secs = time()
if exists(otufolder + "clusters.txt"):
clustersin = open(otufolder + "clusters.txt")
currclust = ""
for header, seq in MinimalFastaParser(clustersin):
if "cluster_" in header:
currclust = header
clusters[currclust] = []
else:
clusters[currclust].append((header, seq))
clustersin.close()
print "Sequences previously clustered,", len(clusters), "clusters"
else:
print "Running uclust over sequences"
#cluster the initial sequences by sequence simmilarity
clusters = cluster_seqs(args.i, args.sim, folderout=args.o,
gapopen='10.0', gapext='10.0')
#print that shit to file
cout = open(otufolder + "clusters.txt", 'w')
hold = clusters.keys()
hold.sort()
for cluster in hold:
cout.write(">%s\n%s\n" % (cluster, cluster))
for seq in clusters[cluster]:
cout.write(">%s\n%s\n" % seq)
cout.close()
print str(len(clusters)) + " clusters"
print "Runtime: " + str((time() - secs)/60) + " min"
if not exists(otufolder + "cluster_structs.fasta"):
#create file to write to if not already there
# dont need to do anything since already folded by next step
print "Sequences previously clustered"
with open(clustfile) as fin:
numclusts = int(fin.readline().strip())
elif exists(clustfile):
# already clustered but not folded, so read in clusters
with open(clustfile) as fin:
clusters, numclusts = read_clusters(fin)
print "Sequences previously clustered, %i clusters" % numclusts
else:
print "Running uclust over sequences"
# cluster the initial sequences by sequence simmilarity
clusters = cluster_seqs(args.i,
args.sim,
folderout=args.o,
gapopen='1.0',
gapext='1.0')
with open(clustfile, 'w') as fout:
write_clusters(clusters, fout)
numclusts = len(clusters)
clusters.clear()
del clusters
print "Runtime: %0.2f min" % ((time() - secs) / 60)
if not exists(structfile):
# create file to write to if not already there
with open(structfile, 'w'):
pass
print "Running BayesFold over %i clusters" % numclusts
secs = time()
