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        "description": "# Annotate Gene Fusion (AGFusion)\nAGFusion is a python package for annotating gene fusions from the human or mouse genomes. AGFusion simply needs the reference genome, the two gene partners, and the fusion junction coordinates as input, and outputs the following:\n\n* FASTA files of cDNA, CDS, and protein sequences.\n* Visualizes the protein domain and exon architectures of the fusion transcripts.\n* Saves tables listing the coordinates of protein features and exons included in the fusion.\n* Optional exon structure and protein domain visualization of the wild-type  version of the fusion gene partners.\n\nSome other things to know:\n\n* AGFusion automatically predicts the functional effect of the gene fusion (e.g. in-frame, out-of-frame, etc.).\n* Annotation is by default done only for canonical gene isoforms, but there is the option to annotate all gene non-canonical isoform combinations.\n* All gene and protein annotation is from Ensembl\n* Supports up to Ensembl release 95\n\n\n## Table of Contents\n\n- [Examples](#examples)\n  * [Basic Usage](#basic-usage)\n  * [Plotting wild-type protein and exon structure](#plotting-wild-type-protein-and-exon-structure)\n  * [Canonical gene isoforms](#canonical-gene-isoforms)\n  * [Input from fusion-finding algorithms](#input-from-fusion-finding-algorithms)\n  * [Graphical parameters](#graphical-parameters)\n- [Installation](#installation)\n- [Dependencies](#dependencies)\n- [Troubleshooting](#troubleshooting)\n- [License](#license)\n- [Citing AGFusion](#citing-agfusion)\n\n\n## Examples\n\n### Basic Usage\n\nYou just need to provide the two fusion gene partners (gene symbol, Ensembl ID, or Entrez gene ID), their predicted fusion junctions in genomic coordinates, and the genome build. You can also specify certain transcripts with Ensembl transcript ID or RefSeq ID\n\nExample usage from the command line:\n\n```\nagfusion annotate \\\n  --gene5prime DLG1 \\\n  --gene3prime BRAF \\\n  --junction5prime 31684294 \\\n  --junction3prime 39648486 \\\n  -db agfusion.mus_musculus.87.db \\\n  -o DLG1-BRAF\n```\n\nThe protein domain structure of the DLG1-BRAF fusion:\n\n![alt tag](https://github.com/murphycj/AGFusion/blob/master/doc/ENSMUST00000064477-ENSMUST00000002487.png)\n\nThe exon structure of the DLG1-BRAF fusion:\n\n![alt tag](https://github.com/murphycj/AGFusion/blob/master/doc/ENSMUST00000064477-ENSMUST00000002487.exon.png)\n\n### Plotting wild-type protein and exon structure\n\nYou can additionally plot the wild-type proteins and exon structures for each gene with --WT flag.\n\n```\nagfusion annotate \\\n   -g5 ENSMUSG00000022770 \\\n   -g3 ENSMUSG00000002413 \\\n   -j5 31684294 \\\n   -j3 39648486 \\\n   -db agfusion.mus_musculus.87.db \\\n   -o DLG1-BRAF \\\n   --WT\n```\n\n### Canonical gene isoforms\n\nBy default AGFusion only plots the [canonical](http://useast.ensembl.org/Help/Glossary?id=346) gene isoforms, but you can tell AGFusion to include non-canonical isoform with the --noncanonical flag.\n\n```\nagfusion annotate \\\n  -g5 ENSMUSG00000022770 \\\n  -g3 ENSMUSG00000002413 \\\n  -j5 31684294 \\\n  -j3 39648486 \\\n  -db agfusion.mus_musculus.87.db \\\n  -o DLG1-BRAF \\\n  --noncanonical\n```\n\n### Input from fusion-finding algorithms\n\nYou can provide as input output files from fusion-finding algorithms. Currently supported algorithms are:\n\n* Bellerophontes\n* BreakFusion\n* ChimeraScan\n* ChimeRScope\n* deFuse\n* EricScript\n* FusionCatcher\n* FusionHunter\n* FusionMap\n* InFusion\n* JAFFA\n* MapSplice (only if --gene-gtf specified)\n* STAR-Fusion\n* TopHat-Fusion\n\n\n\nBelow is an example for FusionCatcher.\n\n```\nagfusion batch \\\n  -f final-list_candidate-fusion-genes.txt \\\n  -a fusioncatcher \\\n  -o test \\\n  -db agfusion.mus_musculus.87.db\n```\n\n### Graphical parameters\n\nYou can change domain names and colors:\n\n```\nagfusion annotate \\\n  -g5 ENSMUSG00000022770 \\\n  -g3 ENSMUSG00000002413 \\\n  -j5 31684294 \\\n  -j3 39648486 \\\n  -db agfusion.mus_musculus.87.db \\\n  -o DLG1-BRAF \\\n  --recolor \"Pkinase_Tyr;red\" --recolor \"L27_1;blue\" \\\n  --rename \"Pkinase_Tyr;Kinase\" --rename \"L27_1;L27\"\n```\n\n![alt tag](https://github.com/murphycj/AGFusion/blob/master/doc/ENSMUST00000064477-ENSMUST00000002487-recolorRename.png)\n\nYou can rescale the protein length so that images of two different fusions have appropriate relative lengths when plotted side by side:\n\n```\nagfusion annotate \\\n  -g5 ENSMUSG00000022770 \\\n  -g3 ENSMUSG00000002413 \\\n  -j5 31684294 \\\n  -j3 39648486 \\\n  -db agfusion.mus_musculus.87.db \\\n  -o DLG1-BRAF \\\n  --recolor \"Pkinase_Tyr;red\" --recolor \"L27_1;blue\" \\\n  --rename \"Pkinase_Tyr;Kinase\" --rename \"L27_1;L27\" \\\n  --scale 2000\nagfusion annotate \\\n  -g5 FGFR2 \\\n  -g3 DNM3 \\\n  -j5 130167703 \\\n  -j3 162019992 \\\n  -db agfusion.mus_musculus.87.db \\\n  -o FGFR2-DNM3 \\\n  --recolor \"Pkinase_Tyr;red\" \\\n  --rename \"Pkinase_Tyr;Kinase\" \\\n  --scale 2000\n```\n\n![alt tag](https://github.com/murphycj/AGFusion/blob/master/doc/ENSMUST00000064477-ENSMUST00000002487-rescale.png)\n![alt tag](https://github.com/murphycj/AGFusion/blob/master/doc/ENSMUST00000122054-ENSMUST00000070330-rescale.png)\n\n# Installation\n\nFirst you need to install pyensembl (and the other dependencies listed at the bottom) and download the reference genome you will use by running one of the following.\n\n```\nFor GRCh38/hg38:\npyensembl install --species homo_sapiens --release 87\n\nFor GRCh37/hg19:\npyensembl install --species homo_sapiens --release 75\n\nFor GRCm38/mm10:\npyensembl install --species mus_musculus --release 87\n```\n\nThen you can install AGFusion:\n\n```\npip install agfusion\n```\n\nFinally, download the AGFusion database for your reference genome (downloaded from [here](https://github.com/murphycj/AGFusionDB)).\n\n```\nFor GRCh38/hg38:\nagfusion download -g hg38\n\nFor GRCh37/hg19:\nagfusion download -g hg19\n\nFor GRCm38/mm10:\nagfusion download -g mm10\n```\n\nYou can view all supported species and ensembl releases with ```agfusion download -a```. Due to limitations in pyensembl, the maximum supported Ensembl release is 87.\n\n# Dependencies\n\n- python 2.7, 3.5\n- matplotlib>=1.5.0\n- pandas>=0.18.1\n- biopython>=1.67\n- future>=0.16.0\n- pyensembl>=1.1.0\n\n# Troubleshooting\n\n**Problem:** I get a warning message like the following:\n\n\n> 2017-08-28 15:02:51,377 - AGFusion - WARNING - No cDNA sequence available for AC073283.4! Will not print cDNA sequence for the AC073283.4-MSH2 fusion. You might be working with an outdated pyensembl. Update the package and rerun 'pyensembl install'\n\n**Solution:** Run the following to update pyensembl package and database:\n\n```\ngit clone git@github.com:hammerlab/pyensembl.git\ncd pyensembl\nsudo pip install .\npyensembl install --release (your-release) --species (your-species)\n```\n\n# License\n\nMIT license\n\n# Citing AGFusion\n\nYou can cite bioRxiv: http://dx.doi.org/10.1101/080903",
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