Update README

README.md

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-# generate_panels
+# Generate Panel
+
+Here's a script for generating bed files to create templates for capture-targeted high-throughput sequencing.
+
+## Usage
+
+```
+Generate a bed panel from a GTF file
+
+options:
+  -h, --help            show this help message and exit
+  -v, --verbose         Enable verbose mode (default: False)
+  -o OUTPUT, --output OUTPUT
+                        Specify an output file for gene information (default: /Users/Charles/Documents/codes/generate_panels/src)
+  --gtf GTF             Specify the gtf file to use (default: None)
+
+GTF options:
+  -s SOURCE [SOURCE ...], --source SOURCE [SOURCE ...]
+                        Specify the source(s) to use ("BestRefSeq", "Curated", "Gnomon", "RefSeq", "cmsearch", "tRNAscan-SE") (default: ['BestRefSeq'])
+  -t TYPE [TYPE ...], --type TYPE [TYPE ...]
+                        Specify the sequence type to analyze ("CDS", "exon", "gene", "start_codon", "stop_codon", "transcript") (default: ['exon'])
+
+Genes options:
+  -g [GENE ...], --gene [GENE ...]
+                        Specify the gene(s) (default: None)
+  --genes-list GENES_LIST
+                        Specify the gene(s) (default: None)
+
+Chromosomes options:
+  --chromosomes CHROMOSOMES
+                        Specify the file with chromosome correspondences (default: None)
+  --usable-chromosomes USABLE_CHROMOSOMES [USABLE_CHROMOSOMES ...]
+                        Specify the chromosomes you want to use (default: ['1', '2', '3', '4', '5', '6', '7', '8', '9', '10', '11', '12', '13', '14', '15', '16', '17', '18', '19', '20', '21', '22', 'X', 'Y'])
+  -w, --without-chr     Specify the chromosome format (default: True)
+
+Variant (ClinVar/LOVD) options:
+  -c CLINVAR, --clinvar CLINVAR
+                        Specify the ClinVar vcf file (default: None)
+  --clinvar-type CLINVAR_TYPE [CLINVAR_TYPE ...]
+                        Specify the sequence type to check on ClinVar ("CDS", "exon", "gene", "start_codon", "stop_codon", "transcript") (default: ['gene'])
+  --clinvar-clnsig CLINVAR_CLNSIG [CLINVAR_CLNSIG ...]
+                        Specify the significance levels for ClinVar ("Pathogenic", "Likely_pathogenic", "Pathogenic_low_penetrance", "Likely_pathogenic_low_penetrance", "Established_risk_allele", "Likely_risk_allele") (default:
+                        ['Pathogenic', 'Likely_pathogenic', 'Pathogenic_low_penetrance', 'Likely_pathogenic_low_penetrance', 'Established_risk_allele', 'Likely_risk_allele'])
+  --lovd LOVD           Specify LOVD file (default: None)
+  --max-len-variants MAX_LEN_VARIANTS
+                        Specify the max length for clinvar variants (default: 150)
+
+Other options:
+  -p PADDING, --padding PADDING
+                        Specify the padding to apply (default: 0)
+```
+
+### GTF file
+
+> Recommended :
+> download the GTF from NCBI (e.g. GRCh38 : https://www.ncbi.nlm.nih.gov/datasets/genome/GCF_000001405.40/)
+
+### Example
+
+- Generate exome
+> `generate-panel --gtf /ncbi_dataset/ncbi_dataset/data/GCF_000001405.40/genomic.gtf `
+
+- Generate panel of genes with only coding region with a pdding of 50
+
+> `generate-panel --gtf /ncbi_dataset/ncbi_dataset/data/GCF_000001405.40/genomic.gtf -g TP53 TNF EGFR VEGFA APOE IL6 TGFB1 MTHFR ESR1 AKT1 -t CDS -p 50`