def generateJSON(geneDot, count, name, out_file_name):
'''
generate JSON file for uploading into RNA 2D browser for visualization
'''
RNA = {}
count = [int(x) for x in count]
RNA["ideograms"] = [{"id": name, "length": len(geneDot), "color": "grey"}]
RNA["tracks"] = [{
"name": "coverage",
"color": "blue",
"type": "plot",
"values": [{
"chr": name,
"values": count
}]
}]
stems = dot2block(geneDot, name)
RNA["tracks"].append({
"name": "stems",
"color": "green",
"type": "links",
"values": stems
})
out = open(out_file_name, 'w')
print >> out, json.dumps(RNA, indent=2)
def generateJSON(geneDot,count,name,out_file_name):
'''
generate JSON file for uploading into RNA 2D browser for visualization
'''
RNA = {}
count=[int(x) for x in count]
RNA["ideograms"]=[{"id":name,"length":len(geneDot),"color":"grey"}]
RNA["tracks"]=[{"name":"coverage","color":"blue","type":"plot","values":[{"chr":name,"values":count}]}]
stems = dot2block(geneDot,name)
RNA["tracks"].append({"name":"stems","color":"green","type":"links","values":stems})
out = open(out_file_name,'w')
print >>out, json.dumps(RNA, indent=2)
import sys from RNAstructure import dot2block stems = dot2block(sys.argv[1],"test") print stems
import sys from RNAstructure import dot2block stems = dot2block(sys.argv[1], "test") print stems
