_quick_setup.log`   
 
 
 
@@ -754,7 +760,7 @@ By default if no positional arguments are supplied, rolypoly is installed into t
 curl -fsSL https://pixi.sh/install.sh | bash
 
 # Clone the repository
-git clone https://code.jgi.doe.gov/rolypoly/rolypoly.git
+git clone https://github.com/UriNeri/rolypoly.git
 cd rolypoly
 
 # Install for specific functionality (examples):
@@ -794,11 +800,11 @@ Legend:
 
 #### Raw-Reads
 - ✅ [`filter-reads`](https://urineri.github.io/rolypoly/commands/read_processing) — Host/rRNA/adapters/artifact filtering and QC (bbmap, falco, etc.)
-- ✅ [`shrink-reads`](https://urineri.github.io/rolypoly/commands/shrink_reads) — Downsample or subsample reads. Useful for testing or normalizing coverage across samples.
-- ✅ [`mask-dna`](https://urineri.github.io/rolypoly/commands/mask_dna) — Mask DNA regions in RNA-seq reads (bbmap, seqkit). Useful for avoiding mis-filtering of RNA virus reads in because of potential matches to EVEs.
+- ✅ [`shrink-reads`](https://urineri.github.io/rolypoly/commands/read_processing) — Downsample or subsample reads. Useful for testing or normalizing coverage across samples.
+- ✅ [`mask-dna`](https://urineri.github.io/rolypoly/commands/read_processing) — Mask DNA regions in RNA-seq reads (bbmap, seqkit). Useful for avoiding mis-filtering of RNA virus reads in because of potential matches to EVEs.
 
 #### Annotation
-- ✅ [`annotate`](https://urineri.github.io/rolypoly/commands/annotate) — Genome feature annotation (wraps the rna and prot commands)
+- ✅ [`annotate`](https://urineri.github.io/rolypoly/commands/annotate_rna/#annotate-rna) — Genome feature annotation (wraps the rna and prot commands)
 - ✅ [`annotate-rna`](https://urineri.github.io/rolypoly/commands/annotate_rna) — RNA secondary structure labelling and ribozyme detection (Infernal, ViennaRNA/linearfold, cmsearch on Rfam...)
 - 🧪 [`annotate-prot`](https://urineri.github.io/rolypoly/commands/annotate_prot) — Gene calling and Protein domain annotation and functional prediction (HMMER, Pfam, custom).
 
@@ -809,22 +815,22 @@ Legend:
 #### RNA Virus Identification
 - ✅ [`marker-search`](https://urineri.github.io/rolypoly/commands/marker_search) — Search for viral markers (mainly RdRps, genomad VVs, or user-provided), using profile-based methods (HMMER / MMseqs2). 
 - ✅ [`virus-mapping`](https://urineri.github.io/rolypoly/commands/search_viruses) — Map and identify viruses using nucleic acid search (MMseqs2).
-- ✅ `rdrp-motif-search` — Search RdRp motifs (A/B/C/D) in nucleotide or amino acid sequences.
+- ✅ [`rdrp-motif-search`](https://urineri.github.io/rolypoly/commands/rdrp_motif_search) — Search RdRp motifs (A/B/C/D) in nucleotide or amino acid sequences.
 
 #### Bining / Clustering
-- 🧪 `cluster` — Average Nucleic identity (ANI) based contig gropuing. Supports several common backends and methods.
-- 🧪 `extend` — Extend sequences by pile-up/assembly. Useful for combining assemblies of with low abundance viruses, or those with high microdiversity, at the cost of worse strain/sub-species resolution (i.e. can condense to a consenus). 
-- 🧪 `termini` — Shared termini grouping and motif reporting. Writes assignments + groups tables (TSV/CSV/Parquet/JSONL) and motif FASTA by default.
-- 🧪 `correlate` — group contigs based on co-occurence, co-abundance, minimal correlation (Spearman's) of these, or both.
-- 🤔 `binit` — Combines the above commands with sample information and genome attributes (e.g. require a shared termini AND protein complementarity, like CP + RdRp). See [notebooks/Exprimental/partiti_usecase/partiti_segment_workflow_experimental.ipynb](notebooks/Exprimental/partiti_usecase/partiti_segment_workflow_experimental.ipynb) for candidate workflow.
+- 🧪 [`cluster`](https://urineri.github.io/rolypoly/commands/cluster) — Average Nucleic identity (ANI) based contig grouping. Supports several common backends and methods.
+- 🧪 [`extend`](https://urineri.github.io/rolypoly/commands/extend) — Extend sequences by pile-up/assembly. Useful for combining assemblies of with low abundance viruses, or those with high microdiversity, at the cost of worse strain/sub-species resolution (i.e. can condense to a consensus).
+- 🧪 [`termini`](https://urineri.github.io/rolypoly/commands/binning_termini) — Shared termini grouping and motif reporting. Writes assignments + groups tables (TSV/CSV/Parquet/JSONL) and motif FASTA by default.
+- 🧪 [`correlate`](https://urineri.github.io/rolypoly/commands/binning_correlate) — Group contigs based on co-occurrence, co-abundance, minimal correlation (Spearman's) of these, or both.
+- 🤔 [`binit`](https://urineri.github.io/rolypoly/commands/binit) — Combines the above commands with sample information and genome attributes (e.g. require a shared termini AND protein complementarity, like CP + RdRp). See [notebooks/Exprimental/partiti_usecase/partiti_segment_workflow_experimental.ipynb](notebooks/Exprimental/partiti_usecase/partiti_segment_workflow_experimental.ipynb) for candidate workflow.
 
 #### Miscellaneous
-- ✅ `roll` — Run an end-to-end pipeline (before v0.7.1, named `end2end`).
-- ✅ `fetch-sra` — Download SRA fastq files (from ENA)
-- ✅ `fastx-calc` — Calculate per-sequence metrics (length, GC content, hash, ...)
-- ✅ `fastx-stats` — Calculate (-->aggregate) statistics for sequences (min, max, mean, median, ...) (input is file/s)
-- ✅ `rename-seqs` — Rename sequences (add a prefix, suffix, hash, running number, etc.)
-- 🚧 `quick-taxonomy` — Quick taxonomy assignment. Candidate workflows are [github.com/UriNeri/ictv-mmseqs2-protein-database](https://github.com/UriNeri/ictv-mmseqs2-protein-database) and [github.com/apcamargo/ictv-mmseqs2-protein-database](https://github.com/apcamargo/ictv-mmseqs2-protein-database) 
+- ✅ [`roll`](https://urineri.github.io/rolypoly/commands/end_to_end) — Run an end-to-end pipeline (before v0.7.1, named `end2end`).
+- ✅ [`fetch-sra`](https://urineri.github.io/rolypoly/commands/misc) — Download SRA fastq files (from ENA)
+- ✅ [`fastx-calc`](https://urineri.github.io/rolypoly/commands/misc) — Calculate per-sequence metrics (length, GC content, hash, ...)
+- ✅ [`fastx-stats`](https://urineri.github.io/rolypoly/commands/misc) — Calculate (-->aggregate) statistics for sequences (min, max, mean, median, ...) (input is file/s)
+- ✅ [`rename-seqs`](https://urineri.github.io/rolypoly/commands/misc) — Rename sequences (add a prefix, suffix, hash, running number, etc.)
+- 🚧 [`quick-taxonomy`](https://urineri.github.io/rolypoly/commands/misc) — Quick taxonomy assignment. Candidate workflows are [github.com/UriNeri/ictv-mmseqs2-protein-database](https://github.com/UriNeri/ictv-mmseqs2-protein-database) and [github.com/apcamargo/ictv-mmseqs2-protein-database](https://github.com/apcamargo/ictv-mmseqs2-protein-database) 
 - 🤔 support for [genotate](https://github.com/deprekate/genotate) for gene prediction.
 - 🤔 Genome refinement / strain de-entalgement / variant calling?
 - 🤔 Virus feature prediction (+/-ssRNA/dsRNA, circular/linear, mono/poly-segmented, capsid type, etc.)
@@ -835,7 +841,7 @@ If you have suggestions for additional commands or features, or want to implemen
 
 ## Dependencies
 
-**📦 Modular Installation Available**: RolyPoly supports both quick setup (one environment with all dependecies for all commands) and modular installation (command-specific environments). The modular approach is particularly useful for software developers who want to integrate specific rolypoly features with minimal dependency conflicts. See the [installation documentation](./docs/docs/mkdocs_docs/installation.md) for details.
+**📦 Modular Installation Available**: RolyPoly supports both quick setup (one environment with all dependecies for all commands) and modular installation (command-specific environments). The modular approach is particularly useful for software developers who want to integrate specific rolypoly features with minimal dependency conflicts. See the [installation documentation](https://urineri.github.io/rolypoly/installation/) for details.
 
 Not all 3rd party software is used by all the different commands. RolyPoly includes a "citation reminder" that will try to list all the external software used by a command. The "reminded citations" are pretty printed to console (stdout) and to a logfile. To shut off the terminal citation reminder printing, set `ROLYPOLY_REMIND_CITATIONS` to false in your `rpconfig.json` file.
 

{rolypoly_tk-0.7.2 → rolypoly_tk-0.7.4}/README.md

@@ -1,13 +1,15 @@
-![RolyPoly Logo](https://code.jgi.doe.gov/rolypoly/docs/-/raw/main/docs/rolypoly_logo.png?ref_type=heads)
+![RolyPoly Logo](https://raw.githubusercontent.com/UriNeri/rolypoly/main/docs/rolypoly_logo.png)
 
 # RolyPoly
 
+[![PyPI version](https://img.shields.io/pypi/v/rolypoly-tk.svg?cacheSeconds=300)](https://pypi.org/project/rolypoly-tk/) [![Python versions](https://img.shields.io/pypi/pyversions/rolypoly-tk.svg?cacheSeconds=300)](https://pypi.org/project/rolypoly-tk/) [![PyPI Downloads](https://static.pepy.tech/personalized-badge/rolypoly-tk?period=monthly&units=INTERNATIONAL_SYSTEM&left_color=BLACK&right_color=GREEN&left_text=Downloads+%28month%29)](https://pepy.tech/projects/rolypoly-tk) [![License](https://img.shields.io/github/license/UriNeri/rolypoly.svg)](LICENSE) [![Docs](https://img.shields.io/badge/docs-urineri.github.io%2Frolypoly-blue)](https://urineri.github.io/rolypoly/)
+
 RolyPoly is an RNA virus analysis toolkit, meant to be a "swiss-army knife" for RNA virus discovery and characterization by including a variety of commands, wrappers, parsers, automations, and some "quality of life" features for any many of a virus investigation process (from raw read processing to genome annotation). While it includes an "end-2-end" command that employs an entire pipeline, the main goals of rolypoly are:
 - Help non-computational researchers take a deep dive into their data without compromising on using tools that are non-techie friendly.  
 - Help (software) developers of virus analysis pipeline "plug" holes missing from their framework, by using specific RolyPoly commands to add features to their existing code base.
 
 ## Note - Rolypoly is still under development (contributions welcome!)
-RolyPoly is an open, still in progress project - I aim to summarise the main functionality into a manuscript ~early 2026. Pull requests and contributions are welcome and will be considered (see [CONTRIBUTING.md](CONTRIBUTING.md)).  
+RolyPoly is an open, still in progress project - I aim to summarise the main functionality into a manuscript ~mid 2026. Pull requests and contributions are welcome and will be considered (see [CONTRIBUTING.md](CONTRIBUTING.md)).  
 This also means that there are bugs, verbose logging even for non debug mode, and some place holders and TODOs here and there.
 
 ## Installation
@@ -16,23 +18,27 @@ This also means that there are bugs, verbose logging even for non debug mode, an
 **Recommended for most users** who want a "just works" solution and primarily intend to use rolypoly as a CLI tool in an independent environment.
 
 We hope to have rolypoly available from bioconda in the near future.  
-In the meantime, it can be installed with the [`quick_setup.sh`](https://code.jgi.doe.gov/rolypoly/rolypoly/-/raw/main/src/setup/quick_setup.sh) script, which will also fetch the pre-generated data rolypoly requires.
+In the meantime, it can be installed with the [`quick_setup.sh`](https://raw.githubusercontent.com/UriNeri/rolypoly/main/src/setup/quick_setup.sh) script, which is Conda/Mamba-based (uses `mamba` or `micromamba`) and also fetches the pre-generated data rolypoly requires.
 
 ```bash
-curl -O https://code.jgi.doe.gov/rolypoly/rolypoly/-/raw/main/src/setup/quick_setup.sh && \
+curl -O https://raw.githubusercontent.com/UriNeri/rolypoly/main/src/setup/quick_setup.sh && \
 bash quick_setup.sh 
 ```
 
 #### Quick Setup - Additional Options
-You can specify custom paths for the code, databases, and conda environment location:
+You can specify custom paths for the code, databases, and Conda/Mamba environment location (this is also how you "name" the environment by choosing its path):
 ```bash
 bash quick_setup.sh /path/to/conda/env /path/to/install/rolypoly_code /path/to/store/databases /path/to/logfile
 ```
+Example with an explicit environment path:
+```bash
+bash quick_setup.sh "$HOME/mamba_envs/rolypoly"
+```
 By default if no positional arguments are supplied, rolypoly is installed into the session current folder (path the quick_setup.sh is called from):   
 - database in `./rolypoly/data/`  
 - code in `./rolypoly/code/ `  
 - conda environment in `./rolypoly/env/`  
-- log file in `./RolyPoly_quick_setup.log`   
+- log file in `./rolypoly/RolyPoly_quick_setup.log`   
 
 
 
@@ -44,7 +50,7 @@ By default if no positional arguments are supplied, rolypoly is installed into t
 curl -fsSL https://pixi.sh/install.sh | bash
 
 # Clone the repository
-git clone https://code.jgi.doe.gov/rolypoly/rolypoly.git
+git clone https://github.com/UriNeri/rolypoly.git
 cd rolypoly
 
 # Install for specific functionality (examples):
@@ -84,11 +90,11 @@ Legend:
 
 #### Raw-Reads
 - ✅ [`filter-reads`](https://urineri.github.io/rolypoly/commands/read_processing) — Host/rRNA/adapters/artifact filtering and QC (bbmap, falco, etc.)
-- ✅ [`shrink-reads`](https://urineri.github.io/rolypoly/commands/shrink_reads) — Downsample or subsample reads. Useful for testing or normalizing coverage across samples.
-- ✅ [`mask-dna`](https://urineri.github.io/rolypoly/commands/mask_dna) — Mask DNA regions in RNA-seq reads (bbmap, seqkit). Useful for avoiding mis-filtering of RNA virus reads in because of potential matches to EVEs.
+- ✅ [`shrink-reads`](https://urineri.github.io/rolypoly/commands/read_processing) — Downsample or subsample reads. Useful for testing or normalizing coverage across samples.
+- ✅ [`mask-dna`](https://urineri.github.io/rolypoly/commands/read_processing) — Mask DNA regions in RNA-seq reads (bbmap, seqkit). Useful for avoiding mis-filtering of RNA virus reads in because of potential matches to EVEs.
 
 #### Annotation
-- ✅ [`annotate`](https://urineri.github.io/rolypoly/commands/annotate) — Genome feature annotation (wraps the rna and prot commands)
+- ✅ [`annotate`](https://urineri.github.io/rolypoly/commands/annotate_rna/#annotate-rna) — Genome feature annotation (wraps the rna and prot commands)
 - ✅ [`annotate-rna`](https://urineri.github.io/rolypoly/commands/annotate_rna) — RNA secondary structure labelling and ribozyme detection (Infernal, ViennaRNA/linearfold, cmsearch on Rfam...)
 - 🧪 [`annotate-prot`](https://urineri.github.io/rolypoly/commands/annotate_prot) — Gene calling and Protein domain annotation and functional prediction (HMMER, Pfam, custom).
 
@@ -99,22 +105,22 @@ Legend:
 #### RNA Virus Identification
 - ✅ [`marker-search`](https://urineri.github.io/rolypoly/commands/marker_search) — Search for viral markers (mainly RdRps, genomad VVs, or user-provided), using profile-based methods (HMMER / MMseqs2). 
 - ✅ [`virus-mapping`](https://urineri.github.io/rolypoly/commands/search_viruses) — Map and identify viruses using nucleic acid search (MMseqs2).
-- ✅ `rdrp-motif-search` — Search RdRp motifs (A/B/C/D) in nucleotide or amino acid sequences.
+- ✅ [`rdrp-motif-search`](https://urineri.github.io/rolypoly/commands/rdrp_motif_search) — Search RdRp motifs (A/B/C/D) in nucleotide or amino acid sequences.
 
 #### Bining / Clustering
-- 🧪 `cluster` — Average Nucleic identity (ANI) based contig gropuing. Supports several common backends and methods.
-- 🧪 `extend` — Extend sequences by pile-up/assembly. Useful for combining assemblies of with low abundance viruses, or those with high microdiversity, at the cost of worse strain/sub-species resolution (i.e. can condense to a consenus). 
-- 🧪 `termini` — Shared termini grouping and motif reporting. Writes assignments + groups tables (TSV/CSV/Parquet/JSONL) and motif FASTA by default.
-- 🧪 `correlate` — group contigs based on co-occurence, co-abundance, minimal correlation (Spearman's) of these, or both.
-- 🤔 `binit` — Combines the above commands with sample information and genome attributes (e.g. require a shared termini AND protein complementarity, like CP + RdRp). See [notebooks/Exprimental/partiti_usecase/partiti_segment_workflow_experimental.ipynb](notebooks/Exprimental/partiti_usecase/partiti_segment_workflow_experimental.ipynb) for candidate workflow.
+- 🧪 [`cluster`](https://urineri.github.io/rolypoly/commands/cluster) — Average Nucleic identity (ANI) based contig grouping. Supports several common backends and methods.
+- 🧪 [`extend`](https://urineri.github.io/rolypoly/commands/extend) — Extend sequences by pile-up/assembly. Useful for combining assemblies of with low abundance viruses, or those with high microdiversity, at the cost of worse strain/sub-species resolution (i.e. can condense to a consensus).
+- 🧪 [`termini`](https://urineri.github.io/rolypoly/commands/binning_termini) — Shared termini grouping and motif reporting. Writes assignments + groups tables (TSV/CSV/Parquet/JSONL) and motif FASTA by default.
+- 🧪 [`correlate`](https://urineri.github.io/rolypoly/commands/binning_correlate) — Group contigs based on co-occurrence, co-abundance, minimal correlation (Spearman's) of these, or both.
+- 🤔 [`binit`](https://urineri.github.io/rolypoly/commands/binit) — Combines the above commands with sample information and genome attributes (e.g. require a shared termini AND protein complementarity, like CP + RdRp). See [notebooks/Exprimental/partiti_usecase/partiti_segment_workflow_experimental.ipynb](notebooks/Exprimental/partiti_usecase/partiti_segment_workflow_experimental.ipynb) for candidate workflow.
 
 #### Miscellaneous
-- ✅ `roll` — Run an end-to-end pipeline (before v0.7.1, named `end2end`).
-- ✅ `fetch-sra` — Download SRA fastq files (from ENA)
-- ✅ `fastx-calc` — Calculate per-sequence metrics (length, GC content, hash, ...)
-- ✅ `fastx-stats` — Calculate (-->aggregate) statistics for sequences (min, max, mean, median, ...) (input is file/s)
-- ✅ `rename-seqs` — Rename sequences (add a prefix, suffix, hash, running number, etc.)
-- 🚧 `quick-taxonomy` — Quick taxonomy assignment. Candidate workflows are [github.com/UriNeri/ictv-mmseqs2-protein-database](https://github.com/UriNeri/ictv-mmseqs2-protein-database) and [github.com/apcamargo/ictv-mmseqs2-protein-database](https://github.com/apcamargo/ictv-mmseqs2-protein-database) 
+- ✅ [`roll`](https://urineri.github.io/rolypoly/commands/end_to_end) — Run an end-to-end pipeline (before v0.7.1, named `end2end`).
+- ✅ [`fetch-sra`](https://urineri.github.io/rolypoly/commands/misc) — Download SRA fastq files (from ENA)
+- ✅ [`fastx-calc`](https://urineri.github.io/rolypoly/commands/misc) — Calculate per-sequence metrics (length, GC content, hash, ...)
+- ✅ [`fastx-stats`](https://urineri.github.io/rolypoly/commands/misc) — Calculate (-->aggregate) statistics for sequences (min, max, mean, median, ...) (input is file/s)
+- ✅ [`rename-seqs`](https://urineri.github.io/rolypoly/commands/misc) — Rename sequences (add a prefix, suffix, hash, running number, etc.)
+- 🚧 [`quick-taxonomy`](https://urineri.github.io/rolypoly/commands/misc) — Quick taxonomy assignment. Candidate workflows are [github.com/UriNeri/ictv-mmseqs2-protein-database](https://github.com/UriNeri/ictv-mmseqs2-protein-database) and [github.com/apcamargo/ictv-mmseqs2-protein-database](https://github.com/apcamargo/ictv-mmseqs2-protein-database) 
 - 🤔 support for [genotate](https://github.com/deprekate/genotate) for gene prediction.
 - 🤔 Genome refinement / strain de-entalgement / variant calling?
 - 🤔 Virus feature prediction (+/-ssRNA/dsRNA, circular/linear, mono/poly-segmented, capsid type, etc.)
@@ -125,7 +131,7 @@ If you have suggestions for additional commands or features, or want to implemen
 
 ## Dependencies
 
-**📦 Modular Installation Available**: RolyPoly supports both quick setup (one environment with all dependecies for all commands) and modular installation (command-specific environments). The modular approach is particularly useful for software developers who want to integrate specific rolypoly features with minimal dependency conflicts. See the [installation documentation](./docs/docs/mkdocs_docs/installation.md) for details.
+**📦 Modular Installation Available**: RolyPoly supports both quick setup (one environment with all dependecies for all commands) and modular installation (command-specific environments). The modular approach is particularly useful for software developers who want to integrate specific rolypoly features with minimal dependency conflicts. See the [installation documentation](https://urineri.github.io/rolypoly/installation/) for details.
 
 Not all 3rd party software is used by all the different commands. RolyPoly includes a "citation reminder" that will try to list all the external software used by a command. The "reminded citations" are pretty printed to console (stdout) and to a logfile. To shut off the terminal citation reminder printing, set `ROLYPOLY_REMIND_CITATIONS` to false in your `rpconfig.json` file.
 

{rolypoly_tk-0.7.2 → rolypoly_tk-0.7.4}/pyproject.toml

@@ -16,7 +16,7 @@ authors = [
 
 description = "RNA virus analysis toolkit"
 readme = "README.md"
-requires-python = ">=3.10"
+requires-python = ">=3.10,<3.14"
 license = { file = "LICENSE" }
 # License-File = "license"
 dependencies = [
@@ -47,7 +47,7 @@ dependencies = [
 
 [project.urls]
 Source = "https://github.com/UriNeri/rolypoly"
-Documentation = "https://pages.jgi.doe.gov/rolypoly/docs/"
+Documentation = "https://urineri.github.io/rolypoly/"
 pypi = "https://pypi.org/project/rolypoly-tk/"
 
 [project.scripts]
@@ -160,6 +160,13 @@ aria2 = ">=1.37.0,<2"
 [tool.pixi.feature.dev.pypi-dependencies]
 lets-plot = ">=4.8.2,<5"
 
+[tool.pixi.feature.docs.pypi-dependencies]
+mkdocs = "*"
+mkdocs-material = "*"
+mkdocs-mermaid2-plugin = "*"
+mkdocstrings = "*"
+mkdocstrings-python = "*"
+
 [tool.pixi.feature.py310.dependencies]
 python = "~=3.10.0"
 
@@ -193,6 +200,7 @@ dev = { features = [
     "format",
     "publish",
     "dev",
+    "docs",
 ] }
 
 # Specific command group environments for targeted installations
@@ -234,6 +242,10 @@ test-import = "python -c 'import rolypoly; print(rolypoly.__version__)'"
 test-cli = "pytest -q src/tests/test_cli_contracts.py"
 bump-commit-publish = "bash src/setup/bump_commit_publish.sh"
 
+[tool.pixi.feature.docs.tasks]
+docs-serve = "mkdocs serve -f docs/mkdocs.yml"
+docs-build = "mkdocs build -f docs/mkdocs.yml"
+
 [tool.ruff]
 exclude = [
     ".bzr",

{rolypoly_tk-0.7.2 → rolypoly_tk-0.7.4}/rolypoly/__init__.py

@@ -1,4 +1,4 @@
 """rolypoly: RNA virus analysis toolkit"""
 
-__version__ = "0.7.2"
+__version__ = "0.7.4"
 __name__ = "rolypoly-tk"

{rolypoly_tk-0.7.2 → rolypoly_tk-0.7.4}/rolypoly/commands/annotation/annotate.py

@@ -177,7 +177,15 @@ def annotate(
     log_level,
     search_tool,
 ):
-    """Functionally and structurally annotate RNA viral sequence(s) (Wrapper for annotate_prot, annotate_RNA)"""
+    """Run combined RNA + protein annotation on nucleotide viral sequences.
+
+    This command orchestrates `annotate-rna` and `annotate-prot` into a single
+    workflow and writes results into `rna_annotation/` and
+    `protein_annotation/` subdirectories under the selected output path.
+
+    Use `--skip-steps` to disable specific stages and `--override-parameters`
+    to forward JSON overrides to sub-tools.
+    """
     import json
 
     from rolypoly.utils.logging.loggit import log_start_info

{rolypoly_tk-0.7.2 → rolypoly_tk-0.7.4}/rolypoly/commands/annotation/annotate_RNA.py

@@ -228,10 +228,15 @@ def annotate_RNA(
     resolve_mode,
     min_overlap_positions,
 ):
-    """Predict viral sequence RNA secondary structure, search for ribozymes, IRES, tRNAs, and other RNA structural elements.
-    By default, the following steps are run in the following order: predict_secondary_structure (LinearFold), search_ribozymes (Rfam via cmscan), predict_trnas (tRNAscan-SE).
-    Additional steps (detect_ires, search_rna_motifs, search_rna_elements) are currently disabled as they are under development.
-    Use --skip-steps to skip specific steps."""
+    """Annotate RNA structural features and motifs on viral nucleotide inputs.
+
+    The default pipeline runs secondary-structure prediction, ribozyme/CM
+    search, and tRNA detection, while optional modules can add IRES and motif
+    analyses depending on selected tools and skip settings.
+
+    Use `--skip-steps` to disable modules and `--override-parameters` to pass
+    tool-specific tuning values for individual stages.
+    """
     import json
 
     config = RNAAnnotationConfig(

{rolypoly_tk-0.7.2 → rolypoly_tk-0.7.4}/rolypoly/commands/assembly/assemble.py

@@ -530,7 +530,16 @@ def assembly(
     overwrite,
     log_level,
 ):
-    """Assembly wrapper - takes in reads, assembles them using one or more assemblers, then performs post-assembly processing."""
+    """Assemble reads/contigs with one or more backends and optional post-processing.
+
+    Inputs can be provided explicitly (`--paired-end`, `--single-end`,
+    `--merged`, `--long-read`, `--raw-fasta`) and/or discovered from
+    `--input-dir`.
+
+    Selected assembler outputs are normalized and optionally post-processed
+    (for example `rmdup` or `linclust`) before writing final contigs and run
+    metadata to the output directory.
+    """
     import shutil
 
     import polars as pl

{rolypoly_tk-0.7.2 → rolypoly_tk-0.7.4}/rolypoly/commands/assembly/filter_contigs.py

@@ -167,7 +167,13 @@ def filter_contigs(
     log_level,
 ):
     """
-    Filter contigs based on user-supplied host sequences. Wrapper for both nucleotide and amino acid filtering.
+    Filter contigs against user-supplied host/contamination references.
+
+    Depending on `--mode`, the command applies nucleotide filtering, protein
+    filtering, or both, using two-stage rule sets (`filter1_*` and
+    `filter2_*`) to retain likely non-host contigs.
+
+    Host references can be masked first (default) unless `--dont-mask` is set.
     """
     from rolypoly.utils.logging.citation_reminder import remind_citations
     from rolypoly.utils.logging.loggit import log_start_info

{rolypoly_tk-0.7.2 → rolypoly_tk-0.7.4}/rolypoly/commands/bining/binit.py

@@ -432,7 +432,12 @@ def binit(
 	log_file: Path | None,
 	log_level: str,
 ) -> None:
-	"""Run a first integrated segment-binning workflow over RdRp and CP contigs."""
+	"""Run an integrated segment-binning workflow over RdRp and CP contigs.
+
+	The workflow chains cluster, correlate, extend, and termini steps, then
+	joins their outputs to report candidate segment pairs with supporting
+	evidence from abundance/correlation and termini/motif consistency.
+	"""
 	logger = setup_logging(log_file, log_level)
 	log_start_info(logger, locals())
 

{rolypoly_tk-0.7.2 → rolypoly_tk-0.7.4}/rolypoly/commands/bining/correlate.py

@@ -296,7 +296,14 @@ def correlate(
     log_file,
     log_level,
 ):
-    """Correlate and cluster contigs by cross-sample co-occurrence patterns."""
+    """Group contigs by cross-sample association patterns.
+
+    Supports correlation-based edges, co-occurrence-based edges, or both,
+    with prevalence and shared-sample thresholds to reduce spurious links.
+
+    Writes pairwise edge tables and connected-component style groups using the
+    selected output prefix.
+    """
     logger = setup_logging(log_file, log_level)
     log_start_info(logger, locals())
 

{rolypoly_tk-0.7.2 → rolypoly_tk-0.7.4}/rolypoly/commands/identify_virus/search_viruses.py

@@ -48,7 +48,13 @@ tools = []
 def virus_mapping(
     threads, memory, output, keep_tmp, db, db_path, log_file, log_level, input
 ):
-    """MMseqs2 Virus mapping/search wrapper - takes in reads/contigs (i.e. nucs), and search them against precompiled virus databases OR user-supplied databases."""
+    """Search nucleotide reads/contigs against virus reference databases.
+
+    Input can be FASTA/FASTQ or an existing MMseqs2 database. The command
+    converts sequence inputs to MMseqs2 format as needed and runs searches
+    against built-in viral databases (`RVMT`, `NCBI_Ribovirus`, or `all`) or a
+    user-supplied target via `--db other --db-path`.
+    """
     import shutil
     import subprocess
 

{rolypoly_tk-0.7.2 → rolypoly_tk-0.7.4}/rolypoly/commands/misc/fastx_stats.py

@@ -82,8 +82,10 @@ def fastx_stats(
     """
     Calculate aggregate statistics for sequences (min, max, mean, median, etc.).
 
-    This command computes summary statistics across all sequences in a FASTA/FASTQ file.
-    For per-sequence calculations, use the 'fastx-calc' command instead.
+    This command computes dataset-level summaries across sequences in one or
+    more FASTA/FASTQ inputs, including count, length, and composition fields.
+
+    For per-sequence annotations instead of aggregates, use `fastx-calc`.
     """
     from rolypoly.utils.bio.polars_fastx import (
         compute_aggregate_stats,

{rolypoly_tk-0.7.2 → rolypoly_tk-0.7.4}/rolypoly/commands/reads/filter_reads.py

@@ -463,8 +463,14 @@ def filter_reads(
     temp_dir,
 ):
     """
-    Process RNA-seq (transcriptome, RNA virome, metatranscriptomes) Illumina raw reads.
-    Removes host reads, synthetic artifacts, and unknown DNA, corrects sequencing errors, trims adapters and low quality reads.
+    Process RNA-seq Illumina reads through the read-cleaning pipeline.
+
+    The workflow combines host/contaminant removal, optional fetched-reference
+    filtering, adapter/quality trimming, and optional error correction based on
+    configured steps and speed presets.
+
+    Input can be a single file, paired files, or a directory of FASTQ files.
+    Use `--skip-steps` and `--override-parameters` to tailor the workflow.
     """
     from rolypoly.utils.logging.citation_reminder import remind_citations
     from rolypoly.utils.logging.loggit import log_start_info

{rolypoly_tk-0.7.2 → rolypoly_tk-0.7.4}/rolypoly/commands/reads/shrink_reads.py

@@ -65,11 +65,13 @@ def shrink_reads(
     log_level,
 ):
     """
-    Subsets data from an input FASTQ file(s) based on the provided options.
-    Supports random sampling (when sample_size < 1) and fixed number read sampling
-    (i.e. first n reads)
-    NOTE: UNLESS --keep-matching-pairs is used, the output may not be very useful in practice.
-    TODO: no real threading support yet, maybe will have it if multiple input files are used (one per thread)
+    Subset FASTQ reads by count or fraction for lightweight test datasets.
+
+    Supports deterministic head-style subsampling (`first_n`) and random
+    sampling (`random`) for single-end, interleaved, and paired-end layouts.
+
+    This command is intended for quick dry runs and resource-reduced tests,
+    not as a full read-normalization strategy.
     """
     # Initialise logger
     logger = setup_logging(log_file=log_file, log_level=log_level)

{rolypoly_tk-0.7.2 → rolypoly_tk-0.7.4}/rolypoly/rolypoly.py

@@ -109,7 +109,6 @@ CONTEXT_SETTINGS = dict(
                 "fastx-stats": "rolypoly.commands.misc.fastx_stats.fastx_stats",
                 "fastx-calc": "rolypoly.commands.misc.fastx_calc.fastx_calc",
                 "rename-seqs": "rolypoly.commands.misc.rename_seqs.rename_seqs",
-                "quick-taxonomy": "rolypoly.commands.misc.quick_taxonomy.quick_taxonomy",
                 "help": "rolypoly.rolypoly.rolypoly",
             },
         },
@@ -126,7 +125,6 @@ CONTEXT_SETTINGS = dict(
         #     "name": "Characterisation",
         #     "commands": {
         #         "characterise": "hidden:rolypoly.commands.virotype.predict_characteristics.predict_characteristics",
-        #         "predict-host": "hidden:rolypoly.commands.host.classify.predict_host_range",
         #         # Commenting out unimplemented/broken commands
         #         # "summarize": "rolypoly.commands.virotype.summarize.summarize"
         #     },
@@ -156,7 +154,10 @@ def rolypoly():
 )
 def version(log_level):
     """
-    Print code version (commit or semvar) and data (date) information.
+    Print RolyPoly code and data version details.
+
+    This is a command-form wrapper around top-level `--version` output, useful
+    in scripted workflows that call `rolypoly version` explicitly.
     """
     setup_logging(None, log_level)
     # click wrapper for version/data information, so it could be called vai rolypoly version (on top of rolypoly --version)

rolypoly_tk-0.7.2/rolypoly/commands/host/classify.py

@@ -1,47 +0,0 @@
-"""
-This is a place holder script.
-"""
-
-import os
-
-import rich_click as click
-
-# from rich.console import Console
-
-# console = Console()
-
-
-@click.command()
-@click.option(
-    "-i",
-    "--input",
-    required=True,
-    help="Input directory containing rolypoly's virus identification and annotation results",
-)
-@click.option(
-    "-o",
-    "--output",
-    default=lambda: f"{os.getcwd()}_predict_host_range.tsv",
-    help="output path",
-)
-@click.option("-t", "--threads", default=1, help="Number of threads")
-@click.option(
-    "-g",
-    "--log-file",
-    default=lambda: f"{os.getcwd()}/predict_host_range_logfile.txt",
-    help="Path to log file",
-)
-@click.option(
-    "-ll", "--log-level", hidden=True, default="INFO", help="Log level"
-)
-def predict_host_range(input, output, threads, log_file, log_level):
-    """WIP WIP WIP Predict a viral seq host range - caution! this is not definitive"""
-    from rolypoly.utils.logging.loggit import setup_logging
-
-    logger = setup_logging(log_file, log_level)
-    logger.info("Starting to predict      ")
-    logger.info("Sorry! command not yet implemented!")
-
-
-if __name__ == "main":
-    predict_host_range()

rolypoly_tk-0.7.2/rolypoly/commands/misc/quick_taxonomy.py

@@ -1,372 +0,0 @@
-"""
-this script is a place holder
-"""
-
-from pathlib import Path
-
-import rich_click as click
-from rich.console import Console
-
-from rolypoly.utils.logging.citation_reminder import remind_citations
-
-console = Console()
-
-
-def parse_marker_results(marker_file):
-    """Parse marker search results file.
-
-    Args:
-        marker_file (str): Path to marker search results
-
-    Returns:
-        pl.DataFrame: DataFrame with marker results
-    """
-    import json
-
-    import polars as pl
-
-    if marker_file.endswith(".tsv"):
-        return pl.read_csv(marker_file, separator="\t")
-    elif marker_file.endswith(".json"):
-        with open(marker_file) as f:
-            data = json.load(f)
-        return pl.DataFrame(data)
-    else:
-        raise ValueError(f"Unsupported file format for {marker_file}")
-
-
-def run_genomad_hmm_search(input_fasta, output_dir, threads, logger):
-    """Run genomad RNA viral HMM search.
-
-    Args:
-        input_fasta (str): Path to input fasta file
-        output_dir (Path): Output directory
-        threads (int): Number of threads to use
-        logger (Logger): Logger object
-
-    Returns:
-        pl.DataFrame: DataFrame with HMM search results
-    """
-    import os
-
-    import polars as pl
-
-    from rolypoly.utils.bio.alignments import search_hmmdb
-
-    hmm_db = (
-        Path(os.environ["ROLYPOLY_DATA"])
-        / "hmmdbs"
-        / "genomad_rna_viral_markers.hmm"
-    )
-    output_file = output_dir / "genomad_hmm_results.txt"
-
-    # Use existing HMM search functionality
-    try:
-        search_hmmdb(
-            amino_file=input_fasta,
-            db_path=str(hmm_db),
-            output=str(output_file),
-            threads=threads,
-            logger=logger,
-            output_format="tblout",
-        )
-
-        # Parse results
-        results = []
-        with open(output_file) as f:
-            for line in f:
-                if line.startswith("#"):
-                    continue
-                parts = line.split()
-                if len(parts) >= 5:
-                    results.append(
-                        {
-                            "query": parts[0],
-                            "target": parts[2],
-                            "evalue": float(parts[4]),
-                            "score": float(parts[5]),
-                        }
-                    )
-
-        return pl.DataFrame(results)
-    except Exception as e:
-        logger.error(f"HMM search failed: {e}")
-        return pl.DataFrame()
-
-
-def assign_taxonomy(sequence_id, markers, hmm_results, min_score=50):
-    """Assign taxonomy based on marker and HMM results.
-
-    Args:
-        sequence_id (str): Sequence identifier
-        markers (pl.DataFrame): Marker search results
-        hmm_results (pl.DataFrame): HMM search results
-        min_score (float): Minimum score threshold
-
-    Returns:
-        dict: Taxonomy assignment
-    """
-    import polars as pl
-
-    # Filter results by score
-    seq_markers = markers.filter(pl.col("query") == sequence_id)
-    seq_hmms = hmm_results.filter(
-        (pl.col("query") == sequence_id) & (pl.col("score") >= min_score)
-    )
-
-    # Initialize taxonomy assignment
-    tax = {
-        "sequence_id": sequence_id,
-        "confidence": 0.0,
-        "taxonomy": "Unknown",
-        "evidence": [],
-    }
-
-    # Look for RdRP markers first (highest confidence)
-    rdrp_markers = seq_markers.filter(
-        pl.col("target").str.contains("RdRP|RdRp|rdrp")
-    )
-    if not rdrp_markers.is_empty():
-        best_hit = rdrp_markers.sort("score", descending=True).row(0)
-        tax["taxonomy"] = (
-            best_hit["taxonomy"] if "taxonomy" in best_hit else "RNA virus"
-        )
-        tax["confidence"] = min(1.0, best_hit["score"] / 100)
-        tax["evidence"].append(f"RdRP marker: {best_hit['target']}")
-
-    # Check genomad HMM results
-    if not seq_hmms.is_empty():
-        hmm_hits = seq_hmms.sort("score", descending=True)
-        for hit in hmm_hits.iter_rows():
-            tax["evidence"].append(f"RNA viral marker: {hit['target']}")
-            if (
-                tax["confidence"] < 0.8
-            ):  # Only update if current confidence is low
-                tax["confidence"] = min(0.8, hit["score"] / 100)
-
-    # Check other viral markers
-    other_markers = seq_markers.filter(
-        ~pl.col("target").str.contains("RdRP|RdRp|rdrp")
-    )
-    if not other_markers.is_empty():
-        for hit in other_markers.iter_rows():
-            tax["evidence"].append(f"Other marker: {hit['target']}")
-            if (
-                tax["confidence"] < 0.6
-            ):  # Only update if current confidence is low
-                tax["confidence"] = min(0.6, hit["score"] / 100)
-
-    return tax
-
-
-def summarize_taxonomy(assignments):
-    """Generate taxonomy summary statistics.
-
-    Args:
-        assignments (list): List of taxonomy assignments
-
-    Returns:
-        dict: Summary statistics
-    """
-    from collections import defaultdict
-
-    total = len(assignments)
-    assigned = sum(1 for a in assignments if a["taxonomy"] != "Unknown")
-
-    # Count taxonomy levels
-    tax_counts = defaultdict(int)
-    confidence_sum = 0
-
-    for assign in assignments:
-        if assign["taxonomy"] != "Unknown":
-            tax_counts[assign["taxonomy"]] += 1
-            confidence_sum += assign["confidence"]
-
-    return {
-        "total_sequences": total,
-        "assigned_sequences": assigned,
-        "percent_assigned": (assigned / total * 100) if total > 0 else 0,
-        "mean_confidence": confidence_sum / assigned if assigned > 0 else 0,
-        "taxonomy_distribution": dict(tax_counts),
-    }
-
-
-@click.command()
-@click.option("-i", "--input", required=True, help="Input file or directory")
-@click.option("-o", "--output", default="output", help="Output directory")
-@click.option("-t", "--threads", default=1, help="Number of threads")
-@click.option("--log-file", default="command.log", help="Path to log file")
-@click.option(
-    "-ll", "--log-level", hidden=True, default="INFO", help="Log level"
-)
-@click.option("--marker_results", default=None, type=str, help="marker_results")
-@click.option(
-    "--format",
-    default="text",
-    type=click.Choice(["text", "json", "tsv"]),
-    help="format",
-)
-@click.option("--min_score", default=50.0, type=float, help="min_score")
-@click.option("--summarize", default=True, type=bool, help="summarize")
-def quick_taxonomy(
-    input,
-    output,
-    threads,
-    log_file,
-    log_level,
-    marker_results,
-    format,
-    min_score,
-    summarize,
-):
-    """
-    Rapid taxonomy assignment for viral sequences using marker search results and genomad RNA viral HMMs
-    """
-    import json
-
-    import polars as pl
-    from needletail import parse_fastx_file
-    from rich.table import Table
-
-    from rolypoly.utils.logging.loggit import log_start_info, setup_logging
-
-    logger = setup_logging(log_file, log_level)
-    log_start_info(logger, locals())
-
-    # Create output directory
-    output_path = Path(output)
-    output_path.mkdir(parents=True, exist_ok=True)
-
-    sequences = []
-    for record in parse_fastx_file(input):
-        sequences.append({"id": record.id, "seq": record.seq})  # type: ignore
-
-    if not sequences:
-        logger.error(f"No sequences found in {input}")
-        return
-
-    # Parse marker results if provided
-    markers_df = None
-    if marker_results:
-        try:
-            markers_df = parse_marker_results(marker_results)
-        except Exception as e:
-            logger.warning(f"Error parsing marker results: {e}")
-
-    # Run genomad HMM search
-    logger.info("Running genomad RNA viral HMM search...")
-    hmm_results = run_genomad_hmm_search(input, output_path, threads, logger)
-
-    # Assign taxonomy
-    logger.info("Assigning taxonomy...")
-    assignments = []
-    for seq in sequences:
-        tax = assign_taxonomy(
-            seq["id"],
-            markers_df if markers_df is not None else pl.DataFrame(),
-            hmm_results,
-            min_score,
-        )
-        assignments.append(tax)
-
-    # Generate summary if requested
-    if summarize:
-        summary = summarize_taxonomy(assignments)
-
-    # Output results based on format
-    if format == "json":
-        results = {
-            "assignments": assignments,
-            "summary": summary if summarize else None,
-        }
-        with open(output_path / "taxonomy_assignments.json", "w") as f:
-            json.dump(results, f, indent=2)
-
-    elif format == "tsv":
-        # Flatten assignments for TSV
-        flat_assignments = []
-        for assign in assignments:
-            flat_assign = {
-                "sequence_id": assign["sequence_id"],
-                "taxonomy": assign["taxonomy"],
-                "confidence": assign["confidence"],
-                "evidence": ";".join(assign["evidence"]),
-            }
-            flat_assignments.append(flat_assign)
-
-        pl.DataFrame(flat_assignments).write_csv(
-            output_path / "taxonomy_assignments.tsv", separator="\t"
-        )
-
-        if summarize:
-            with open(output_path / "taxonomy_summary.tsv", "w") as f:
-                for k, v in summary.items():
-                    if k != "taxonomy_distribution":
-                        f.write(f"{k}\t{v}\n")
-                f.write("\nTaxonomy distribution:\n")
-                for tax, count in summary["taxonomy_distribution"].items():
-                    f.write(f"{tax}\t{count}\n")
-
-    else:  # text format
-        # Create assignments table
-        assign_table = Table(title="Taxonomy Assignments")
-        assign_table.add_column("Sequence ID")
-        assign_table.add_column("Taxonomy")
-        assign_table.add_column("Confidence")
-        assign_table.add_column("Evidence")
-
-        for assign in assignments:
-            assign_table.add_row(
-                assign["sequence_id"],
-                assign["taxonomy"],
-                f"{assign['confidence']:.2f}",
-                "\n".join(assign["evidence"]),
-            )
-
-        console.print(assign_table)
-
-        if summarize:
-            # Create summary table
-            summary_table = Table(title="Taxonomy Summary")
-            summary_table.add_column("Metric")
-            summary_table.add_column("Value")
-
-            for k, v in summary.items():
-                if k != "taxonomy_distribution":
-                    summary_table.add_row(
-                        k, f"{v:.1f}" if isinstance(v, float) else str(v)
-                    )
-
-            console.print(summary_table)
-
-            # Create taxonomy distribution table
-            dist_table = Table(title="Taxonomy Distribution")
-            dist_table.add_column("Taxonomy")
-            dist_table.add_column("Count")
-            dist_table.add_column("Percentage")
-
-            total = sum(summary["taxonomy_distribution"].values())
-            for tax, count in summary["taxonomy_distribution"].items():
-                dist_table.add_row(
-                    tax, str(count), f"{count / total * 100:.1f}%"
-                )
-
-            console.print(dist_table)
-
-            # Save to file
-            with open(output_path / "taxonomy_assignments.txt", "w") as f:
-                file_console = Console(file=f)
-                file_console.print(assign_table)
-                if summarize:
-                    file_console.print("\n")
-                    file_console.print(summary_table)
-                    file_console.print("\n")
-                    file_console.print(dist_table)
-
-    logger.info("quick-taxonomy completed successfully!")
-    tools = ["HMMER", "geNomad"]
-    remind_citations(tools)
-
-
-if __name__ == "__main__":
-    quick_taxonomy()