Source code for bripipetools.io.sexcheck

"""
Class for reading and parsing sex check validation files.
"""
import logging

logger = logging.getLogger(__name__)


class SexcheckFile(object):
    """
    Parser to read tables of metrics generated by custom Tophat Stats PE tool,
    stored in a tab-delimited text file.
    """
    def __init__(self, path):
        self.path = path
        self.data = {}

    def _read_file(self):
        """
        Read file into list of raw strings.
        """
        logger.debug("reading file '{}' to raw string list".format(self.path))
        with open(self.path) as f:
            self.data['raw'] = f.readlines()

    def _parse_lines(self):
        """
        Get key-value pairs from text lines and return dictionary.
        """
        rows = [l.rstrip().split(',') for l in self.data['raw']]
        self.data['table'] = dict(list(zip(rows[0], rows[1])))

    def parse(self):
        """
        Parse metrics table and return dictionary.
        """
        self._read_file()
        self._parse_lines()

        return self.data['table']