def enrich_kegg(): "use the input key and value to find contigs, then based on type to generate enrich_info" args = query_format(['key','value']) if args: t_op = 'eq' if type(args['value'])!=list else 'in_' ctg_set = views.contig_v().filter(args['key'],t_op,args['value']) res = views.contig_v(ctg_set).enrich_kegg() return jsonify(res)
def contig_seq():
args = query_format(['key','value','seq_type'])
if args:
t_op = 'eq' if type(args['value'])!=list else 'in_'
ctg_set = views.contig_v().filter(args['key'],t_op,args['value'])
res = views.contig_v(ctg_set).seq_info(args.get('seq_type',None))
if res:
return jsonify({'seqs':res})
def contig_detail():
"based key and value to search contig model, if value contain ',', the operator will be 'in_', not 'eq'"
args = query_format(['key','value'])
res={}
if args:
t_op = 'eq' if type(args['value'])==str else 'in_'
t_contig = views.contig_v().filter(args['key'],t_op,args['value'])
if t_contig.count():
res['ids'] = [x.id for x in t_contig]
res['seqs']=views.contig_v(t_contig).seq_info()
res['count_info']=views.count_v([x.counts.get() for x in t_contig]).data()
res['taxa']=views.contig_v(t_contig).lineage_info()
return jsonify(res)
def contig_fpkm(): args = query_format(['key','value']) if args: t_op = 'eq' if type(args['value'])==str else 'in_' t_contig = views.contig_v().filter(args['key'],t_op,args['value']) t_fpkm = [x.fpkms.get() for x in t_contig if x.fpkms.count()] if t_fpkm: return jsonify(views.fpkm_v(t_fpkm).fpkm())
def contig_search():
"search contig by name"
args = query_format(['name'])
if args:
res = views.contig_v().text_search('name',args['name'])
return jsonify(views.contig_v(res).search_info())