def main():
parser = optparse.OptionParser()
parser.add_option('-S', '--sam', action="store_true", dest="is_sam")
parser.add_option('-B', '--bam', action="store_true", dest="is_bam")
options, args = parser.parse_args()
if options.is_bam:
input_fname = args[0]
index_fname = args[1]
out_fname = args[2]
samfile = csamtools.Samfile(filename=input_fname,
mode='rb',
index_filename=index_fname)
elif options.is_sam:
input_fname = args[0]
out_fname = args[1]
samfile = csamtools.Samfile(filename=input_fname, mode='r')
st = SummaryTree(block_size=25,
levels=6,
draw_cutoff=150,
detail_cutoff=30)
for read in samfile.fetch():
st.insert_range(samfile.getrname(read.rname), read.pos,
read.pos + read.rlen)
st.write(out_fname)
finally:
os.unlink(dataset_symlink)
stderr = open(stderr_name).read().strip()
if stderr:
if exit_code != 0:
os.unlink(stderr_name) # clean up
raise Exception("Error Setting BAM Metadata: %s" % stderr)
else:
print stderr
dataset.metadata.bam_index = index_file
# Remove temp file
os.unlink(stderr_name)
# Now use pysam with BAI index to determine additional metadata
try:
bam_file = csamtools.Samfile(filename=dataset.file_name,
mode='rb',
index_filename=index_file.file_name)
dataset.metadata.reference_names = list(bam_file.references)
dataset.metadata.reference_lengths = list(bam_file.lengths)
dataset.metadata.bam_header = bam_file.header
dataset.metadata.read_groups = [
read_group['ID']
for read_group in dataset.metadata.bam_header.get('RG', [])
if 'ID' in read_group
]
dataset.metadata.sort_order = dataset.metadata.bam_header.get(
'HD', {}).get('SO', None)
dataset.metadata.bam_version = dataset.metadata.bam_header.get(
'HD', {}).get('VN', None)
except:
pass
def set_meta(self, dataset, overwrite=True, **kwd):
""" Creates the index for the BAM file. """
# These metadata values are not accessible by users, always overwrite
index_file = dataset.metadata.bam_index
if not index_file:
index_file = dataset.metadata.spec['bam_index'].param.new_file(
dataset=dataset)
# Create the Bam index
# $ samtools index
# Usage: samtools index <in.bam> [<out.index>]
stderr_name = tempfile.NamedTemporaryFile(
prefix="bam_index_stderr").name
command = [
'samtools', 'index', dataset.file_name, index_file.file_name
]
exit_code = subprocess.call(args=command,
stderr=open(stderr_name, 'wb'))
# Did index succeed?
if exit_code == -6:
# SIGABRT, most likely samtools 1.0+ which does not accept the index name parameter.
dataset_symlink = os.path.join(
os.path.dirname(index_file.file_name), '__dataset_%d_%s' %
(dataset.id, os.path.basename(index_file.file_name)))
os.symlink(dataset.file_name, dataset_symlink)
try:
command = ['samtools', 'index', dataset_symlink]
exit_code = subprocess.call(args=command,
stderr=open(stderr_name, 'wb'))
shutil.move(dataset_symlink + '.bai', index_file.file_name)
except Exception as e:
open(stderr_name, 'ab+').write(
'Galaxy attempted to build the BAM index with samtools 1.0+ but failed: %s\n'
% e)
exit_code = 1 # Make sure an exception raised by shutil.move() is re-raised below
finally:
os.unlink(dataset_symlink)
stderr = open(stderr_name).read().strip()
if stderr:
if exit_code != 0:
os.unlink(stderr_name) # clean up
raise Exception("Error Setting BAM Metadata: %s" % stderr)
else:
print stderr
dataset.metadata.bam_index = index_file
# Remove temp file
os.unlink(stderr_name)
# Now use pysam with BAI index to determine additional metadata
try:
bam_file = csamtools.Samfile(filename=dataset.file_name,
mode='rb',
index_filename=index_file.file_name)
dataset.metadata.reference_names = list(bam_file.references)
dataset.metadata.reference_lengths = list(bam_file.lengths)
dataset.metadata.bam_header = bam_file.header
dataset.metadata.read_groups = [
read_group['ID']
for read_group in dataset.metadata.bam_header.get('RG', [])
if 'ID' in read_group
]
dataset.metadata.sort_order = dataset.metadata.bam_header.get(
'HD', {}).get('SO', None)
dataset.metadata.bam_version = dataset.metadata.bam_header.get(
'HD', {}).get('VN', None)
except:
pass