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import os
import shutil
import logging
#try:
# from bcbio.install import _set_matplotlib_default_backend
# _set_matplotlib_default_backend()
#except (ImportError, OSError, IOError):
# pass
#import matplotlib
#matplotlib.use('Agg', force=True)
from seqcluster.libs.read import load_data
from seqcluster.libs.report import make_profile
from seqcluster.libs.utils import safe_dirs
from seqcluster.db import make_database
from seqcluster import templates
logger = logging.getLogger('report')
def report(args):
"""
Create report in html format
"""
logger.info("Reading sequences")
data = load_data(args.json)
profilesDir=os.path.join(args.out, "profiles")
logger.info("Creating profile (%s)" % profilesDir)
data = make_profile(data, profilesDir, args)
logger.info("Creating database")
make_database(data, "seqcluster.db", args.out, True)
logger.info("Done. Download https://github.com/lpantano/seqclusterViz/archive/master.zip to browse the output.")
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