Python get_samtools_opts Examples

Example #1

File: wrapper.py Project: tdayris/snakemake-wrappers

__author__ = "Filipe G. Vieira"
__copyright__ = "Copyright 2020, Filipe G. Vieira"
__license__ = "MIT"

from snakemake.shell import shell
from snakemake_wrapper_utils.samtools import get_samtools_opts

samtools_opts = get_samtools_opts(snakemake,
                                  parse_write_index=False,
                                  parse_output=False)
extra = snakemake.params.get("extra", "")
log = snakemake.log_fmt_shell(stdout=False, stderr=True)

shell(
    "samtools calmd {samtools_opts} {extra} {snakemake.input.aln} {snakemake.input.ref} > {snakemake.output[0]} {log}"
)

Example #2

File: wrapper.py Project: yztxwd/snakemake-wrappers

__author__ = "Johannes Köster"
__copyright__ = "Copyright 2016, Johannes Köster"
__email__ = "*****@*****.**"
__license__ = "MIT"


from snakemake.shell import shell
from snakemake_wrapper_utils.samtools import get_samtools_opts


samtools_opts = get_samtools_opts(snakemake)
log = snakemake.log_fmt_shell(stdout=True, stderr=True, append=True)


shell(
    "samtools view {snakemake.params.extra} {samtools_opts} -o {snakemake.output[0]} {snakemake.input[0]} {log}"
)

Example #3

File: wrapper.py Project: tdayris/snakemake-wrappers

__author__ = "Michael Chambers"
__copyright__ = "Copyright 2019, Michael Chambers"
__email__ = "*****@*****.**"
__license__ = "MIT"

from snakemake.shell import shell
from snakemake_wrapper_utils.samtools import get_samtools_opts

samtools_opts = get_samtools_opts(snakemake,
                                  parse_threads=False,
                                  parse_write_index=False,
                                  parse_output_format=False)
extra = snakemake.params.get("extra", "")
log = snakemake.log_fmt_shell(stdout=True, stderr=True)

shell("samtools faidx {samtools_opts} {extra} {snakemake.input[0]} {log}")