variant.py

from verum.common import ITestRecord, IValidationRecord, getPass
logger = logging.getLogger(__name__)

class VariantTestRecord(ITestRecord):
    def __init__(self, variant, success=False):
        self.variant = variant
        self.success = success
        self.ident = "{}:{}".format(variant.CHROM, variant.POS)

class VariantMatch(VariantTestRecord):
    def __init__(self, expected_variant, expected_filename, matched_variant, matched_filename, agi, consensus, success=True):
        super(VariantMatch, self).__init__(expected_variant, success=success)

    def getSummary(self):
        message = ("{passed}: {expected_ident} in {e_filename} to {working_ident} in {w_filename}"
                   .format(passed=getPass(self.success),
                           expected_ident=self.ident,
                           e_filename=self.filename,
                           working_ident="{}:{}".format(self.matched_variant.CHROM,
                                                        self.matched_variant.POS),

                           "PASS: chr5:345987 in blahblah.vcf to chr5:345987 in summary.vcf"
                           "FAIL: chr5:345987 in blahblah.vcf to chr5:345987 in summary.vcf"

class VariantWorkingOrphan(VariantTestRecord):
    pass

class VariantExpectedOrphan(VariantTestRecord):
    def __init__(self, variant, success=False, filename, amplicon_group_id, consensus):
        super(VariantExpectedOrphan, self).__init__(variant, sucess)

        self.filename = filename
        self.amplicon_group_id = amplicon_group_id
        self.consensus = consensus

        self.ident = "{}:{}, {}".format(self.variant.CHROM, self.variant.POS, self.amplicon_group_id[:9])


class VariantSNPMismatch(VariantTestRecord):
    pass

class VariantIndelMismatch(VariantTestRecord):
    pass