9409416133

Committed 07 Jun 2024 12:01AM UTC coverage: 94.434%. Remained the same

Build # 9409416133

Build Type

Pull #132

github

Committed by

web-flow

Commit Message

Merge 85d054b54 into 61b51548b

Pull Request Pull Request #132: ⬆️ Bump tornado from 6.4 to 6.4.1

Run Details

3071 of 3252 relevant lines covered (94.43%)

0.94 hits per line

Source File
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86.49

/src/data/import_manifest.py

#!/usr/bin/env python3
# -*- coding: utf-8 -*-
"""
Created on Tue Mar  2 10:38:05 2021

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

import click
import logging

from src.features.illumina import read_Manifest
from src.features.smarterdb import (
    Location, global_connection, SupportedChip)
from src.data.common import get_variant_species, update_variant, new_variant

logger = logging.getLogger(__name__)


@click.command()
@click.option('--species_class', type=str, required=True)
@click.option('--manifest', type=str, required=True)
@click.option('--chip_name', type=str, required=True)
@click.option('--version', type=str, required=True)
@click.option('--sender', type=str, required=True)
def main(species_class, manifest, chip_name, version, sender):
    """Load SNP data from Illumina manifest file into SMARTER-database"""

    # determining the proper VariantSpecies class
    VariantSpecie = get_variant_species(species_class)

    # check chip_name
    illumina_chip = SupportedChip.objects(name=chip_name).get()

    # reset chip data (if any)
    illumina_chip.n_of_snps = 0

    logger.info(f"Reading from {manifest}")

    # grep a sample SNP
    for i, record in enumerate(read_Manifest(manifest, delimiter=",")):
        # update chip data indipendentely if it is an update or not
        illumina_chip.n_of_snps += 1

        # create a location object
        location = Location(
            version=version,
            chrom=record.chr,
            position=record.mapinfo,
            illumina=record.snp,
            illumina_strand=record.ilmnstrand,
            strand=record.sourcestrand,
            imported_from="manifest",
            date=record.date,
        )

        variant = VariantSpecie(
            chip_name=[chip_name],
            name=record.name,
            sequence={chip_name: record.sourceseq},
            sender=sender
        )

        # search for a snp in database (relying on name)
        qs = VariantSpecie.objects.filter(name=record.name)

        if qs.count() == 1:
            update_variant(qs, variant, location)

        elif qs.count() == 0:
            new_variant(variant, location)

        if (i+1) % 5000 == 0:
            logger.info(f"{i+1} variants processed")

    # update chip info
    illumina_chip.save()

    logger.info(f"{i+1} variants processed")

    logger.info("Completed")


if __name__ == '__main__':
    log_fmt = '%(asctime)s - %(name)s - %(levelname)s - %(message)s'
    logging.basicConfig(level=logging.INFO, format=log_fmt)

    # connect to database
    global_connection()

    main()

1	#!/usr/bin/env python3
2	# -- coding: utf-8 --
3	"""	1✔
4	Created on Tue Mar 2 10:38:05 2021
5
6	@author: Paolo Cozzi <paolo.cozzi@ibba.cnr.it>
7	"""
8
9	import click	1✔
10	import logging	1✔
11
12	from src.features.illumina import read_Manifest	1✔
13	from src.features.smarterdb import (	1✔
14	Location, global_connection, SupportedChip)
15	from src.data.common import get_variant_species, update_variant, new_variant	1✔
16
17	logger = logging.getLogger(__name__)	1✔
18
19
20	@click.command()	1✔
21	@click.option('--species_class', type=str, required=True)	1✔
22	@click.option('--manifest', type=str, required=True)	1✔
23	@click.option('--chip_name', type=str, required=True)	1✔
24	@click.option('--version', type=str, required=True)	1✔
25	@click.option('--sender', type=str, required=True)	1✔
26	def main(species_class, manifest, chip_name, version, sender):	1✔
27	"""Load SNP data from Illumina manifest file into SMARTER-database"""
28
29	# determining the proper VariantSpecies class
30	VariantSpecie = get_variant_species(species_class)	1✔
31
32	# check chip_name
33	illumina_chip = SupportedChip.objects(name=chip_name).get()	1✔
34
35	# reset chip data (if any)
36	illumina_chip.n_of_snps = 0	1✔
37
38	logger.info(f"Reading from {manifest}")	1✔
39
40	# grep a sample SNP
41	for i, record in enumerate(read_Manifest(manifest, delimiter=",")):	1✔
42	# update chip data indipendentely if it is an update or not
43	illumina_chip.n_of_snps += 1	1✔
44
45	# create a location object
46	location = Location(	1✔
47	version=version,
48	chrom=record.chr,
49	position=record.mapinfo,
50	illumina=record.snp,
51	illumina_strand=record.ilmnstrand,
52	strand=record.sourcestrand,
53	imported_from="manifest",
54	date=record.date,
55	)
56
57	variant = VariantSpecie(	1✔
58	chip_name=[chip_name],
59	name=record.name,
60	sequence={chip_name: record.sourceseq},
61	sender=sender
62	)
63
64	# search for a snp in database (relying on name)
65	qs = VariantSpecie.objects.filter(name=record.name)	1✔
66
67	if qs.count() == 1:	1✔
68	update_variant(qs, variant, location)	1✔
69
70	elif qs.count() == 0:	1✔
71	new_variant(variant, location)	1✔
72
73	if (i+1) % 5000 == 0:	1✔
74	logger.info(f"{i+1} variants processed")	×
75
76	# update chip info
77	illumina_chip.save()	1✔
78
79	logger.info(f"{i+1} variants processed")	1✔
80
81	logger.info("Completed")	1✔
82
83
84	if __name__ == '__main__':	1✔
85	log_fmt = '%(asctime)s - %(name)s - %(levelname)s - %(message)s'	×
86	logging.basicConfig(level=logging.INFO, format=log_fmt)	×
87
88	# connect to database
89	global_connection()	×
90
91	main()	×

cnr-ibba / SMARTER-database / 9409416133

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