PyBRAID 1.0.0__tar.gz

pybraid-1.0.0/LICENSE

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+MIT License
+
+Copyright (c) 2026 Yuefan Huang
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in all
+copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+SOFTWARE.

pybraid-1.0.0/PKG-INFO

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+Metadata-Version: 2.4
+Name: PyBRAID
+Version: 1.0.0
+Summary: Block Resolution and Annotation of Integrated DNA
+Author: Yuefan Huang
+License: MIT
+Requires-Python: >=3.8
+Description-Content-Type: text/markdown
+License-File: LICENSE
+Requires-Dist: pysam>=0.17.0
+Requires-Dist: biopython>=1.80
+Dynamic: license-file
+
+# BRAID
+**Block Resolution and Annotation of Integrated DNA**
+
+![Python Version](https://img.shields.io/badge/python-3.8%2B-blue)
+![License](https://img.shields.io/badge/license-MIT-green)
+![Status](https://img.shields.io/badge/status-active-success)
+
+> **Analyze phased VCF data to predict variant effects on protein sequences for each haplotype.**
+
+## Overview
+
+**BRAID** is a bioinformatics tool designed to go beyond isolated mutations annotation. By utilizing **phased VCF data**, this tool reconstructs the combination of mutations present on each chromosome (haplotype) to predict the actual protein sequence produced.
+
+This allows for the detection of complex effects, such as:
+* **Compound Heterozygosity:** Understanding how multiple mutations on the same haplotype interact.
+* **Haplotype-specific LOF:** Determining if a combination effect of mutations leads to a Loss of Function.
+* **Protein Structure Changes:** Visualizing the exact amino acid sequence changes.
+
+<div align="center">
+<img width="256.5" height="113.5" alt="Image" src="https://github.com/user-attachments/assets/55e71e73-1e83-44f2-9f62-187104f54523" />
+</div>
+
+
+## Installation & Requirements
+
+BRAID is a software that requires standard bioinformatics libraries.
+
+**Prerequisites:**
+> * Python >= 3.8
+> * `pysam`
+> * `biopython`
+
+**installation**
+
+**Dowload via pip**
+> ```
+> pip install pybraid
+> ```
+
+**Dowload via conda**
+> ```
+> conda install braid
+> ```
+
+**Dowload via wget**
+> ```
+> wget https://github.com/YuefanHuang1998/BRAID/archive/refs/tags/braid-v1.0.1.tar.gz
+> tar -zxvf braid-v1.0.1
+> cd BRAID-1.0.1/
+> pip install .
+> ```
+
+**Dowload via git**
+> ```
+> git clone https://github.com/YuefanHuang1998/BRAID.git
+> cd BRAID
+> pip install .
+> ```
+
+**To verify the installation was successful, run:**
+> braid test
+
+## Usage
+**Run the script from the command line by providing the GFF3 annotation, Reference Genome, and Phased VCF.**
+
+`braid -r reference.fa -g annotation.gff3 -v phased_variants.vcf.gz`
+
+### Example for test dataset
+`braid -r test.fasta -g test.gff3 -v test.vcf.gz`
+> ```
+> You should have three output files and one log file:
+> variant_analysis_output.tsv
+> variant_analysis_output.alignment.txt
+> variant_analysis_output.sample.txt
+> variant_analysis_output.log
+> ```
+
+## Arguments Parameter Table
+| **Short** | **Long** | **Description** |       |
+|:-----:|:------:|:-------------:|:-------------:|
+| **-g** | **--gff** | Path to the GFF3 annotation file. | Required |
+| **-r** | **--reference** | Path to the Reference Genome FASTA (must be indexed: .fai). | Required |
+| **-v** | **--vcf** | Path to the Phased VCF file (must be indexed: .tbi/.csi). | Required |
+| **-o** | **--output** | Output file name (default: variant_analysis_output.tsv). | Optional |
+| **-s** | **--sample** | Path to file containing specific sample IDs to analyze (one per line, no header). | Optional |
+|  | **--gene** | Path to file with specific gene IDs to analyze (one per line, no header). | Optional |
+|  | **--lof-threshold** | Custom threshold for Loss-of-Function classification (e.g., 0.1; default: 0.3). | Optional |
+|  | **--force-unphased** | Skip phasing check (forces run on unphased VCF). | Optional |
+|  | **--ignore-intron** | Ignore variants marked strictly as intronic. | Optional |
+
+## Output Files Explaination
+
+**BRAID generates three main files to assist in your analysis.**
+
+**1. Summary Table**
+
+A comprehensive table detailing the protein changes for every haplotype (default: variant_analysis_output.tsv).
+
+Example View:
+| Gene_ID | Haplotype_ID | mRNA | Haplotype_Count | Frequency | Variant_Type | Protein_Changes | Haplotype_Mutations | Sample_Sources | Ref_Protein | Alt_Protein | Ref_CDS | Alt_CDS | Aligned_Ref | Comparison_String | Aligned_Alt |
+|:-----|:------|:------|:-----|:------|:------|:-----|:------|:------|:-----|:------|:------|:-----|:------|:------|:-----|
+| gene1 | transcript1:REF | transcript1 | . | . | NoLOF(non_identity_rate:0.00%,non_identical_AAs:0,total_ref_AAs:27) `\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|` | . | . | . | MSLASSANDMIDRSIDRSIDRSIDRS* | MSLASSANDMIDRSIDRSIDRSIDRS* | ATGAGCTTAGCTAGCTCAGCTAACGATATGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGTGA | ATGAGCTTAGCTAGCTCAGCTAACGATATGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGTGA | MSLASSANDMIDRSIDRSIDRSIDRS* | `\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|` | MSLASSANDMIDRSIDRSIDRSIDRS* |
+| gene1 | transcript1:1 | transcript1 | 4 | 0.500000 | NoLOF(non_identity_rate:3.70%,non_identical_AAs:1,total_ref_AAs:27)`\|\|\|`deletion `\|\|\|\|\|\|\|\|\|\|\|\|\|\|` | Del(5)S | 1:17_CTTAG>C[CDS,EXON];1:27_T>TT[CDS,EXON] | sample1(Hap2);sample2(Hap1);sample3(Homo) | MSLASSANDMIDRSIDRSIDRSIDRS* | MSLASANDMIDRSIDRSIDRSIDRS* | ATGAGCTTAGCTAGCTCAGCTAACGATATGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGTGA | ATGAGCCTAGCTTCAGCTAACGATATGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGTGA | MSLASSANDMIDRSIDRSIDRSIDRS* | `\|\|\|\| \|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|` | MSLA-SANDMIDRSIDRSIDRSIDRS* |
+
+**Explanation for each column**
+
+| **Column** | **Example** | **Explanation** |
+|:-----|:-----|:-------------|
+| **Gene_ID** | gene1 | The gene to which this haplotype belongs. |
+| **Haplotype_ID** | transcript1:REF;transcript1:1 | transcript:REF indicates the reference haplotype; others (e.g. transcript1:1) are alternative haplotypes. |
+| **mRNA** | transcript1 | The transcript to which this haplotype belongs. |
+| **Haplotype_Count** | 4 | Number of samples carrying this haplotype. |
+| **Frequency** | 0.500000 | Population frequency of this haplotype. |
+| **Variant_Type** | LOF/NoLoF (Please see <br>the detailed information below.) | Functional classification of the haplotype	and indicates LOF status. |
+| **Protein_Changes** | Del(5)S | Protein-level consequence	HGVS format description. |
+| **Haplotype_Mutations** | 1:17_CTTAG>C[CDS,EXON];<br>1:27_T>TT[CDS,EXON] | List of variants defining the haplotype. |
+| **Sample_Sources** | sample1(Hap2);sample2(Hap1);<br>sample3(Homo) | Samples carrying this haplotype, including haplotype phase (Hap1, Hap2) or homozygous status (Homo). |
+| **Ref_Protein** | MSLASSANDIDRSIDRS* | Reference protein sequence. |
+| **Alt_Protein** | MSLASANDIDRSIDRS* | Alternative protein sequence. |
+| **Ref_CDS** | ATGAGCTTAGCTAGCTCAGCTAACGATATCG<br>ATCGATCGATCGATCGATCGTGA | Reference CDS sequence. |
+| **Alt_CDS** | ATGAGCCTAGCTTCAGCTAACGATATCG<br>ATCGATCGATCGATCGATCGTGA | Haplotype-specific CDS sequence. |
+| **Aligned_Ref** | MSLASSANDIDRSIDRS* | Aligned reference protein, protein alignment string for visualization: `-` → Gap (insertion or deletion). |
+| **Comparison_String** | MSLASANDIDRSIDRS* | Alignment comparison symbols: `*` → Different amino acid, `\|` → Same amino acid. |
+| **Aligned_Alt** | MSLASANDIDRSIDRS* | Aligned alternative protein, shows amino acid changes: `-` → Gap (insertion or deletion). |
+
+**Detail information for Variant_Type**
+
+| **Column** | **Explanation** |
+|:-----|:-------------|
+| **LOF_Info** | LOF indicates haplotypes predicted to cause protein loss of function, whereas NoLOF indicates haplotypes without LOF effects. non_identity_rate represents the proportion of amino acid differences between ALT and REF proteins; non_identical_AAs is the corresponding count, and total_ref_AAs denotes the length of the REF protein. e.g., NoLOF(non_identity_rate:5.56%,non_identical_AAs:1,total_ref_AAs:18). |
+| **missense** | A nucleotide variant that results in the substitution of one amino acid by another in the protein sequence. |
+| **insertion** | An insertion of one or more nucleotides that alters the coding sequence and may affect the resulting protein sequence. |
+| **deletion** | A deletion of one or more nucleotides from the coding sequence, potentially altering the protein sequence or reading frame. |
+| **complex_indel** | A combined insertion and deletion event that cannot be represented as a simple insertion or deletion and may cause complex changes to the coding sequence. |
+| **exon_skip** | A splicing event in which one or more exons are completely skipped in the transcript, leading to an altered mRNA and protein sequence. |
+| **skipped_exons_detail** | Detailed information specifying which exon is skipped in the exon-skipping event, SITE_PRESERVED, SITE_SHIFT, SITE_DESTROYED. e.g., SkippedExon:[1:51-77`\|`SITE_SHIFT]. |
+| **intron_retention** | A splicing event in which one or more introns are retained in the mature transcript, potentially disrupting the coding sequence. |
+| **retained_introns_detail** | Detailed information specifying which intron(s) are retained in the intron-retention event, SITE_PRESERVED, SITE_SHIFT, SITE_DESTROYED. e.g., RetainedIntron:[1:78-90`\|`SITE_DESTROYED]. |
+| **start_codon_loss** | A variant that disrupts the canonical start codon, potentially preventing translation initiation. |
+| **stop_loss** | A variant that removes or alters the stop codon, resulting in translational read-through and an extended protein. |
+| **No_start_codon_for_reference** | The reference transcript or protein sequence lacks an annotated start codon. |
+| **same_as_other_transcript** | The variant effect on this protein is identical to that observed in another transcript's protein of the same gene. |
+| **protein_loss** | The variant or variant combination results in the complete loss of the predicted protein product. |
+| **ref_protein_empty** | The reference transcript does not produce a protein sequence (e.g., non-coding or incomplete annotation). |
+| **alignment_failed** | The reference and alternative protein sequences could not be reliably aligned, preventing accurate variant effect annotation. |
+
+**Log information for splice sites mutations**
+
+**SITE_PRESERVED**: The splice site is unaltered, with both its position and sequence conserved; normal splicing is expected.
+> ```
+> [transcript1] (strand +) Splice site 'GT' at 39 PRESERVED by mutation 1:39_GTCG>G.
+>   - Original Window Seq  : GATGTCGTTAAG     - Mutated Window Seq  : GATGTTAAG.
+> ```
+
+**SITE_SHIFT**: The splice site may move to a nearby position due to the variant, potentially altering the exon–intron boundary.
+> ```
+> WARNING - [transcript1] Splice site may SHIFT for mutation 1:44_TAAGTA>A.
+>   - Splice Site          : 'AG' (Original genomic pos: 49)
+>   - Mutation             : TAAGTA -> A (Genomic pos: 44)
+>   - Window               : 1:42-53
+>   - Original Window Seq  : GTTAAGTAGATG
+>   - Mutated Window Seq   : GTAGATG
+> ```
+
+**SITE_DESTROYED**: The splice site is disrupted or abolished by the variant, likely preventing normal splicing at this site.
+> ```
+> [transcript1] (strand +) Splice site 'GT' at 78 DESTROYED by mutation 1:50_GATGATCGATCGATCGATCGATCGATCGG>GG. It was 'GT', became 'AT'.
+>   - Original Window Seq  : TCGGTCGATCGA     - Mutated Window Seq  : TCGATCGA
+> ```
+
+**2. Alignment Visualization (.alignment.txt)**
+
+A text file showing the pairwise alignment of the Reference vs. Alternative protein.
+Use the Haplotype_ID to match the haplotype in the summary table.
+
+Example View:
+> ```
+> Haplotype_ID: transcript1:1
+> Gene: gene1 | mRNA: transcript1
+> Haplotype_Mutations: 1:17_CTTAG>C[CDS,EXON];1:27_T>TT[CDS,EXON]
+> Variant_Type: NoLOF(non_identity_rate:3.70%,non_identical_AAs:1,total_ref_AAs:27)|||deletion||||||||||||||
+> Protein_Changes: Del(5)S
+> Alignment:
+>   Ref: MSLASSANDMIDRSIDRSIDRSIDRS*
+>        |||| ||||||||||||||||||||||
+>   Alt: MSLA-SANDMIDRSIDRSIDRSIDRS*
+> ```
+
+**3. Sample Matrix (.sample.txt)**
+
+A matrix format ideal for heatmaps or downstream programmatic analysis.
+
+Example View:
+| Gene_ID | mRNA_ID | Ref_ID | Alt_IDs | sample1 | sample2 | sample3 |
+|:-----|:------|:------|:-----|:------|:------|:------|
+| gene1	| transcript1 |	transcript1:REF |	transcript1:1	| 0`\|`1 |	1`\|`0 | 1`\|`1 |
+
+>```
+> Gene_ID  mRNA_ID      Ref_ID           Alt_IDs         sample1 sample2 sample3
+> gene1    transcript1  transcript1:REF  transcript1:1	  0|1	    1|0     1|1
+>```
+
+| **Column** | **Explanation** |
+|:-----|:-------------|
+| **Gene_ID** | The identifier of the gene being analyzed. |
+| **mRNA_ID** | The identifier of the specific transcript of that gene. |
+| **Ref_ID** | Reference haplotype ID, labeled as transcript:REF. |
+| **Alt_IDs** | Alternative haplotype IDs observed in the samples, with numbering to distinguish multiple haplotypes. |
+| **samples** | The haplotype presence/absence in each sample. Each entry corresponds to the Ref or Alt haplotype. `0` represents REF. |
+
+## Citation
+
+If you use BRAID in your research, please cite our paper:
+> *   

pybraid-1.0.0/README.md

@@ -0,0 +1,214 @@
+# BRAID
+**Block Resolution and Annotation of Integrated DNA**
+
+![Python Version](https://img.shields.io/badge/python-3.8%2B-blue)
+![License](https://img.shields.io/badge/license-MIT-green)
+![Status](https://img.shields.io/badge/status-active-success)
+
+> **Analyze phased VCF data to predict variant effects on protein sequences for each haplotype.**
+
+## Overview
+
+**BRAID** is a bioinformatics tool designed to go beyond isolated mutations annotation. By utilizing **phased VCF data**, this tool reconstructs the combination of mutations present on each chromosome (haplotype) to predict the actual protein sequence produced.
+
+This allows for the detection of complex effects, such as:
+* **Compound Heterozygosity:** Understanding how multiple mutations on the same haplotype interact.
+* **Haplotype-specific LOF:** Determining if a combination effect of mutations leads to a Loss of Function.
+* **Protein Structure Changes:** Visualizing the exact amino acid sequence changes.
+
+<div align="center">
+<img width="256.5" height="113.5" alt="Image" src="https://github.com/user-attachments/assets/55e71e73-1e83-44f2-9f62-187104f54523" />
+</div>
+
+
+## Installation & Requirements
+
+BRAID is a software that requires standard bioinformatics libraries.
+
+**Prerequisites:**
+> * Python >= 3.8
+> * `pysam`
+> * `biopython`
+
+**installation**
+
+**Dowload via pip**
+> ```
+> pip install pybraid
+> ```
+
+**Dowload via conda**
+> ```
+> conda install braid
+> ```
+
+**Dowload via wget**
+> ```
+> wget https://github.com/YuefanHuang1998/BRAID/archive/refs/tags/braid-v1.0.1.tar.gz
+> tar -zxvf braid-v1.0.1
+> cd BRAID-1.0.1/
+> pip install .
+> ```
+
+**Dowload via git**
+> ```
+> git clone https://github.com/YuefanHuang1998/BRAID.git
+> cd BRAID
+> pip install .
+> ```
+
+**To verify the installation was successful, run:**
+> braid test
+
+## Usage
+**Run the script from the command line by providing the GFF3 annotation, Reference Genome, and Phased VCF.**
+
+`braid -r reference.fa -g annotation.gff3 -v phased_variants.vcf.gz`
+
+### Example for test dataset
+`braid -r test.fasta -g test.gff3 -v test.vcf.gz`
+> ```
+> You should have three output files and one log file:
+> variant_analysis_output.tsv
+> variant_analysis_output.alignment.txt
+> variant_analysis_output.sample.txt
+> variant_analysis_output.log
+> ```
+
+## Arguments Parameter Table
+| **Short** | **Long** | **Description** |       |
+|:-----:|:------:|:-------------:|:-------------:|
+| **-g** | **--gff** | Path to the GFF3 annotation file. | Required |
+| **-r** | **--reference** | Path to the Reference Genome FASTA (must be indexed: .fai). | Required |
+| **-v** | **--vcf** | Path to the Phased VCF file (must be indexed: .tbi/.csi). | Required |
+| **-o** | **--output** | Output file name (default: variant_analysis_output.tsv). | Optional |
+| **-s** | **--sample** | Path to file containing specific sample IDs to analyze (one per line, no header). | Optional |
+|  | **--gene** | Path to file with specific gene IDs to analyze (one per line, no header). | Optional |
+|  | **--lof-threshold** | Custom threshold for Loss-of-Function classification (e.g., 0.1; default: 0.3). | Optional |
+|  | **--force-unphased** | Skip phasing check (forces run on unphased VCF). | Optional |
+|  | **--ignore-intron** | Ignore variants marked strictly as intronic. | Optional |
+
+## Output Files Explaination
+
+**BRAID generates three main files to assist in your analysis.**
+
+**1. Summary Table**
+
+A comprehensive table detailing the protein changes for every haplotype (default: variant_analysis_output.tsv).
+
+Example View:
+| Gene_ID | Haplotype_ID | mRNA | Haplotype_Count | Frequency | Variant_Type | Protein_Changes | Haplotype_Mutations | Sample_Sources | Ref_Protein | Alt_Protein | Ref_CDS | Alt_CDS | Aligned_Ref | Comparison_String | Aligned_Alt |
+|:-----|:------|:------|:-----|:------|:------|:-----|:------|:------|:-----|:------|:------|:-----|:------|:------|:-----|
+| gene1 | transcript1:REF | transcript1 | . | . | NoLOF(non_identity_rate:0.00%,non_identical_AAs:0,total_ref_AAs:27) `\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|` | . | . | . | MSLASSANDMIDRSIDRSIDRSIDRS* | MSLASSANDMIDRSIDRSIDRSIDRS* | ATGAGCTTAGCTAGCTCAGCTAACGATATGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGTGA | ATGAGCTTAGCTAGCTCAGCTAACGATATGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGTGA | MSLASSANDMIDRSIDRSIDRSIDRS* | `\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|` | MSLASSANDMIDRSIDRSIDRSIDRS* |
+| gene1 | transcript1:1 | transcript1 | 4 | 0.500000 | NoLOF(non_identity_rate:3.70%,non_identical_AAs:1,total_ref_AAs:27)`\|\|\|`deletion `\|\|\|\|\|\|\|\|\|\|\|\|\|\|` | Del(5)S | 1:17_CTTAG>C[CDS,EXON];1:27_T>TT[CDS,EXON] | sample1(Hap2);sample2(Hap1);sample3(Homo) | MSLASSANDMIDRSIDRSIDRSIDRS* | MSLASANDMIDRSIDRSIDRSIDRS* | ATGAGCTTAGCTAGCTCAGCTAACGATATGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGTGA | ATGAGCCTAGCTTCAGCTAACGATATGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGTGA | MSLASSANDMIDRSIDRSIDRSIDRS* | `\|\|\|\| \|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|` | MSLA-SANDMIDRSIDRSIDRSIDRS* |
+
+**Explanation for each column**
+
+| **Column** | **Example** | **Explanation** |
+|:-----|:-----|:-------------|
+| **Gene_ID** | gene1 | The gene to which this haplotype belongs. |
+| **Haplotype_ID** | transcript1:REF;transcript1:1 | transcript:REF indicates the reference haplotype; others (e.g. transcript1:1) are alternative haplotypes. |
+| **mRNA** | transcript1 | The transcript to which this haplotype belongs. |
+| **Haplotype_Count** | 4 | Number of samples carrying this haplotype. |
+| **Frequency** | 0.500000 | Population frequency of this haplotype. |
+| **Variant_Type** | LOF/NoLoF (Please see <br>the detailed information below.) | Functional classification of the haplotype	and indicates LOF status. |
+| **Protein_Changes** | Del(5)S | Protein-level consequence	HGVS format description. |
+| **Haplotype_Mutations** | 1:17_CTTAG>C[CDS,EXON];<br>1:27_T>TT[CDS,EXON] | List of variants defining the haplotype. |
+| **Sample_Sources** | sample1(Hap2);sample2(Hap1);<br>sample3(Homo) | Samples carrying this haplotype, including haplotype phase (Hap1, Hap2) or homozygous status (Homo). |
+| **Ref_Protein** | MSLASSANDIDRSIDRS* | Reference protein sequence. |
+| **Alt_Protein** | MSLASANDIDRSIDRS* | Alternative protein sequence. |
+| **Ref_CDS** | ATGAGCTTAGCTAGCTCAGCTAACGATATCG<br>ATCGATCGATCGATCGATCGTGA | Reference CDS sequence. |
+| **Alt_CDS** | ATGAGCCTAGCTTCAGCTAACGATATCG<br>ATCGATCGATCGATCGATCGTGA | Haplotype-specific CDS sequence. |
+| **Aligned_Ref** | MSLASSANDIDRSIDRS* | Aligned reference protein, protein alignment string for visualization: `-` → Gap (insertion or deletion). |
+| **Comparison_String** | MSLASANDIDRSIDRS* | Alignment comparison symbols: `*` → Different amino acid, `\|` → Same amino acid. |
+| **Aligned_Alt** | MSLASANDIDRSIDRS* | Aligned alternative protein, shows amino acid changes: `-` → Gap (insertion or deletion). |
+
+**Detail information for Variant_Type**
+
+| **Column** | **Explanation** |
+|:-----|:-------------|
+| **LOF_Info** | LOF indicates haplotypes predicted to cause protein loss of function, whereas NoLOF indicates haplotypes without LOF effects. non_identity_rate represents the proportion of amino acid differences between ALT and REF proteins; non_identical_AAs is the corresponding count, and total_ref_AAs denotes the length of the REF protein. e.g., NoLOF(non_identity_rate:5.56%,non_identical_AAs:1,total_ref_AAs:18). |
+| **missense** | A nucleotide variant that results in the substitution of one amino acid by another in the protein sequence. |
+| **insertion** | An insertion of one or more nucleotides that alters the coding sequence and may affect the resulting protein sequence. |
+| **deletion** | A deletion of one or more nucleotides from the coding sequence, potentially altering the protein sequence or reading frame. |
+| **complex_indel** | A combined insertion and deletion event that cannot be represented as a simple insertion or deletion and may cause complex changes to the coding sequence. |
+| **exon_skip** | A splicing event in which one or more exons are completely skipped in the transcript, leading to an altered mRNA and protein sequence. |
+| **skipped_exons_detail** | Detailed information specifying which exon is skipped in the exon-skipping event, SITE_PRESERVED, SITE_SHIFT, SITE_DESTROYED. e.g., SkippedExon:[1:51-77`\|`SITE_SHIFT]. |
+| **intron_retention** | A splicing event in which one or more introns are retained in the mature transcript, potentially disrupting the coding sequence. |
+| **retained_introns_detail** | Detailed information specifying which intron(s) are retained in the intron-retention event, SITE_PRESERVED, SITE_SHIFT, SITE_DESTROYED. e.g., RetainedIntron:[1:78-90`\|`SITE_DESTROYED]. |
+| **start_codon_loss** | A variant that disrupts the canonical start codon, potentially preventing translation initiation. |
+| **stop_loss** | A variant that removes or alters the stop codon, resulting in translational read-through and an extended protein. |
+| **No_start_codon_for_reference** | The reference transcript or protein sequence lacks an annotated start codon. |
+| **same_as_other_transcript** | The variant effect on this protein is identical to that observed in another transcript's protein of the same gene. |
+| **protein_loss** | The variant or variant combination results in the complete loss of the predicted protein product. |
+| **ref_protein_empty** | The reference transcript does not produce a protein sequence (e.g., non-coding or incomplete annotation). |
+| **alignment_failed** | The reference and alternative protein sequences could not be reliably aligned, preventing accurate variant effect annotation. |
+
+**Log information for splice sites mutations**
+
+**SITE_PRESERVED**: The splice site is unaltered, with both its position and sequence conserved; normal splicing is expected.
+> ```
+> [transcript1] (strand +) Splice site 'GT' at 39 PRESERVED by mutation 1:39_GTCG>G.
+>   - Original Window Seq  : GATGTCGTTAAG     - Mutated Window Seq  : GATGTTAAG.
+> ```
+
+**SITE_SHIFT**: The splice site may move to a nearby position due to the variant, potentially altering the exon–intron boundary.
+> ```
+> WARNING - [transcript1] Splice site may SHIFT for mutation 1:44_TAAGTA>A.
+>   - Splice Site          : 'AG' (Original genomic pos: 49)
+>   - Mutation             : TAAGTA -> A (Genomic pos: 44)
+>   - Window               : 1:42-53
+>   - Original Window Seq  : GTTAAGTAGATG
+>   - Mutated Window Seq   : GTAGATG
+> ```
+
+**SITE_DESTROYED**: The splice site is disrupted or abolished by the variant, likely preventing normal splicing at this site.
+> ```
+> [transcript1] (strand +) Splice site 'GT' at 78 DESTROYED by mutation 1:50_GATGATCGATCGATCGATCGATCGATCGG>GG. It was 'GT', became 'AT'.
+>   - Original Window Seq  : TCGGTCGATCGA     - Mutated Window Seq  : TCGATCGA
+> ```
+
+**2. Alignment Visualization (.alignment.txt)**
+
+A text file showing the pairwise alignment of the Reference vs. Alternative protein.
+Use the Haplotype_ID to match the haplotype in the summary table.
+
+Example View:
+> ```
+> Haplotype_ID: transcript1:1
+> Gene: gene1 | mRNA: transcript1
+> Haplotype_Mutations: 1:17_CTTAG>C[CDS,EXON];1:27_T>TT[CDS,EXON]
+> Variant_Type: NoLOF(non_identity_rate:3.70%,non_identical_AAs:1,total_ref_AAs:27)|||deletion||||||||||||||
+> Protein_Changes: Del(5)S
+> Alignment:
+>   Ref: MSLASSANDMIDRSIDRSIDRSIDRS*
+>        |||| ||||||||||||||||||||||
+>   Alt: MSLA-SANDMIDRSIDRSIDRSIDRS*
+> ```
+
+**3. Sample Matrix (.sample.txt)**
+
+A matrix format ideal for heatmaps or downstream programmatic analysis.
+
+Example View:
+| Gene_ID | mRNA_ID | Ref_ID | Alt_IDs | sample1 | sample2 | sample3 |
+|:-----|:------|:------|:-----|:------|:------|:------|
+| gene1	| transcript1 |	transcript1:REF |	transcript1:1	| 0`\|`1 |	1`\|`0 | 1`\|`1 |
+
+>```
+> Gene_ID  mRNA_ID      Ref_ID           Alt_IDs         sample1 sample2 sample3
+> gene1    transcript1  transcript1:REF  transcript1:1	  0|1	    1|0     1|1
+>```
+
+| **Column** | **Explanation** |
+|:-----|:-------------|
+| **Gene_ID** | The identifier of the gene being analyzed. |
+| **mRNA_ID** | The identifier of the specific transcript of that gene. |
+| **Ref_ID** | Reference haplotype ID, labeled as transcript:REF. |
+| **Alt_IDs** | Alternative haplotype IDs observed in the samples, with numbering to distinguish multiple haplotypes. |
+| **samples** | The haplotype presence/absence in each sample. Each entry corresponds to the Ref or Alt haplotype. `0` represents REF. |
+
+## Citation
+
+If you use BRAID in your research, please cite our paper:
+> *   

pybraid-1.0.0/pyproject.toml

@@ -0,0 +1,26 @@
+[build-system]
+requires = ["setuptools>=61.0"]
+build-backend = "setuptools.build_meta"
+
+[project]
+name = "PyBRAID"
+version = "1.0.0"
+description = "Block Resolution and Annotation of Integrated DNA"
+authors = [
+  { name = "Yuefan Huang" },
+]
+license = { text = "MIT" }
+readme = "README.md"
+requires-python = ">=3.8"
+dependencies = [
+    "pysam>=0.17.0",
+    "biopython>=1.80",
+]
+
+[project.scripts]
+braid = "braid.cli:main"
+
+[tool.setuptools.packages.find]
+where = ["src"]
+[tool.setuptools.package-data]
+braid = ["data/*"]

pybraid-1.0.0/setup.cfg

@@ -0,0 +1,4 @@
+[egg_info]
+tag_build = 
+tag_date = 0
+