4627485829

Build Type

push

github-actions

Committed by karlnyr

Commit Message

remova conda stuff, expand aliases

Run Details

501 of 941 relevant lines covered (53.24%)

0.53 hits per line

Source File
Press 'n' to go to next uncovered line, 'b' for previous

35.48

/demux/utils/hiseq2500_samplesheet.py

"""
    Create a samplesheet for 2500 flowcells
"""

from ..constants.constants import DASH, COMMA, LIMS_KEYS
from .samplesheet import Samplesheet


class Create2500Samplesheet:
    """Create a raw sample sheet for 2500 flowcells"""

    def __init__(self, flowcell: str, index_length: int, raw_samplesheet: list):
        self.flowcell = flowcell
        self.index_length = index_length
        self.raw_samplesheet = raw_samplesheet

    @property
    def header(self) -> list:
        """Create the sample sheet header"""
        return list(Samplesheet.header_map.values())

    @staticmethod
    def is_dual_index(index: str, delimiter=DASH) -> bool:
        """Determines if an index in the raw samplesheet is dual index or not"""
        return delimiter in index

    def remove_unwanted_indexes(self, raw_samplesheet: list) -> list:
        """Remove indexes with length unequal to index_length"""
        raw_samplesheet = [
            line
            for line in raw_samplesheet
            if len(line["index"].replace("-", "")) == self.index_length
        ]

        return raw_samplesheet

    def split_dual_indexes(self, raw_samplesheet: list) -> list:
        """Splits dual indexes"""
        for line in raw_samplesheet:
            if self.is_dual_index(line["index"]):
                index1, index2 = line["index"].split("-")
                line["index"], line["index2"] = index1, index2
        return raw_samplesheet

    def construct_samplesheet(self, end="\n", delimiter=COMMA) -> str:
        """Construct the sample sheet"""
        demux_samplesheet = [delimiter.join(self.header)]
        raw_samplesheet = self.raw_samplesheet
        raw_samplesheet = self.remove_unwanted_indexes(raw_samplesheet)
        raw_samplesheet = self.split_dual_indexes(raw_samplesheet)
        for line in raw_samplesheet:
            line["sample_name"] = line["project"]
            demux_samplesheet.append(
                delimiter.join([str(line[lims_key]) for lims_key in LIMS_KEYS])
            )

        return end.join(demux_samplesheet)

1	"""
2	Create a samplesheet for 2500 flowcells
3	"""
4
5	from ..constants.constants import DASH, COMMA, LIMS_KEYS	1✔
6	from .samplesheet import Samplesheet	1✔
7
8
9	class Create2500Samplesheet:	1✔
10	"""Create a raw sample sheet for 2500 flowcells"""
11
12	def __init__(self, flowcell: str, index_length: int, raw_samplesheet: list):	1✔
13	self.flowcell = flowcell	×
14	self.index_length = index_length	×
15	self.raw_samplesheet = raw_samplesheet	×
16
17	@property	1✔
18	def header(self) -> list:	1✔
19	"""Create the sample sheet header"""
20	return list(Samplesheet.header_map.values())	×
21
22	@staticmethod	1✔
23	def is_dual_index(index: str, delimiter=DASH) -> bool:	1✔
24	"""Determines if an index in the raw samplesheet is dual index or not"""
25	return delimiter in index	×
26
27	def remove_unwanted_indexes(self, raw_samplesheet: list) -> list:	1✔
28	"""Remove indexes with length unequal to index_length"""
29	raw_samplesheet = [	×
30	line
31	for line in raw_samplesheet
32	if len(line["index"].replace("-", "")) == self.index_length
33	]
34
35	return raw_samplesheet	×
36
37	def split_dual_indexes(self, raw_samplesheet: list) -> list:	1✔
38	"""Splits dual indexes"""
39	for line in raw_samplesheet:	×
40	if self.is_dual_index(line["index"]):	×
41	index1, index2 = line["index"].split("-")	×
42	line["index"], line["index2"] = index1, index2	×
43	return raw_samplesheet	×
44
45	def construct_samplesheet(self, end="\n", delimiter=COMMA) -> str:	1✔
46	"""Construct the sample sheet"""
47	demux_samplesheet = [delimiter.join(self.header)]	×
48	raw_samplesheet = self.raw_samplesheet	×
49	raw_samplesheet = self.remove_unwanted_indexes(raw_samplesheet)	×
50	raw_samplesheet = self.split_dual_indexes(raw_samplesheet)	×
51	for line in raw_samplesheet:	×
52	line["sample_name"] = line["project"]	×
53	demux_samplesheet.append(	×
54	delimiter.join([str(line[lims_key]) for lims_key in LIMS_KEYS])
55	)
56
57	return end.join(demux_samplesheet)	×

Clinical-Genomics / demultiplexing / 4627485829

Source File Press 'n' to go to next uncovered line, 'b' for previous

Source File
Press 'n' to go to next uncovered line, 'b' for previous