def do_pred_bam(self, inpath_bam, outpath_npy):
if os.stat(inpath_bam).st_size != 0:
pre, ext = os.path.splitext(inpath_bam)
temp_fasta = "{}.fasta".format(pre)
# create the file upfront, so pysam can open it
with open(temp_fasta, 'w') as fp:
pass
pysam.fasta("-@", str(self.cores - 1), inpath_bam, save_stdout=temp_fasta)
self.do_pred_fasta(temp_fasta, outpath_npy)
else:
np.save(outpath_npy, np.empty(0))
def get_mapped_fasta(self, inpath, outpath, single=False):
# set output in both pysam wrapper and samtools argument list
outpath_fasta_1 = outpath + "_1.fasta"
# create the file upfront, so pysam can open it
with open(outpath_fasta_1, 'w') as fp:
pass
if single:
pysam.fasta("-G 4", "-@", self.c_threads, inpath, save_stdout=outpath_fasta_1)
return outpath_fasta_1, ""
else:
pysam.fasta("-NG 12", "-f 64", "-@", self.c_threads, inpath, save_stdout=outpath_fasta_1)
outpath_fasta_2 = outpath + "_2.fasta"
# create the file upfront, so pysam can open it
with open(outpath_fasta_2, 'w') as fp:
pass
pysam.fasta("-NG 12", "-f 128", "-@", self.c_threads, inpath, save_stdout=outpath_fasta_2)
return outpath_fasta_1, outpath_fasta_2
def setUpClass(cls):
# convert bam to reads
pysam.fasta(cls.__reads_bam__, save_stdout=cls.__reads_fasta__.name)