Merge pull request #26 from JbaptisteLam/master

Version 1.1 release
bioinfo-chru-strasbourg · Mar 29, 2023 · 3dee9ce · 3dee9ce
2 parents 96c1c14 + 87a61ca
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diff --git a/.gitignore b/.gitignore
@@ -0,0 +1,3 @@
+__pycache__/
+*.egg-info/
+*.tar.gz
diff --git a/Dockerfile b/Dockerfile
@@ -0,0 +1,19 @@
+FROM python:3.9.16
+
+LABEL maintainer="Jean-Baptiste Lamouche"
+LABEL name="[email protected]"
+
+#Install vcf2circos
+RUN pip install git+https://github.com/JbaptisteLam/vcf2circos@manuscript
+
+#Download config
+RUN wget https://www.lbgi.fr/~lamouche/vcf2circos/config_vcf2circos_29032023.tar.gz
+
+#Untar config
+RUN tar -xzf config_vcf2circos_29032023.tar.gz
+
+#Set configuration path
+RUN sed -i 's,\"Static\": \"/enadisk/maison/lamouche/dev_vcf2circos/Static\"\,,\"Static\": \"/Static\"\,,' /Static/options.json
+
+ENTRYPOINT ["vcf2circos"]
+
diff --git a/README.md b/README.md
@@ -6,34 +6,74 @@ See documentation and code in [GitHub vcf2circos](https://github.com/bioinfo-chr
 
 This package is based on [PCircos](https://github.com/CJinnny/PCircos) code
 
+```
+-._    _.--'"`'--._    _.--'"`'--._    _.--'"`'--._    _
+    '-:`.'|`|"':-.  '-:`.'|`|"':-.  '-:`.'|`|"':-.  '.` : '.
+  '.  '.  | |  | |'.  '.  | |  | |'.  '.  | |  | |'.  '.:   '.  '.
+  : '.  '.| |  | |  '.  '.| |  | |  '.  '.| |  | |  '.  '.  : '.  `.
+  '   '.  `.:_ | :_.' '.  `.:_ | :_.' '.  `.:_ | :_.' '.  `.'   `.
+         `-..,..-'       `-..,..-'       `-..,..-'       `         `
+
+                     __ ___      _
+                    / _|__ \    (_)
+         __   _____| |_   ) |___ _ _ __ ___ ___  ___
+         \ \ / / __|  _| / // __| | '__/ __/ _ \/ __|
+          \ V / (__| |  / /| (__| | | | (_| (_) \__ \
+           \_/ \___|_| |____\___|_|_|  \___\___/|___/
+
+
+
+Author: Jean-Baptiste Lamouche, Antony Le Bechec, Jin Cui
+Version: 1.1
+Last update: Mars 26 2023
+
+
+usage: python vcf2circos.py [-h] -i INPUT -o OUTPUT [-e EXPORT] [-p OPTIONS] [-a ASSEMBLY]
+
+optional arguments:
+  -h, --help            show this help message and exit
+  -i INPUT, --input INPUT
+                        Input vcf File
+                        VCF SHOULD be multiallelic split to avoid trouble in vcf2circos
+                        example: bcftools -m -any <vcf>
+                        Format will be autodetected from file path.
+                        Supported format:
+                           'vcf.gz', 'vcf'
+  -o OUTPUT, --output OUTPUT
+                        Output file.
+                        Format will be autodetected from file path.
+                        Supported format:
+                           'png', 'jpg', 'jpeg', 'webp', 'svg', 'pdf', 'eps', 'json'
+  -e EXPORT, --export EXPORT
+                        Export file.
+                        Format is 'json'.
+                        Generate json file from VCF input file
+  -p OPTIONS, --options OPTIONS
+                        Options file in json format
+  -a ASSEMBLY, --assembly ASSEMBLY
+                        Genome assembly to use for now values available (hg19, hg38)
+```
 
-![Doc Circos](docs/circos_help.png)
 <br/>
 
 # Installation
 
-## Git clone
+## Git clone and Pip
 
 Download package source files.
 
 ```
 $ git clone https://github.com/bioinfo-chru-strasbourg/vcf2circos.git .
-```
-
-## Pip
-
-Compile source using Pip to generate binary "vcf2circos"
-
-```
 $ python -m pip install -e .
 ```
 
 ## Docker
 
-Build docker image "vcf2circos:latest"
+Build docker image "vcf2circos:latest"  
+From inside cloned repository
 
 ```
-$ docker-compose build
+$ docker image build -t vcf2circos:latest .
 ```
 
 ## Configuration folder
@@ -42,8 +82,7 @@ Configuration files could be download here: [vcf2circos-config](http://www.lbgi.
 ```
 tar -xzf <tarballname> <folder>
 ```
-Regarding where you place your configuration folder previously downloaded, you need to specify the absolute path of the Static folder in "Static" json key (which will replace default value "config/Static")<br><br>
-An <b>example VCF</b> is also available in the configuration folder called example.vcf
+Regarding where you place your configuration folder previously downloaded, you need to specify the absolute path of the Static folder in "Static" json key (which will replace default value)<br><br>
 
 <br/>
 
@@ -52,35 +91,21 @@ An <b>example VCF</b> is also available in the configuration folder called examp
 ## Binary 
 
 ```
-$ vcf2circos --input config/Static/example.vcf.gz --options config/Static/options.json --output <outputpath>.html
+$ vcf2circos --input config/Static/example.vcf.gz --options <jsonfile> --output <outputpath>.html -a <assembly hg19 or hg38>
 
 ```
 
 ## Docker
 
 ```
-$ docker run -v $(pwd):/data vcf2circos:latest --input=demo_data/example.vcf.gz --output=/data/example.vcf.gz.html --options=demo_data/options.example.json
-
-```
-
-## Python 
-
-```
-$ python vcf2circos/__main__.py --input config/Static/example.vcf.gz --options config/Static/options.json --output <outputpath>.html
+$ docker run -it --rm vcf2circos:1.1 -i <input.vcf> -o <output.html> -p /Static/options.json -a hg19
 
 ```
 
-<br/>
-
-
 # Input
 
 This package allows multiple input formats:
-- VCF including SNV/InDel/SV (see [VCF specifications](https://samtools.github.io/hts-specs/VCFv4.2.pdf)). Header needs to contain contigs (in order of appearance). See [VCF example](demo_data/example.vcf.gz).
-- JSON configuration file (see [PCircos](https://github.com/CJinnny/PCircos) documentation). See [JSON configuration example](demo_data/demo_params.json).
-
-Format will be autodetected from file path.
-
+- VCF including SNV/InDel/SV (see [VCF specifications](https://samtools.github.io/hts-specs/VCFv4.2.pdf)). Header needs to contain contigs (in order of appearance). See [VCF example](tests/example.vcf).
 
 <br/>
 
@@ -91,17 +116,9 @@ This package generates Circos plot in multiple formats (html, png, jpg, jpeg, we
 - Image files (i.e. png, jpg, jpeg, webp, svg, pdf, eps). See [PNG example](docs/refontcircos.png) and [PDF example](docs/refontcircos.pdf)
 - JSON Plotly file (see [Plotly documentation](https://plotly.com/)). 
 
-Format will be autodetected from file path.
 
 Output Circos plot sections from a VCF file:
-![Doc Circos](docs/docs.circos.png)
-
-
-<br/>
-
-# Export
-
-Circos plot generated from VCF file can be exported as JSON configuration file, for further use. See [JSON configuration export example](demo_data/example.vcf.gz.export.json)
+![Doc Circos](docs/circos.png)
 
 
 <br/>
@@ -113,36 +130,53 @@ Circos plot generated from a VCF file can be configured using a JSON options fil
 Here is an example of a JSON options file:
 ```
 {
-	"General": {
-		"title": "",
-		"width": 1200,
-		"height": 1200,
-		"plot_bgcolor": "white"
-	},
-	"Static": "config/Static",
-	"Assembly": "hg19",
-	"Chromosomes": {
-		"cytoband": "True",
-		"list": ["chr1", "chrX"]
-	},
-	"Genes": {
-		"only_snv_in_sv_genes": false
-	},
-	"Variants": {
-		"annotations": {
-			"fields": ["SVTYPE", "SVLEN"]
-		},
-		"rings": {
-			"position": 0.4,
-			"height": 0.04,
-			"space": 0.01,
-			"nrings": 6
-		}
-	},
-	"Extra": [
-		"gc"
-	]
-}
+    "General": {
+        "title": "",
+        "width": 1000,
+        "height": 1000,
+        "plot_bgcolor": "white"
+    },
+    "Static": "<path of config>",
+    "Assembly": "hg19",
+    "Chromosomes": {
+        "list": ["chrX"],
+        "all": false
+    },
+    "Genes": {
+        "only_snv_in_sv_genes": false,
+        "extend": false
+    },
+    "Variants": {
+        "annotations": {
+            "fields": [
+                "REF",
+                "ALT",
+                "Tx",
+                "SV_length",
+                "SVLEN",
+                "END",
+                "CN",
+                "Gene_name",
+                "Gene_count",
+                "DDD_HI_percent",
+                "OMIM_morbid",
+                "GnomAD_pLI",
+                "LOEUF_bin",
+                "AnnotSV_ranking_criteria",
+                "ACMG_class"
+            ]
+        },
+        "rings": {
+            "position": 0.5,
+            "height": 0.04,
+            "space": 0.01,
+            "nrings": 6
+        }
+    },
+    "Extra": [
+        "gc"
+    ],
+
 ```
 
 <br/>
@@ -174,8 +208,8 @@ Example:
 ```
 "General": {
     "title": "",
-    "width": 1400,
-    "height": 1400,
+    "width": 1000,
+    "height": 1000,
     "plot_bgcolor": "white"
 }
 ```
@@ -202,17 +236,20 @@ The "list" option define the list of chromosomes to show in the Circos plot. Ord
 
 ## Genes section
 
-The "Genes" section defines information about Genes (e.g. refGene data, list of genes to show). These information are used to annnotate variants (SNV and SV), and are used with algorithms highlight interesting information (e.g. only SNV on CNV genes). They also can be shown in the Circos plot (below Chromosomes ring)
+The "Genes" section defines information about Genes (e.g. refGene data, list of genes to show). These information are used to annnotate variants (SNV and SV), and are used with algorithms highlight interesting information (e.g. only SNV on CNV genes). They also can be shown in the Circos plot (below Chromosomes ring)  
+only_snv_in_sv_genes: display only snv indels located inside SV boundaries  
+extend: display genes located 1Mb in upstream and downstream of SV boundaries
 
 ```
-    "only_snv_in_sv_genes": true
-}
+    "only_snv_in_sv_genes": true,
+    "extend": true
 ```
 ### List of genes
 
 The "list" option defines the list of genes to show in the Circos plot, below Chromosomes/Cytoband ring. This list refers to the "gene" column in the data.
-
 <br>
+</br>
+
 ### Filter SNV on CNV genes
 
 The "only_snv_in_sv_genes" option will select (and show) only SNV that are located on genes mutated with at least 1 SV.

diff --git a/dist/vcf2circos-2.1.1-py3-none-any.whl b/dist/vcf2circos-2.1.1-py3-none-any.whl
diff --git a/docker-compose.yml b/docker-compose.yml
diff --git a/docker/.env b/docker/.env