# This lets us handle whether to write to a log file or to write to stdout.
# See snakemake.script.log_fmt_shell for details.
if snakemake.log:
snakemake.log = os.path.realpath(str(snakemake.log))
log = snakemake.log_fmt_shell(stdout=False)
# Get directories that I need to move between
cwd = os.getcwd()
tmpdir = gettempdir()
# tin uses the name of the BAM to create outputs. In order to write outputs to
# tmp I need to copy the BAM over to tmp.
bam = NamedTemporaryFile(suffix='.bam').name
bed = NamedTemporaryFile(suffix='.bed').name
name = bam.rstrip('.bam')
shell('cp {snakemake.input.bam} {bam} '
'&& cp {snakemake.input.bam}.bai {bam}.bai '
'&& cp {snakemake.input.bed} {bed}')
os.chdir(tmpdir)
shell('tin.py ' '-i {bam} ' '-r {bed} ' '{extra} ' '{log}')
# Cleanup 1
shell('rm {bam} ' '&& rm {bam}.bai ' '&& rm {bed}')
# Move outputs
os.chdir(cwd)
shell('cp {name}.tin.xls {snakemake.output.table} '
'&& cp {name}.summary.txt {snakemake.output.summary} '
