configuration file format

PISCES is driven by JSON configuration files. The key:value pairs in this configuration file then are used by all subsequent pisces subcommands. Paths can be either local files, or HTTP/FTP URLs. Notice that chimeric organisms such as a human/mouse xenograft organisms are easily defined by specifying each transcriptome as a separate GTF/FASTA pair. Example transcriptomes for human, mouse, and human/mouse xenograft are included in the default PISCES distribution. If you need to support another organism, this can easily be accomplished by adding your transcriptome of interest in a new configuration file. The configuration file format follows:

{
    "human": {
        "downloads": "$HOME/pisces/downloads",
        "index_dir": "$HOME/pisces",
        "default": "gencode_basic",
        "index": {
            "gencode_basic": {
                "gtfs": ["ftp://ftp.ebi.ac.uk/pub/databases/gencode/Gencode_human/release_32/gencode.v32.basic.annotation.gtf.gz"],
                "fastas": ["ftp://ftp.ebi.ac.uk/pub/databases/gencode/Gencode_human/release_32/GRCh38.p13.genome.fa.gz"],
                "extra_fastas": [],
                "options": {
                    "-k": 31,
                    "infer_features": false
                }
            }
        }
    },
    "mouse": {
        "downloads": "$HOME/pisces/downloads",
        "index_dir": "$HOME/pisces",
        "default": "gencode_basic",
        "index": {
            "gencode_basic": {
                "gtfs": ["ftp://ftp.ebi.ac.uk/pub/databases/gencode/Gencode_mouse/release_M23/gencode.vM23.basic.annotation.gtf.gz"],
                "fastas": ["ftp://ftp.ebi.ac.uk/pub/databases/gencode/Gencode_mouse/release_M23/GRCm38.p6.genome.fa.gz"],
                "extra_fastas": [],
                "options": {
                    "-k": 31,
                    "infer_features": false
                }
            }
        }
    },
    "human-mouse": {
        "downloads": "$HOME/pisces/downloads",
        "index_dir": "$HOME/pisces",
        "default": "gencode_basic",
        "index": {
            "gencode_basic": {
                "gtfs": ["ftp://ftp.ebi.ac.uk/pub/databases/gencode/Gencode_mouse/release_M23/gencode.vM23.basic.annotation.gtf.gz",
                    "ftp://ftp.ebi.ac.uk/pub/databases/gencode/Gencode_human/release_32/gencode.v32.basic.annotation.gtf.gz"
                ],
                "fastas": ["ftp://ftp.ebi.ac.uk/pub/databases/gencode/Gencode_mouse/release_M23/GRCm38.p6.genome.fa.gz", "ftp://ftp.ebi.ac.uk/pub/databases/gencode/Gencode_human/release_32/GRCh38.p13.genome.fa.gz"],
                "extra_fastas": [],
                "options": {
                    "-k": 31,
                    "infer_features": false
                }
            }
        }
    }
}