germlines.data 2.24 KB
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// This file gives the description of germlines and "pseudo-germlines" for incomplete/irregular rearrangements

germlines = {
    
    // TRA
    
    "TRA": {
	"shortcut": "A",
	"description": "Human T-cell receptor, alpha locus (14q11.2)",
	"5": ["TRAV.fa"],
	"3": ["TRAJ.fa"],
	"parameters": {
	    "seed": "13s"
	}
    },
    
    // TRB
    
    "TRB": {
	"shortcut": "B",
	"description": "Human T-cell receptor, beta locus (7q34)",
	"5": ["TRBV.fa"],
	"4": ["TRBD.fa"],
	"3": ["TRBJ.fa"],
	"parameters": {
	    "seed": "12s"
	}
    },
    
    // TRG
    
    "TRG": {
	"shortcut": "G",
	"description": "Human T-cell receptor, gamma locus (7p14)",
	"5": ["TRGJ.fa"],
	"3": ["TRGV.fa"],
	"parameters": {
	    "seed": "10s"
	}
    },
    
    // TRD
    
    "TRD": {
	"shortcut": "D",
	"description": "Human T-cell receptor, delta locus (14q11.2)",
	"5": ["TRDV.fa"],
	"4": ["TRDD.fa"],
	"3": ["TRDJ.fa"],
	"parameters": {
	    "seed": "10s"
	}
    },
    "TRD+": {
	"shortcut": "d",
	"description": "Human T-cell receptor, delta locus (14q11.2), incomplete Dd2-Dd3 rearrangements",
	"follows": "TRD",
	"5": ["TRDD-d2.fa"],
	"3": ["TRDD-d3.fa"]
	// "seed": "8" ? (pipeline.py)
    },
    
    // IGH
    
    "IGH": {
	"shortcut": "H",
	"description": "Human immunoglobulin, heavy locus (14q32.33)",
	"5": ["IGHV.fa"],
	"4": ["IGHD.fa"],
	"3": ["IGHJ.fa"],
	"parameters": {
	    "seed": "12s"
	}
    },
    "IGH+": { // "DHJH" ?
	"shortcut": "h",
	"description": "Human immunoglobulin, heavy locus (14q32.33), incomplete DH-JH rearrangements",
	"follows": "IGH",
	"5": ["IGHD.fa"],
	"3": ["IGHJ.fa"]
	// "seed": "10s" ? (pipeline.py)
    },
    
    // IGK
    
    "IGK": {
	"shortcut": "K",
	"description": "Human immunoglobulin, kappa locus (2p11.2)",
	"5": ["IGKV.fa"],
	"3": ["IGKJ.fa"],
	"parameters": {
	    "seed": "11s"
	}
    },
    "IGK+": {
	"shortcut": "k",
	"description": "Human immunoglobulin, kappa locus (2p11.2), Vk-KDE and Intron-KDE rearrangements",
	"follows": "IGK",
	"5": ["IGKV.fa", "INTRON.fa"],
	"3": ["KDE.fa"]
	// "seed": "10s" ? (pipeline.py)
    },
    
    // IGL
    
    "IGL": {
	"shortcut": "L",
	"description": "Human immunoglobulin, lambda locus (22q11.2)",
	"5": ["IGLV.fa"],
	"3": ["IGLJ.fa"],
	"parameters": {
	    "seed": "11s"
	}
    }
    
}