AgeseqConfig.py

# -*- coding: utf-8 -*-


class ASConfig(object):
    """
    This is a AGESeqConfig class for saving AGEseq Configuration
    """

    def __init__(self, mismatch_cutoff, min_cutoff,
                 wt_like_report, indel_report, remove_files,
                 READ_SNP_MINR_FREQ, READ_INDEL_MINR_FREQ,
                 READ_SNP_MINIMAL_SUPPORT, READ_INDEL_MINIMAL_SUPPORT,
                 WOBBLE_BASE, WOBBLE_FREQ_HIGH, WOBBLE_FREQ_LOW):
        self.mismatch_cutoff = mismatch_cutoff
        self.min_cutoff = min_cutoff
        self.wt_like_report = wt_like_report
        self.indel_report = indel_report
        self.remove_files = remove_files
        self.READ_SNP_MINR_FREQ = float(READ_SNP_MINR_FREQ)
        self.READ_INDEL_MINR_FREQ = float(READ_INDEL_MINR_FREQ)
        self.READ_SNP_MINIMAL_SUPPORT = int(READ_SNP_MINIMAL_SUPPORT)
        self.READ_INDEL_MINIMAL_SUPPORT = int(READ_INDEL_MINIMAL_SUPPORT)
        self.WOBBLE_BASE = WOBBLE_BASE
        self.WOBBLE_FREQ_HIGH = float(WOBBLE_FREQ_HIGH)
        self.WOBBLE_FREQ_LOW = float(WOBBLE_FREQ_LOW)

    def returnConfig(self):
        return self.__dict__



class BLATConfig(object):
    """
    This is a BLATConfig class for saving BLAT Configuration
    """

    def __init__(self, tileSize, oneOff,
                 maxGap, minIdentity, minScore):
        self.tileSize = tileSize
        self.oneOff = oneOff
        self.maxGap = maxGap
        self.minIdentity = minIdentity
        self.minScore = minScore

    def returnBLATConfig(self):
        return self.__dict__


# Preset:
ASPRESET = ASConfig(mismatch_cutoff=0.1,
                    min_cutoff=0,
                    wt_like_report=20,
                    indel_report=50,
                    remove_files=True,
                    READ_SNP_MINR_FREQ=0.05,
                    READ_INDEL_MINR_FREQ=0.01,
                    READ_SNP_MINIMAL_SUPPORT=3,
                    READ_INDEL_MINIMAL_SUPPORT=5,
                    WOBBLE_BASE=True,
                    WOBBLE_FREQ_HIGH=0.65,
                    WOBBLE_FREQ_LOW=0.35)

BLATPRESET = BLATConfig(tileSize=7,
                        oneOff=1,
                        maxGap=20,
                        minIdentity=70,
                        minScore=80)

PRESET_PAM = {
    "SpCas9": "NGG",
    "SaCas9": "NGRRN",
    "NmeCas9": "NNNNGATT",
    "CjCas9": "NNNNRYAC",
    "StCas9": "NNAGAAW",
    "LbCpf1": "TTTV",
    "AsCpf1": "TTTV"
}


def readConfigFile(configFile):
    """
    Reading configuration from the configFile
    Return an instance of ASConfig and a BLATConfig instance
    via a tuple.
    """
    cfile = open(configFile, "r")
    paradict = dict()
    # print("Reading Configuration as following!")
    for cfileline in cfile:
        if cfileline.startswith("#") or not cfileline.strip():
            pass
        else:
            spline = cfileline.split()
            paradict[spline[0]] = spline[2]
            # print(spline[0]+"\t"+spline[2])

    USER_ASCONF = ASConfig(mismatch_cutoff=paradict['mismatch_cutoff'],
                           min_cutoff=paradict['min_cutoff'],
                           wt_like_report=paradict['wt_like_report'],
                           indel_report=paradict['indel_report'],
                           remove_files=paradict['remove_files'],
                           READ_SNP_MINR_FREQ=paradict['READ_SNP_MINR_FREQ'],
                           READ_INDEL_MINR_FREQ=paradict['READ_INDEL_MINR_FREQ'],
                           READ_SNP_MINIMAL_SUPPORT=paradict['READ_SNP_MINIMAL_SUPPORT'],
                           READ_INDEL_MINIMAL_SUPPORT=paradict['READ_INDEL_MINIMAL_SUPPORT'],
                           WOBBLE_BASE=paradict['WOBBLE_BASE'],
                           WOBBLE_FREQ_HIGH=float(paradict['WOBBLE_FREQ_HIGH']),
                           WOBBLE_FREQ_LOW=float(paradict['WOBBLE_FREQ_LOW']))

    USER_BLCONF = BLATConfig(tileSize=paradict['blat_tileSize'],
                             oneOff=paradict['blat_oneOff'],
                             maxGap=paradict['blat_maxGap'],
                             minIdentity=paradict['blat_minIdentity'],
                             minScore=paradict['blat_minScore'])
    return (USER_ASCONF, USER_BLCONF)


if __name__ == '__main__':
    # print("Default presets for AGEseq are:")
    ASPRESET.returnConfig()
    BLATPRESET.returnBLATConfig()