src.features.illumina

Created on Mon Feb 8 17:15:26 2021

@author: Paolo Cozzi <paolo.cozzi@ibba.cnr.it>

class src.features.illumina.IlluSNP(sequence=None, max_iter=10)

Bases: object

__init__(sequence=None, max_iter=10)

Define a IlluSNP class

findSNP(sequence)

Find snp (eg [A/G] in sequence (0-based)

fromSequence(sequence, max_iter=10)

Define a IlluSNP from a sequence

isUnambiguous(snp)

Return True if snp is unambiguous

toTop()

Convert a BOT sequence into TOP

exception src.features.illumina.IlluSNPException(value=None)

Bases: Exception

Base exception class for IlluSNP

__init__(value=None)

src.features.illumina.read_Manifest(path: str, size=2048, skip=0, delimiter=None)

src.features.illumina.read_illuminaRow(path: str, size=2048)

src.features.illumina.read_snpList(path: str, size=2048, skip=0, delimiter=None)

src.features.illumina.read_snpMap(path: str, size=2048, skip=0, delimiter=None)

src.features.illumina.search_manifactured_date(header: list) → datetime | None

Grep manifactured date from illumina header

Parameters:

header (list) – the illumina header skipped lines

Returns:

a datetime object

Return type:

datetime.datetime

src.features.illumina.skip_lines(handle, skip) → Tuple[int, list]

src.features.illumina.skip_until_section(handle, section) → Tuple[int, list]

Ignore lines until a precise sections

src.features.illumina.sniff_file(handle, size, position=0)