def load(filepath, db, action=None):
samfile = _load_sam(filepath, db)
sam_data = Sam(db)
chromosome_data = Chromosome(db)
chromosomes = []
for ref in samfile.references:
name = trim_chromosome_name(ref)
c = chromosome_data.get_by_name(name)
c['ref'] = ref
chromosomes.append(c)
filename = os.path.basename(filepath)
sam = sam_data.get_by_filename(filename)
if sam is None:
logging.error('Error : please load "%s" first' % filename)
samId = sam['id']
# cypileup
cypileup.pileup(samfile, chromosomes, samId, db, action)
samfile.close()
def load(filepath, db):
filename = os.path.basename(filepath)
base, ext = os.path.splitext(filepath)
if not re.match('^\.(sam|bam)', ext):
raise UnsupportedFileError('ERROR: Not supported file format')
sam_data = Sam(db)
chr_data = Chromosome(db)
if sam_data.get_by_filename(filename) is not None:
raise AlreadyLoadedError('WARNING: Already loaded "%s"' % filename)
logging.info("Begin to load '%s'" % filename)
# Convert sam to bam
if ext == '.sam':
insam = pysam.Samfile(filepath, 'r')
filepath = base + '.bam'
outbam = pysam.Samfile(filepath, 'wb', template=insam)
for s in insam:
outbam.write(s)
# Create index if not exist
bai = filepath + '.bai'
if not os.path.isfile(bai):
logging.info("Create index '%s'" % os.path.basename(bai))
pysam.index(filepath)
# load sam
samfile = pysam.Samfile(filepath)
sam_data.append(filename,
samfile.header, samfile.lengths,
samfile.mapped,
samfile.nreferences, samfile.references)
# load chromosome
for ref in samfile.references:
chr_data.append(trim_chromosome_name(ref))