def test_run_sambamba():
bam = 'tests/fixtures/ccds.mini.sorted.bam'
bed = 'tests/fixtures/CCDS.mini.bed'
out = '/tmp/ccds.coverage.bed'
thresholds = (10, 20)
run_sambamba(bam, bed, outfile=out, cov_treshold=thresholds)
assert os.path.exists(out)
def sambamba():
"""Run Sambamba for an alignment."""
bam_file = request.form['bam']
region_bed = request.form['bed']
cov_thresholds = request.form.getlist('threshold')
out_file = request.form['out']
run_sambamba(bam_file, region_bed, out_file, cov_thresholds)
return jsonify(success=True)
def sambamba(context, bam_file, exon_bed, gene_bed, cov_treshold, outfile):
"""Run Sambamba from chanjo."""
logger = logging.getLogger(__name__)
# For testing only:
logger = logging.getLogger("chanjo.cli.sambamba")
logger.info("Running chanjo sambamba")
if not (exon_bed or gene_bed):
logger.warning("Please provide a region file in BED format")
sys.exit()
if exon_bed and gene_bed:
logger.warning("Only one region file at a time")
sys.exit()
region_file = exon_bed
if gene_bed:
region_file = gene_bed
try:
run_sambamba(bam_file, region_file, outfile, cov_treshold)
except Exception as e:
logger.debug(e)
click.Abort()
def sambamba(context, bam_file, exon_bed, gene_bed, cov_treshold, outfile):
"""Run Sambamba from chanjo."""
logger = logging.getLogger(__name__)
# For testing only:
logger = logging.getLogger("chanjo.cli.sambamba")
logger.info("Running chanjo sambamba")
if not (exon_bed or gene_bed):
logger.warning("Please provide a region file in BED format")
sys.exit()
if exon_bed and gene_bed:
logger.warning("Only one region file at a time")
sys.exit()
region_file = exon_bed
if gene_bed:
region_file = gene_bed
try:
run_sambamba(bam_file, region_file, outfile, cov_treshold)
except Exception as e:
logger.debug(e)
click.Abort()
