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from optparse import OptionParser
usagetxt = "usage: %prog -r res_seqcluster -c clusters_id -o outputdir"
parser = OptionParser(usage=usagetxt, version="%prog 0.1")
parser.add_option("-c", "--clusterid", dest="clus",
help="", metavar="FILE")
parser.add_option("-r", "--results", dest="res",
help="", metavar="FILE")
parser.add_option("-o", "--output", dest="out",
help="", metavar="FILE")
(options, args) = parser.parse_args()
clus = {}
c = open(options.clus, 'r')
for line in c:
line = line.strip()
clus[line] = 0
c.close()
isin = 0
f = open(options.res, 'r')
for line in f:
line = line.strip()
if not "#" in line:
if "C:" in line:
if isin==1:
out.close()
outfa.close()
isin = 0
if line in clus:
out = open(options.out+"/"+line, 'w')
outfa = open(options.out+"/"+line+".fa", 'w')
out.write(line+"\n")
isin = 1
else:
if isin == 1:
out.write(line+"\n")
if "seq_" in line:
cols = line.split(" ")
outfa.write(">"+cols[0]+"\n"+cols[1]+"\n")
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