Skip to content

mavis.tools.vcf

mavis.tools.vcf.parse_bnd_alt()

parses the alt statement from vcf files using the specification in vcf 4.2/4.2.

Assumes that the reference base is always the outermost base (this is based on the spec and also manta results as the spec was missing some cases)

r = reference base/seq u = untemplated sequence/alternate sequence p = chromosome:position

alt format orients
ru[p[ LR
[p[ur RR
]p]ur RL
ru]p] LL 
def parse_bnd_alt(alt):

Args

  • alt

mavis.tools.vcf.convert_record()

converts a vcf record

def convert_record(record, record_mapping={}, log=DEVNULL):

Args

  • record
  • record_mapping
  • log

Note

CT = connection type, If given this field will be used in determining the orientation at the breakpoints. From https://groups.google.com/forum/#!topic/delly-users/6Mq2juBraRY, we can expect certain CT types for certain event types - translocation/inverted translocation: 3to3, 3to5, 5to3, 5to5 - inversion: 3to3, 5to5 - deletion: 3to5 - duplication: 5to3

mavis.tools.vcf.convert_file()

process a VCF file

def convert_file(input_file: str, file_type: str, log):

Args

  • input_file (str): the input file name
  • file_type (str): the input type
  • log

Raises

  • err: [description]