priorcons 0.1.0__tar.gz

priorcons-0.1.0/LICENSE

@@ -0,0 +1,29 @@
+Attribution Permissive License (APL) 1.0
+
+Copyright (c) 2025 Germán Vallejo Palma
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to use,
+copy, modify, merge, publish, distribute, sublicense, and/or sell copies of the
+Software, and to permit persons to whom the Software is furnished to do so,
+subject to the following condition:
+
+  * ATTRIBUTION: Redistributions of source or binary form, modified or
+    unmodified, must retain the following attribution notice in a conspicuous
+    location (for example, in the repository README, the package metadata,
+    or in a NOTICE file shipped with binaries):
+
+      "This software was developed by Germán Vallejo Palma at the Instituto de
+       Salud Carlos III — National Centre of Microbiology (Respiratory Viruses
+       and Influenza Unit)."
+
+The above copyright notice and this permission notice shall be included in all
+copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+SOFTWARE.

priorcons-0.1.0/PKG-INFO

@@ -0,0 +1,276 @@
+Metadata-Version: 2.4
+Name: priorcons
+Version: 0.1.0
+Summary: Tool for the integration of viral consensus sequences obtained by de novo and mapping strategies, supported by prior information.
+Home-page: https://github.com/GERMAN00VP/priorCons
+Author: Germán Vallejo Palma
+Author-email: Germán Vallejo Palma <german.vallejo@isciii.es>
+License: Attribution Permissive License (APL) 1.0
+        
+        Copyright (c) 2025 Germán Vallejo Palma
+        
+        Permission is hereby granted, free of charge, to any person obtaining a copy
+        of this software and associated documentation files (the "Software"), to use,
+        copy, modify, merge, publish, distribute, sublicense, and/or sell copies of the
+        Software, and to permit persons to whom the Software is furnished to do so,
+        subject to the following condition:
+        
+          * ATTRIBUTION: Redistributions of source or binary form, modified or
+            unmodified, must retain the following attribution notice in a conspicuous
+            location (for example, in the repository README, the package metadata,
+            or in a NOTICE file shipped with binaries):
+        
+              "This software was developed by Germán Vallejo Palma at the Instituto de
+               Salud Carlos III — National Centre of Microbiology (Respiratory Viruses
+               and Influenza Unit)."
+        
+        The above copyright notice and this permission notice shall be included in all
+        copies or substantial portions of the Software.
+        
+        THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+        IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+        FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+        AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+        LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+        OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+        SOFTWARE.
+        
+Project-URL: Homepage, https://github.com/GERMAN00VP/priorCons/
+Requires-Python: >=3.8
+Description-Content-Type: text/markdown
+License-File: LICENSE
+Requires-Dist: biopython>=1.79
+Requires-Dist: numpy>=1.21
+Requires-Dist: pandas>=1.3
+Requires-Dist: pyarrow>=12.0
+Dynamic: license-file
+
+# PriorCons 
+
+This repository provides tools to:
+
+1. **Generate Integrated Consensus (`integrate_consensus.py`)**  
+   Produces a high-quality viral consensus by strategically using **ABACAS** sequences to fill missing regions in the **mapping** consensus. It employs a sliding-window approach that verifies the evolutionary plausibility of ABACAS content against empirical priors before incorporation.
+
+2. **Build Evolutionary Priors (`build_priors.py`)**  
+   Constructs empirical prior distributions from large multiple-sequence alignments. These priors model expected genetic variation across genomic windows and provide likelihood thresholds for quality control during consensus integration.
+
+3. **Access Supporting Utilities (`utils` scripts)**  
+   Provides modular helper functions for alignment processing, window scoring, and consensus construction used by both main workflows.
+
+---
+### Installation
+
+```bash
+pip install priorcons
+```
+---
+
+### CLI usage 
+```bash
+# Create priors
+priorcons build-priors --input sequences.fasta --ref REF_ID --output priors.parquet
+
+# Run consensus integration
+priorcons integrate-consensus --input alignment.aln --ref REF_ID --prior priors.parquet --output_dir results
+
+```
+
+---
+
+## 🚀 Main Script: integrate_consensus.py
+
+This is the entrypoint of the tool. It creates a *integrated consensus sequence* by combining mapping consensus and ABACAS output, both aligned to a reference sequence, but only after performing quality control (QC) at the window level.  
+
+### 🔑 Inputs
+
+- `--input` → path to an alignment file (`.aln`) containing at least:  
+  - **1º Reference sequence**  
+  - **2º Mapping consensus sequence**  
+  - **3º ABACAS consensus sequence**  
+
+ **The sequences in the alignment file must be provided in the specified order, as they will be identified by their position.**
+
+
+- `--ref` → ID of the reference sequence in the alignment.  
+
+- `--prior` → path to a priors table (`.parquet`) generated with `build_priors.py`.  
+
+- `--output_dir` → directory to save the results.  
+
+
+---
+
+### 🧪 Workflow
+
+1. **Start with mapping consensus** as the baseline
+2. **Identify missing/unreliable regions** in mapping consensus
+3. **For each window**:
+   - If mapping has coverage → keep mapping sequence
+   - If mapping has missing data → evaluate ABACAS for that window:
+     * Check fragmentation and quality
+     * Verify evolutionary plausibility using priors [(nLL score)](README.md#-methodology-build_priorspy)
+     * If ABACAS passes QC → use ABACAS to fill missing regions
+4. **Construct final consensus** combining mapping baseline with validated ABACAS fills
+5. **Restore mapping-specific insertions**
+6. **QC reporting**: compute coverage, substitutions, and insertion metrics comparing the final integrated consensus to MAPPING.  
+
+---
+
+### 📦 Outputs
+
+The script produces **three files** inside `--output_dir`:
+
+1. **Integrated consensus FASTA**  
+   - File: `<basename>-INTEGRATED.fasta`  
+   - Contains the final consensus sequence after merging and reinserting insertions.  
+
+2. **Window QC trace (CSV)**  
+   - File: `windows_trace.csv`  
+   - One row per window, recording:  
+     - `start`, `end` → genomic coordinates.  
+     - `MISSING_MAPPING`, `MISSING_ABACAS` → counts of missing bases.  
+     - `ABACAS_MORE_INFO` → whether ABACAS has fewer missing bases than MAPPING.  
+     - `ABACAS_FRAGMENTS` → fragmentation level of ABACAS in this window (keep: 0 < n fragments < 3 ).  
+     - `WINDOW_PRIOR_nLL_p95` → threshold from priors.  
+     - `WINDOW_SCORE_nLL` → score of ABACAS in this window.  
+     - `WINDOW_QC_PASSED` → True/False decision.  
+
+3. **Consensus QC summary (JSON)**  
+   - File: `qc.json`  
+   - Provides overall metrics comparing the MAPPING consensus and the integrated consensus:  
+     - `MAPPING_COVERAGE` → % of genome covered in MAPPING.  
+     - `FINAL_COVERAGE` → % of genome covered in integrated consensus.  
+     - `MAPPING_SUBSTITUTIONS` → substitutions vs. reference in MAPPING.  
+     - `FINAL_SUBSTITUTIONS` → substitutions vs. reference in integrated consensus.  
+     - `EXPECTED_SUBSTITUTIONS` → expected number of substitutions, extrapolated from mapping.  
+     - `OBS-EXP_SUBSTITUTIONS` → difference between observed and expected substitutions.  
+     - `N_INSERTIONS` → number of insertions added back.  
+     - `TOTAL_INSERTIONS_LENGTH` → total inserted length.  
+     - `INSERTIONS` → list of insertions with their coordinates.  
+
+---
+
+### ▶️ Example run
+
+```bash
+python integrate_consensus.py \
+  --input /path/to/<sample_name>.aln \
+  --ref RSV_BD \
+  --prior /path/to/RSVBD_win100_ovlp50_priors.parquet \
+  --output_dir results
+```
+----
+
+This will generate:  
+
+- `results/<sample_name>-INTEGRATED.fasta`  
+- `results/windows_trace.csv`  
+- `results/qc.json`  
+
+---
+
+## 🛠 Script: build_priors.py
+
+This script creates **empirical priors** (overlapped windows) from a large multiple sequence alignment.  
+These priors are later used by `integrate_consensus.py` to evaluate windows.
+
+### 🔑 Inputs
+
+- `-i / --input` → aligned FASTA file with multiple sequences.  
+- `-r / --ref` → ID of the reference sequence.  
+- `-o / --output` → output file (`.parquet`).  
+- `--win` → window size (default: 100).  
+- `--overlap` → overlap size (default: 10).  
+
+### ▶️ Example run
+
+```bash
+python build_priors.py \
+  -i alignment.fasta \
+  -r ReferenceID \
+  -o priors.parquet \
+  --win 100 \
+  --overlap 10
+```
+----
+
+### 📦 Output
+
+A `.parquet` file with one row per window, containing:  
+
+- `start`, `end` → window coordinates.  
+- `nLL_p95`, `nLL_p99` → empirical thresholds.  
+- `profile` → base probability distributions for each position in the window.  
+
+## 🧮 Methodology (build_priors.py)
+
+### 1. Probability distributions per position
+
+For each window of size `W` bases (e.g., `W = 100`), and for each position `j` within that window, we compute the probability of observing each nucleotide:
+
+![P_j(b)](https://latex.codecogs.com/png.latex?P_j(b)=\frac{c_j(b)+\alpha}{\sum_{x\in\{A,C,G,T\}}(c_j(x)+\alpha)})
+
+Where:  
+- ![c_j(b)](https://latex.codecogs.com/png.latex?c_j(b)) = number of sequences with base ![b](https://latex.codecogs.com/png.latex?b) at position ![j](https://latex.codecogs.com/png.latex?j).  
+- ![\alpha](https://latex.codecogs.com/png.latex?\alpha) = pseudocount (Laplace smoothing, default ![\alpha=1](https://latex.codecogs.com/png.latex?\alpha=1)) to avoid zero probabilities.  
+- Bases `N` are ignored in the counts.  
+
+This gives a **per-position categorical distribution**.
+
+---
+
+### 2. Log-likelihood of a sequence in a window
+
+Given a query sequence ![Q](https://latex.codecogs.com/png.latex?Q), we compute its probability under the window profile.  
+For each valid (non-`N`) position ![j](https://latex.codecogs.com/png.latex?j) with observed base ![q_j](https://latex.codecogs.com/png.latex?q_j):
+
+![logL](https://latex.codecogs.com/png.latex?\log%20L(Q\mid%20\text{window})=\sum_{j=1}^{W}\log%20P_j(q_j))
+
+The **normalized negative log-likelihood (nLL)** is:
+
+![nLL](https://latex.codecogs.com/png.latex?\text{nLL}(Q)=-\frac{1}{N_{\text{valid}}}\sum_{j=1}^{W}\log%20P_j(q_j))
+
+Where:  
+- ![N_valid](https://latex.codecogs.com/png.latex?N_{\text{valid}}) = number of positions in the window where ![Q](https://latex.codecogs.com/png.latex?Q) has a non-`N` base.  
+
+Smaller nLL values indicate sequences more likely under the empirical profile.
+
+
+### 3. Empirical priors
+
+To characterize "normal variation" for each window:
+
+1. Score **all sequences** from the alignment against the window profile.  
+2. Collect the distribution of nLL values.  
+3. Extract percentiles (e.g., 95th and 99th) to serve as thresholds.  
+
+Thus, for each window we store:  
+- The **distribution (profile)**.  
+- Empirical thresholds: `nLL_p95` and `nLL_p99`.  
+
+A new sequence can later be compared:  
+- If `nLL < nLL_p95` → typical.  
+- If `nLL > nLL_p99` → unusually variable, possibly unreliable region.
+
+---
+
+---
+
+## � Supporting utils
+
+Several utility scripts provide reusable functions for both processes:  
+
+- **utils.py** → basic alignment and scoring functions:  
+  - `load_alignment`, `extract_ref_positions`, `sliding_windows`, `score_window`.  
+
+- **utils_integrate_consensus.py** → additional helpers for consensus integration:  
+  - missingness and fragmentation counts,  
+  - insertion handling,  
+  - QC calculations,  
+  - consensus merging,  
+  - window evaluation wrapper.  
+
+These modular functions keep the pipeline clean and reusable.
+
+

priorcons-0.1.0/README.md

@@ -0,0 +1,229 @@
+# PriorCons 
+
+This repository provides tools to:
+
+1. **Generate Integrated Consensus (`integrate_consensus.py`)**  
+   Produces a high-quality viral consensus by strategically using **ABACAS** sequences to fill missing regions in the **mapping** consensus. It employs a sliding-window approach that verifies the evolutionary plausibility of ABACAS content against empirical priors before incorporation.
+
+2. **Build Evolutionary Priors (`build_priors.py`)**  
+   Constructs empirical prior distributions from large multiple-sequence alignments. These priors model expected genetic variation across genomic windows and provide likelihood thresholds for quality control during consensus integration.
+
+3. **Access Supporting Utilities (`utils` scripts)**  
+   Provides modular helper functions for alignment processing, window scoring, and consensus construction used by both main workflows.
+
+---
+### Installation
+
+```bash
+pip install priorcons
+```
+---
+
+### CLI usage 
+```bash
+# Create priors
+priorcons build-priors --input sequences.fasta --ref REF_ID --output priors.parquet
+
+# Run consensus integration
+priorcons integrate-consensus --input alignment.aln --ref REF_ID --prior priors.parquet --output_dir results
+
+```
+
+---
+
+## 🚀 Main Script: integrate_consensus.py
+
+This is the entrypoint of the tool. It creates a *integrated consensus sequence* by combining mapping consensus and ABACAS output, both aligned to a reference sequence, but only after performing quality control (QC) at the window level.  
+
+### 🔑 Inputs
+
+- `--input` → path to an alignment file (`.aln`) containing at least:  
+  - **1º Reference sequence**  
+  - **2º Mapping consensus sequence**  
+  - **3º ABACAS consensus sequence**  
+
+ **The sequences in the alignment file must be provided in the specified order, as they will be identified by their position.**
+
+
+- `--ref` → ID of the reference sequence in the alignment.  
+
+- `--prior` → path to a priors table (`.parquet`) generated with `build_priors.py`.  
+
+- `--output_dir` → directory to save the results.  
+
+
+---
+
+### 🧪 Workflow
+
+1. **Start with mapping consensus** as the baseline
+2. **Identify missing/unreliable regions** in mapping consensus
+3. **For each window**:
+   - If mapping has coverage → keep mapping sequence
+   - If mapping has missing data → evaluate ABACAS for that window:
+     * Check fragmentation and quality
+     * Verify evolutionary plausibility using priors [(nLL score)](README.md#-methodology-build_priorspy)
+     * If ABACAS passes QC → use ABACAS to fill missing regions
+4. **Construct final consensus** combining mapping baseline with validated ABACAS fills
+5. **Restore mapping-specific insertions**
+6. **QC reporting**: compute coverage, substitutions, and insertion metrics comparing the final integrated consensus to MAPPING.  
+
+---
+
+### 📦 Outputs
+
+The script produces **three files** inside `--output_dir`:
+
+1. **Integrated consensus FASTA**  
+   - File: `<basename>-INTEGRATED.fasta`  
+   - Contains the final consensus sequence after merging and reinserting insertions.  
+
+2. **Window QC trace (CSV)**  
+   - File: `windows_trace.csv`  
+   - One row per window, recording:  
+     - `start`, `end` → genomic coordinates.  
+     - `MISSING_MAPPING`, `MISSING_ABACAS` → counts of missing bases.  
+     - `ABACAS_MORE_INFO` → whether ABACAS has fewer missing bases than MAPPING.  
+     - `ABACAS_FRAGMENTS` → fragmentation level of ABACAS in this window (keep: 0 < n fragments < 3 ).  
+     - `WINDOW_PRIOR_nLL_p95` → threshold from priors.  
+     - `WINDOW_SCORE_nLL` → score of ABACAS in this window.  
+     - `WINDOW_QC_PASSED` → True/False decision.  
+
+3. **Consensus QC summary (JSON)**  
+   - File: `qc.json`  
+   - Provides overall metrics comparing the MAPPING consensus and the integrated consensus:  
+     - `MAPPING_COVERAGE` → % of genome covered in MAPPING.  
+     - `FINAL_COVERAGE` → % of genome covered in integrated consensus.  
+     - `MAPPING_SUBSTITUTIONS` → substitutions vs. reference in MAPPING.  
+     - `FINAL_SUBSTITUTIONS` → substitutions vs. reference in integrated consensus.  
+     - `EXPECTED_SUBSTITUTIONS` → expected number of substitutions, extrapolated from mapping.  
+     - `OBS-EXP_SUBSTITUTIONS` → difference between observed and expected substitutions.  
+     - `N_INSERTIONS` → number of insertions added back.  
+     - `TOTAL_INSERTIONS_LENGTH` → total inserted length.  
+     - `INSERTIONS` → list of insertions with their coordinates.  
+
+---
+
+### ▶️ Example run
+
+```bash
+python integrate_consensus.py \
+  --input /path/to/<sample_name>.aln \
+  --ref RSV_BD \
+  --prior /path/to/RSVBD_win100_ovlp50_priors.parquet \
+  --output_dir results
+```
+----
+
+This will generate:  
+
+- `results/<sample_name>-INTEGRATED.fasta`  
+- `results/windows_trace.csv`  
+- `results/qc.json`  
+
+---
+
+## 🛠 Script: build_priors.py
+
+This script creates **empirical priors** (overlapped windows) from a large multiple sequence alignment.  
+These priors are later used by `integrate_consensus.py` to evaluate windows.
+
+### 🔑 Inputs
+
+- `-i / --input` → aligned FASTA file with multiple sequences.  
+- `-r / --ref` → ID of the reference sequence.  
+- `-o / --output` → output file (`.parquet`).  
+- `--win` → window size (default: 100).  
+- `--overlap` → overlap size (default: 10).  
+
+### ▶️ Example run
+
+```bash
+python build_priors.py \
+  -i alignment.fasta \
+  -r ReferenceID \
+  -o priors.parquet \
+  --win 100 \
+  --overlap 10
+```
+----
+
+### 📦 Output
+
+A `.parquet` file with one row per window, containing:  
+
+- `start`, `end` → window coordinates.  
+- `nLL_p95`, `nLL_p99` → empirical thresholds.  
+- `profile` → base probability distributions for each position in the window.  
+
+## 🧮 Methodology (build_priors.py)
+
+### 1. Probability distributions per position
+
+For each window of size `W` bases (e.g., `W = 100`), and for each position `j` within that window, we compute the probability of observing each nucleotide:
+
+![P_j(b)](https://latex.codecogs.com/png.latex?P_j(b)=\frac{c_j(b)+\alpha}{\sum_{x\in\{A,C,G,T\}}(c_j(x)+\alpha)})
+
+Where:  
+- ![c_j(b)](https://latex.codecogs.com/png.latex?c_j(b)) = number of sequences with base ![b](https://latex.codecogs.com/png.latex?b) at position ![j](https://latex.codecogs.com/png.latex?j).  
+- ![\alpha](https://latex.codecogs.com/png.latex?\alpha) = pseudocount (Laplace smoothing, default ![\alpha=1](https://latex.codecogs.com/png.latex?\alpha=1)) to avoid zero probabilities.  
+- Bases `N` are ignored in the counts.  
+
+This gives a **per-position categorical distribution**.
+
+---
+
+### 2. Log-likelihood of a sequence in a window
+
+Given a query sequence ![Q](https://latex.codecogs.com/png.latex?Q), we compute its probability under the window profile.  
+For each valid (non-`N`) position ![j](https://latex.codecogs.com/png.latex?j) with observed base ![q_j](https://latex.codecogs.com/png.latex?q_j):
+
+![logL](https://latex.codecogs.com/png.latex?\log%20L(Q\mid%20\text{window})=\sum_{j=1}^{W}\log%20P_j(q_j))
+
+The **normalized negative log-likelihood (nLL)** is:
+
+![nLL](https://latex.codecogs.com/png.latex?\text{nLL}(Q)=-\frac{1}{N_{\text{valid}}}\sum_{j=1}^{W}\log%20P_j(q_j))
+
+Where:  
+- ![N_valid](https://latex.codecogs.com/png.latex?N_{\text{valid}}) = number of positions in the window where ![Q](https://latex.codecogs.com/png.latex?Q) has a non-`N` base.  
+
+Smaller nLL values indicate sequences more likely under the empirical profile.
+
+
+### 3. Empirical priors
+
+To characterize "normal variation" for each window:
+
+1. Score **all sequences** from the alignment against the window profile.  
+2. Collect the distribution of nLL values.  
+3. Extract percentiles (e.g., 95th and 99th) to serve as thresholds.  
+
+Thus, for each window we store:  
+- The **distribution (profile)**.  
+- Empirical thresholds: `nLL_p95` and `nLL_p99`.  
+
+A new sequence can later be compared:  
+- If `nLL < nLL_p95` → typical.  
+- If `nLL > nLL_p99` → unusually variable, possibly unreliable region.
+
+---
+
+---
+
+## � Supporting utils
+
+Several utility scripts provide reusable functions for both processes:  
+
+- **utils.py** → basic alignment and scoring functions:  
+  - `load_alignment`, `extract_ref_positions`, `sliding_windows`, `score_window`.  
+
+- **utils_integrate_consensus.py** → additional helpers for consensus integration:  
+  - missingness and fragmentation counts,  
+  - insertion handling,  
+  - QC calculations,  
+  - consensus merging,  
+  - window evaluation wrapper.  
+
+These modular functions keep the pipeline clean and reusable.
+
+

priorcons-0.1.0/priorcons/__init__.py

@@ -0,0 +1,13 @@
+"""
+priorcons package
+Author: Germán Vallejo Palma
+Developed at: Instituto de Salud Carlos III - National Centre of Microbiology
+"""
+
+__version__ = "0.1.0"
+__author__ = "Germán Vallejo Palma"
+__email__ = "german.vallejo@isciii.es"
+
+# Expose key functions/modules for convenience
+from .build_priors import main as build_priors_main
+from .integrate_consensus import main as integrate_consensus_main

priorcons-0.1.0/priorcons/build_priors.py

@@ -0,0 +1,39 @@
+import argparse
+import sys
+from typing import List
+from .utils import (
+    save_priors,
+    load_alignment,
+    build_window_profiles,
+    build_priors
+)
+
+def main(argv: List[str] = None) -> int:
+    parser = argparse.ArgumentParser(description="Build empirical priors from alignment")
+    parser.add_argument("-i", "--input", required=True, help="Input alignment FASTA file")
+    parser.add_argument("-r", "--ref", required=True, help="Reference sequence ID")
+    parser.add_argument("-o", "--output", required=True, help="Output file (.parquet)")
+    parser.add_argument("--win", type=int, default=100, help="Window size (default=100)")
+    parser.add_argument("--overlap", type=int, default=50, help="Window overlap (default=50)")
+    argv = argv if argv is not None else sys.argv[1:]
+    args = parser.parse_args(argv)
+    
+    # Load alignment
+    ids, seqs = load_alignment(args.input)
+
+    # Build window profiles
+    profiles, seqs_filtered, ref_seq = build_window_profiles(
+        ids, seqs, args.ref, args.win, args.overlap
+    )
+
+    # Compute priors
+    df = build_priors(seqs_filtered, profiles)
+
+    # Save to Parquet
+    save_priors(df, args.output)
+
+    return 0
+
+
+if __name__ == "__main__":
+    main()

priorcons-0.1.0/priorcons/cli.py

@@ -0,0 +1,49 @@
+#!/usr/bin/env python3
+"""
+priorCons CLI
+"""
+import sys
+from . import __version__
+from . import build_priors as bp
+from . import integrate_consensus as ic
+
+
+def main(argv=None):
+    argv = argv if argv is not None else sys.argv[1:]
+
+    # si el usuario no da subcomando o pide --help general
+    if len(argv) == 0 or argv[0] in ("-h", "--help"):
+        print(f"""
+priorCons {__version__}
+
+Usage:
+  priorcons <subcommand> [options]
+
+Available subcommands:
+  build-priors         Build priors parquet file
+  integrate-consensus   Run consensus integration workflow
+
+Use 'priorcons <subcommand> -h' for details on each one.
+""")
+        sys.exit(0)
+
+    if argv[0] in ("--version", "-v", "-V"):
+        print(f"priorcons {__version__}")
+        sys.exit(0)
+
+    # delegar completamente al módulo correspondiente
+    subcmd = argv[0]
+    subargs = argv[1:]
+
+    if subcmd == "build-priors":
+        sys.exit(bp.main(subargs))
+    elif subcmd == "integrate-consensus":
+        sys.exit(ic.main(subargs))
+    else:
+        print(f"Unknown command: {subcmd}")
+        print("Use 'priorcons --help' for available commands.")
+        sys.exit(1)
+
+
+if __name__ == "__main__":
+    main()