AmmorFati

Fast and convenient data mining tool for Chip-seq analyses.

'AmmorFati' optimizes peak call tools, like MACS2 or Cisgenome, and increases detection probability by hyper parameter optimization

AmmorFati : 'Amm' is the Korean pronunciation of cancer. 'Fati' means 'fate' in Latin. 'AmmorFati' is a compound word that combines these words'

INSTALL

Dependency

Environment

Ubuntu 18.04 LTS
python2.7
- scipy
- numpy
- pymongo

Install

Install Ammorfati
export env path named 'AMMOR_HOME' where 'AmmorFati' program is located.

$ export AMMOR_HOME=</AmmorFati/root>

Make 'data' diretory and 'tools' diretory

'data' is dir where the chipseq file is located and 'tools' is dir where the 'peak detection tools' like MACS and 'bamtools' are located. If these files are in a different location, you must modify the path inside the script file.

#!bin/sh

CHIPPATH="${AMMOR_HOME}/chipData/" # data dir

export SPEARMINTPATH="${AMMOR_HOME}/spearmint/spearmint/"
SPEARMINTWORK="${AMMOR_HOME}/spearmint/workspace/"

BAMPATH="${AMMOR_HOME}/tools/bamtools/build/install/bin/"
export CISGENOMEPATH="${AMMOR_HOME}/tools/cisgenome/bin/"
export MACS2PATH="${AMMOR_HOME}/tools/macs/bin/"
export SICERPATH="${AMMOR_HOME}/tools/SICERpy/SICERpy/"
export SWEMBLPATH="${AMMOR_HOME}/tools/swembl/"

Install MongoDB & start services

$ mongo
MongoDB shell version v4.0.2
connecting to: mongodb://127.0.0.1:27017
MongoDB server version: 4.0.2
Server has startup warnings:
2018-10-03T12:29:15.474+0900 I STORAGE  [initandlisten]
2018-10-03T12:29:15.474+0900 I STORAGE  [initandlisten] ** WARNING: Using the XFS filesystem is strongly recommended with the WiredTiger storage engine
2018-10-03T12:29:15.474+0900 I STORAGE  [initandlisten] **          See http://dochub.mongodb.org/core/prodnotes-filesystem
2018-10-03T12:29:16.335+0900 I CONTROL  [initandlisten]
2018-10-03T12:29:16.335+0900 I CONTROL  [initandlisten] ** WARNING: Access control is not enabled for the database.
2018-10-03T12:29:16.335+0900 I CONTROL  [initandlisten] **          Read and write access to data and configuration is unrestricted.
2018-10-03T12:29:16.335+0900 I CONTROL  [initandlisten]
---

LABELED DATA

Configuration

If you want to set options about 'spearmint' or other detection tool, check the config files in the 'config' directory. you can change the parameter range for each tool, the maximum number of jobs, and the number of threads.

{
    "language"        : "PYTHON",
    "experiment-name" : "macs2_test",
    "polling-time"    : 1,
    "resources" : {
        "my-machine" : {
            "scheduler"         : "local",
            "max-concurrent"    : 4,
            "max-finished-jobs" : 10
        }
    },

    "variables" : {
        "q" : {
            "type" : "FLOAT",
            "size" : 1,
            "min"  : 0.001,
            "max"  : 0.8
        },
        "m_s" : {
            "type" : "INT",
            "size" : 1,
            "min" : 1,
            "max" : 50
        },
        "m_d" : {
            "type" : "INT",
            "size" : 1,
            "min" : 20,
            "max" : 200
      }
   }
}

Getting started

Run the AmmorFati.

$ sh ammorfati.sh </Treat(input) file of chipseq data/> </Control file of chipseq data/> </train label file/> </test label file/>

You need 4 files (Treat file, Control file, label file for train, label file for test)

CITATION