.info.json

{
  "ymir": {
    "title": "Ymir - a tool for working with probabilistic models of immune receptor assembling",
    "values": {
      "version": "2.0-pre1",
      "release date": "??-??-2016"
    }
  },
  "algos": {
    "title": "Algorithms and their parameters for the statistical inference in Ymir (values for a parameter '-a' for inference.py)",
    "values": {
      "EM": {
        "alias": "em",
        "comment": "Classic EM algorithm for the statistical inference of a model's parameters from (Murugan et al., 2012)",
        "parameters": {
          "niter": {
            "alias": "--niter",
            "comment": "maximum number of iterations to perform (default = 20)"
          }
        }
      }
    }
  },
  "formats": {
    "title": "Possible input formats for Ymir (values for a parameter '-f' for compute.py and inference.py)",
    "values": {
      "ymir": {
        "alias": "ymir",
        "comment": "default format of Ymir datasets",
        "pyclass": "YmirConverter"
      },
      "tcr": {
        "alias": "tcr",
        "comment": "format of data frames from an R package tcR saved with the tcR::repSave() function",
        "pyclass": "tcRConverter"
      },
      "mitcr": {
        "alias": "mitcr",
        "comment": "format for cloneset files outputted by MiTCR",
        "pyclass": "MiTCRConverter"
      },
      "migec": {
        "alias": "migec",
        "comment": "format for cloneset files outputted by MiGEC",
        "pyclass": "MiGECConverter"
      },
      "vdjtools": {
        "alias": "vdjtools",
        "comment": "format for cloneset files outputted by VDJtools",
        "pyclass": "VDJtoolsConverter"
      }
    }
  },
  "models": {
    "title": "Available generation models in the current Ymir distribution (values for a parameter '-m' for scripts)",
    "values": {
      "hTRA": {
        "comment": "human TCR alpha-chain",
        "alias": "htra",
        "path": "./models/hTRA"
      },
      "hTRB": {
        "comment": "human TCR beta-chain",
        "alias": "htrb",
        "path": "./models/hTRB"
      }
    }
  },
  "scripts": {
    "title": "Available ready-to-run scripts",
    "values": {
      "compute": {
        "alias": "compute.py",
        "comment": "A Python 3 script to compute generation probabilities of immune receptors. Run: '$python3 compute.py <parameters>'. To get help: 'run $python3 compute.py -h' to get help"
      },
      "inference": {
        "alias": "inference.py",
        "comment": "A Python 3 script to perform the statistical inference of marginal probabilities of a generation model. To get help: run '$python3 inference.py <parameters>'. Run '$python3 inference.py -h' to get help"
      },
      "generate": {
        "alias": "generate.py",
        "comment": "A Python 3 script for generation a pre-selection repertoire of immunce receptors. Run: '$python3 generate.py <parameters>'. To get help: run '$python3 generate.py -h' to get help"
      }
    }
  }
}