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antonylebechec committed Jan 13, 2025
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38 changes: 23 additions & 15 deletions README.html
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Expand Up @@ -385,21 +385,29 @@ <h3 data-number="2.2.2" id="interactive-terminal"><span
HOWARD::0.12.2.0 [Antony Le Bechec, Jean-Baptiste Lamouche]
HOWARD - Highly Open Workflow for Annotation &amp; Ranking toward genomic variant Discovery

#[2025-01-07 14:19:24] [INFO] Start
#[2025-01-07 14:19:24] [INFO] Loading...
#[2025-01-07 14:19:24] [INFO] End
#[2025-01-07 14:19:24] [INFO] Start interative terminal
#[2025-01-07 14:19:24] [INFO] Interactive DuckDB SQL terminal. Type &#39;exit&#39; to quit.
#[2025-01-07 14:19:24] [INFO] Type &#39;help&#39; for a list of commands.
#[2025-01-07 14:22:25] [SQL]&gt; SELECT &quot;#CHROM&quot;, &quot;POS&quot;, &quot;REF&quot;, &quot;ALT&quot;, &quot;INFO&quot;
#[2025-01-07 14:22:25] [SQL]| FROM variants_view
#[2025-01-07 14:22:25] [SQL]| WHERE DP&gt;30
#[2025-01-07 14:22:25] [SQL]| OR CLNSIG LIKE &#39;pathogenic&#39;;
#CHROM POS REF ALT INFO
0 chr1 28736 A C CLNSIG=pathogenic
1 chr1 69101 A G DP=50
2 chr7 55249063 G A DP=125
#[2025-01-07 14:23:10] [SQL]&gt; </code></pre>
#[2025-01-13 22:18:34] [INFO] Start
#[2025-01-13 22:18:34] [INFO] Loading...
#[2025-01-13 22:18:34] [INFO] End
#[2025-01-13 22:18:34] [INFO] Start interative terminal
#[2025-01-13 22:18:34] [INFO] Interactive DuckDB SQL terminal. Type &#39;exit&#39; to quit.
#[2025-01-13 22:18:34] [INFO] Type &#39;help&#39; for a list of commands.
#[2025-01-13 22:18:34] [SQL]&gt; SELECT
#[2025-01-13 22:18:34] [SQL]| &quot;#CHROM&quot;, &quot;POS&quot;, &quot;REF&quot;, &quot;ALT&quot;,
#[2025-01-13 22:18:34] [SQL]| INFOS.*,
#[2025-01-13 22:18:34] [SQL]| SAMPLES.sample1.GT AS &#39;sample1_GT&#39;,
#[2025-01-13 22:18:34] [SQL]| SAMPLES.sample1.DP AS &#39;sample1_DP&#39;
#[2025-01-13 22:18:34] [SQL]| FROM variants_view
#[2025-01-13 22:18:34] [SQL]| WHERE SAMPLES.sample1.DP &gt; 30
#[2025-01-13 22:18:34] [SQL]| OR INFOS.CLNSIG LIKE &#39;pathogenic&#39;
#[2025-01-13 22:18:34] [SQL]|
#CHROM POS REF ALT NS DP AA CLNSIG SIFT sample1_GT sample1_DP
0 chr1 28736 A C None NaN None pathogenic None 0/1 729
1 chr1 69101 A G None 50.0 None None None 0/1 729
2 chr1 768251 A G None NaN None None None 0/1 729
3 chr1 768252 A G None NaN None None None 0/1 729
4 chr1 768253 A G None NaN None None None 0/1 729
5 chr7 55249063 G A None 125.0 None None None 0/1 729
#[2025-01-13 22:18:38] [SQL]&gt; </code></pre>
<h3 data-number="2.2.3" id="graphical-user-interface"><span
class="header-section-number">2.2.3</span> Graphical User Interface</h3>
<p>Install HOWARD Graphical User Interface using Python Pip tool with
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38 changes: 23 additions & 15 deletions README.md
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Expand Up @@ -160,21 +160,29 @@ howard query --input='tests/data/examples.vcf'
HOWARD::0.12.2.0 [Antony Le Bechec, Jean-Baptiste Lamouche]
HOWARD - Highly Open Workflow for Annotation & Ranking toward genomic variant Discovery
#[2025-01-07 14:19:24] [INFO] Start
#[2025-01-07 14:19:24] [INFO] Loading...
#[2025-01-07 14:19:24] [INFO] End
#[2025-01-07 14:19:24] [INFO] Start interative terminal
#[2025-01-07 14:19:24] [INFO] Interactive DuckDB SQL terminal. Type 'exit' to quit.
#[2025-01-07 14:19:24] [INFO] Type 'help' for a list of commands.
#[2025-01-07 14:22:25] [SQL]> SELECT "#CHROM", "POS", "REF", "ALT", "INFO"
#[2025-01-07 14:22:25] [SQL]| FROM variants_view
#[2025-01-07 14:22:25] [SQL]| WHERE DP>30
#[2025-01-07 14:22:25] [SQL]| OR CLNSIG LIKE 'pathogenic';
#CHROM POS REF ALT INFO
0 chr1 28736 A C CLNSIG=pathogenic
1 chr1 69101 A G DP=50
2 chr7 55249063 G A DP=125
#[2025-01-07 14:23:10] [SQL]>
#[2025-01-13 22:18:34] [INFO] Start
#[2025-01-13 22:18:34] [INFO] Loading...
#[2025-01-13 22:18:34] [INFO] End
#[2025-01-13 22:18:34] [INFO] Start interative terminal
#[2025-01-13 22:18:34] [INFO] Interactive DuckDB SQL terminal. Type 'exit' to quit.
#[2025-01-13 22:18:34] [INFO] Type 'help' for a list of commands.
#[2025-01-13 22:18:34] [SQL]> SELECT
#[2025-01-13 22:18:34] [SQL]| "#CHROM", "POS", "REF", "ALT",
#[2025-01-13 22:18:34] [SQL]| INFOS.*,
#[2025-01-13 22:18:34] [SQL]| SAMPLES.sample1.GT AS 'sample1_GT',
#[2025-01-13 22:18:34] [SQL]| SAMPLES.sample1.DP AS 'sample1_DP'
#[2025-01-13 22:18:34] [SQL]| FROM variants_view
#[2025-01-13 22:18:34] [SQL]| WHERE SAMPLES.sample1.DP > 30
#[2025-01-13 22:18:34] [SQL]| OR INFOS.CLNSIG LIKE 'pathogenic'
#[2025-01-13 22:18:34] [SQL]|
#CHROM POS REF ALT NS DP AA CLNSIG SIFT sample1_GT sample1_DP
0 chr1 28736 A C None NaN None pathogenic None 0/1 729
1 chr1 69101 A G None 50.0 None None None 0/1 729
2 chr1 768251 A G None NaN None None None 0/1 729
3 chr1 768252 A G None NaN None None None 0/1 729
4 chr1 768253 A G None NaN None None None 0/1 729
5 chr7 55249063 G A None 125.0 None None None 0/1 729
#[2025-01-13 22:18:38] [SQL]>
```

### Graphical User Interface
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28 changes: 23 additions & 5 deletions RELEASE_NOTES.html
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Expand Up @@ -176,17 +176,35 @@ <h1 data-number="1" id="release-notes"><span
class="header-section-number">1</span> RELEASE NOTES</h1>
<h2 data-number="1.1" id="section"><span
class="header-section-number">1.1</span> 0.12.2.0</h2>
<p>Few improvements and fixes.</p>
<p>Introduction of interactvie mode to dynamically explore data, using
variants view with columns types (define din VCF header). Improvements
using view duckDB feature, mainly for calculations and prioritizations,
and transcripts mapping.</p>
<h3 data-number="1.1.1" id="news"><span
class="header-section-number">1.1.1</span> News</h3>
<ul>
<li>Interactive mode: add a terminal to execute SQL queries</li>
<li>View variants &#x201C;annotations&#x201D; to:
<li>Interactivity mode:
<ul>
<li>query more easily (with &#x201C;variants_view&#x201D; view loaded by default in
<li>Interactive terminal to execute SQL queries</li>
<li>Completion and history features</li>
<li>Display modes (e.g.&#xA0;&#x2018;dataframe&#x2019;, &#x2018;markdown&#x2019;, &#x2018;simple&#x2019;,
&#x2018;tabulate&#x2019;)</li>
<li>Query result limitation, to speedup exploration</li>
</ul></li>
<li>Variants &#x201C;view&#x201D;:
<ul>
<li>Query more easily (with &#x201C;variants_view&#x201D; view loaded by default in
query tools)</li>
<li>improve performances for annotations, calculations and
<li>INFO/tags and samples structured on specific columns (&#x2018;INFOS&#x2019; and
&#x2018;SAMPLES&#x2019;)</li>
<li>Improve performances for annotations, calculations and
prioritizations</li>
<li>Improve prioritization profiles definition using columns types
(Integer, Float, String) with list type (defined in VCF header)</li>
</ul></li>
<li>Plugins:
<ul>
<li>&#x2018;to_excel&#x2019;: Convert VCF to Excel &#x2018;.xlsx&#x2019; format</li>
</ul></li>
</ul>
<h3 data-number="1.1.2" id="updates"><span
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Expand Up @@ -2,14 +2,26 @@

## 0.12.2.0

Few improvements and fixes.
Introduction of interactvie mode to dynamically explore data, using variants view
with columns types (define din VCF header).
Improvements using view duckDB feature, mainly for calculations and prioritizations,
and transcripts mapping.

### News

- Interactive mode: add a terminal to execute SQL queries
- View variants "annotations" to:
- query more easily (with "variants_view" view loaded by default in query tools)
- improve performances for annotations, calculations and prioritizations
- Interactivity mode:
- Interactive terminal to execute SQL queries
- Completion and history features
- Display modes (e.g. 'dataframe', 'markdown', 'simple', 'tabulate')
- Query result limitation, to speedup exploration
- Variants "view":
- Query more easily (with "variants_view" view loaded by default in query tools)
- INFO/tags and samples structured on specific columns ('INFOS' and 'SAMPLES')
- Improve performances for annotations, calculations and prioritizations
- Improve prioritization profiles definition using columns types
(Integer, Float, String) with list type (defined in VCF header)
- Plugins:
- 'to_excel': Convert VCF to Excel '.xlsx' format

### Updates

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