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# Bioconvert is a project to facilitate the interconversion #
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"""Convert :term:`CRAM` file to :term:`SAM` format"""
import os
import colorlog
from bioconvert import ConvBase
from bioconvert.core.base import ConvArg
from bioconvert.core.decorators import requires
logger = colorlog.getLogger(__name__)
[docs]class CRAM2SAM(ConvBase):
"""Convert :term:`CRAM` file to :term:`SAM` file
The conversion requires the reference corresponding to the input file
It can be provided as an argument with the standalone (*-\\-reference*).
Otherwise, users are asked to provide it.
Methods available are based on samtools [SAMTOOLS]_.
"""
#: Default value
_default_method = "samtools"
_threading = True
def __init__(self, infile, outfile, *args, **kargs):
""".. rubric:: constructor
:param str infile: input CRAM file
:param str outfile: output SAM filename
"""
super(CRAM2SAM, self).__init__(infile, outfile, *args, **kargs)
def _get_reference(self):
# In case the --reference is not used
msg = "Please enter the reference corresponding "
msg += "to the input BAM file:"
reference = input(msg)
if os.path.exists(reference) is False:
raise IOError("Reference required")
else:
logger.debug("Reference exists ({}).".format(reference))
return reference
@classmethod
def get_additional_arguments(cls):
yield ConvArg(
names="--reference",
default=None,
help="the reference used (FASTA format). If not provided, prompt will appear",
)