Module cstag.consensus

Functions

def condense_deletions(s: str) ‑> str

def consensus(cs_tags: list[str], positions: list[int], prefix: bool = False) ‑> str

generate consensus of cs tags

Args

cs_tags : list

cs tags in the long format

positions : list

1-based leftmost mapping position (4th column in SAM file)

prefix : bool, optional

Whether to add the prefix 'cs:Z:' to the cs tag. Defaults to False

Return

str: a consensus of cs tag in the long format

Example

>>> import cstag
>>> cs_tags = ["=ACGT", "=AC*gt=T", "=C*gt=T", "=C*gt=T", "=ACT+ccc=T"]
>>> positions = [1,1,1,2,1]
>>> cstag.consensus(cs_tags, positions)
'=AC*gt=T'

def expand_deletion_tags(tags_combined: list[str]) ‑> list[str]

def get_consensus(cs_tags: list[list[str]]) ‑> str

def normalize_positions(positions: list[int]) ‑> list[int]

Normalize the positions in the given list by shifting them so that the minimum position becomes zero.

def normalize_read_lengths(cs_tags: list[str], positions: list[int]) ‑> list[list[str]]

Normalize the lengths of each read in cs_tags based on their starts positions. If the length is insufficient, fill in with None.

Args

cs_tags : list[str]

list of cs tags.

positions : list[int]

Starting positions of each read.

Returns

list[list[str]]

list of lists representing the reads, now normalized to the same length.

def split_cs_tags(cs_tags: list[str]) ‑> list[list[str]]

Split and process each cs tag in cs_tags.

Args

cs_tags : list[str]

list of cs tags in the long format.

Returns

list[list[str]]

list of processed cs tags.

def split_deletion(cs_tag: str) ‑> list[str]