Commit 98ba0d9a authored by Marc Duez's avatar Marc Duez

germlines.data : convert from js to json

parent 2076b2ea
// 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"
}
"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"
}
"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"
}
"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"
}
"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": ["TRDV.fa", "TRDD-d2.fa"],
"3": ["TRDJ.fa", "TRDD-d3.fa"]
// "seed": "8" ? (pipeline.py)
"shortcut": "d",
"description": "Human T-cell receptor, delta locus (14q11.2), incomplete Dd2-Dd3 rearrangements",
"follows": "TRD",
"5": ["TRDV.fa", "TRDD-d2.fa"],
"3": ["TRDJ.fa", "TRDD-d3.fa"]
},
// IGH
"IGH": {
"shortcut": "H",
"description": "Human immunoglobulin, heavy locus (14q32.33)",
"5": ["IGHV.fa"],
"4": ["IGHD.fa"],
"3": ["IGHJ.fa"],
"parameters": {
"seed": "12s"
}
"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)
"IGH+": {
"shortcut": "h",
"description": "Human immunoglobulin, heavy locus (14q32.33), incomplete DH-JH rearrangements",
"follows": "IGH",
"5": ["IGHD.fa"],
"3": ["IGHJ.fa"]
},
// IGK
"IGK": {
"shortcut": "K",
"description": "Human immunoglobulin, kappa locus (2p11.2)",
"5": ["IGKV.fa"],
"3": ["IGKJ.fa"],
"parameters": {
"seed": "11s"
}
"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)
"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"]
},
// IGL
"IGL": {
"shortcut": "L",
"description": "Human immunoglobulin, lambda locus (22q11.2)",
"5": ["IGLV.fa"],
"3": ["IGLJ.fa"],
"parameters": {
"seed": "11s"
}
"shortcut": "L",
"description": "Human immunoglobulin, lambda locus (22q11.2)",
"5": ["IGLV.fa"],
"3": ["IGLJ.fa"],
"parameters": {
"seed": "11s"
}
}
}
}
\ No newline at end of file
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