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from __future__ import print_function
#import sys
import os
#from os import listdir
#from os.path import isfile, join
import logging
from seqcluster.libs.read import load_data, get_sequences_from_cluster, map_to_precursors, get_precursors_from_cluster
logger = logging.getLogger('explore')
def explore(args):
"""Create mapping of sequences of two clusters
"""
logger.info("Reading sequences")
data = load_data(args.json)
logger.info("Get sequences from json")
#get_sequences_from_cluster()
c1, c2 = args.names.split(",")
seqs, names = get_sequences_from_cluster(c1, c2, data[0])
loci = get_precursors_from_cluster(c1, c2, data[0])
logger.info("Map all sequences to all loci")
print("%s" % (loci))
map_to_precursors(seqs, names, loci, os.path.join(args.out, "map.tsv"), args)
#map_sequences_w_bowtie(sequences, precursors)
logger.info("Plot sequences on loci")
#get_matrix_position()
#plot_sequences()
logger.info("Done")
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