def main(args):
species2counts = {}
for species in args['species']:
hmmoutfiles = glob.glob(args['hmmoutdir'] + "/" + species + "*.hmmout")
if not len(hmmoutfiles) == 1:
sys.exit("ERROR: no single hmmout file found for species %s" %
species)
if args.has_key('pidsfile'):
pidsfiles = glob.glob(args['pidsdir'] + "/" + species + "*.gids")
if not len(pidsfiles) == 1:
sys.exit("ERROR: no single pids file found for species %s" %
species)
pids = get_pids(pidsfiles[0]).keys()
else:
pids = False
species2counts[species] = did2count(hmmoutfiles[0], pids)
ignore = {}
if args.has_key('ignorefile'): ignore = get_pids(args['ignorefile'])
hash = {}
for s, counts in species2counts.iteritems():
for did in counts.keys():
if not ignore.has_key(did): hash[did] = 1
fwt = open("pfam-table", "w")
fwt.write(string.join(["DID"] + args['species'], "\t") + "\n")
for did in hash.keys():
out = did
for species in args['species']:
count = 0
if species2counts[species].has_key(did):
count = species2counts[species][did]
out += "\t" + str(count)
fwt.write(out + "\n")
fwt.close()
fwm = open("pfam-matrix.csv", "w")
fwm.write("," + string.join(args['species'], ",") + "\n")
for i in range(len(args['species'])):
s1 = args['species'][i]
fwm.write(s1)
for j in range(len(args['species'])):
if i == j:
fwm.write(",1")
continue
s2 = args['species'][j]
v1, v2 = [], []
for did in hash.keys():
v1.append(species2counts[s1].get(did, 0))
v2.append(species2counts[s2].get(did, 0))
cor, p = stats.correlate(v1, v2)
fwm.write("," + str(cor))
#print string.join([s1, s2, str(cor), str(p)], "\t")#
fwm.write("\n")
fwm.close()
def score_pair(v1, v2, method=1):
if method == 1:
cor, p = stats.correlate(v1, v2)
return cor
elif method == 2:
x1, x2 = [], []
for i in range(len(v1)):
if v1[i] != 0 or v2[i] != 0: x1.append(v1[i]), x2.append(v2[i])
cor, p = stats.correlate(x1, x2)
return cor
elif method == 3:
up = 0
for i in range(len(v1)):
if v1[i] != 0 and v2[i] != 0: up += 1
return 1.0 * up / len(v1)
elif method == 4:
up = 0
for i in range(len(v1)):
if v1[i] != 0 and v2[i] != 0: up += 1
return up
def score_pair(v1, v2, method=1):
if method == 1:
cor, p = stats.correlate(v1, v2)
return cor
elif method == 2:
x1, x2 = [], []
for i in range(len(v1)):
if v1[i] != 0 or v2[i] != 0: x1.append(v1[i]), x2.append(v2[i])
cor, p = stats.correlate(x1, x2)
return cor
elif method == 3:
up = 0
for i in range(len(v1)):
if v1[i] != 0 and v2[i] != 0: up += 1
return 1.0*up/len(v1)
elif method == 4:
up = 0
for i in range(len(v1)):
if v1[i] != 0 and v2[i] != 0: up += 1
return up
def main( args ):
species2counts = {}
for species in args['species']:
hmmoutfiles = glob.glob(args['hmmoutdir'] + "/" + species + "*.hmmout")
if not len(hmmoutfiles) == 1: sys.exit("ERROR: no single hmmout file found for species %s" % species)
if args.has_key('pidsfile'):
pidsfiles = glob.glob(args['pidsdir'] + "/" + species + "*.gids")
if not len(pidsfiles) == 1: sys.exit("ERROR: no single pids file found for species %s" % species)
pids = get_pids(pidsfiles[0]).keys()
else: pids = False
species2counts[species] = did2count(hmmoutfiles[0], pids)
ignore = {}
if args.has_key('ignorefile'): ignore = get_pids(args['ignorefile'])
hash = {}
for s, counts in species2counts.iteritems():
for did in counts.keys():
if not ignore.has_key(did): hash[did] = 1
fwt = open("pfam-table", "w")
fwt.write(string.join(["DID"] + args['species'], "\t") + "\n")
for did in hash.keys():
out = did
for species in args['species']:
count = 0
if species2counts[species].has_key(did): count = species2counts[species][did]
out += "\t" + str(count)
fwt.write(out + "\n")
fwt.close()
fwm = open("pfam-matrix.csv", "w")
fwm.write("," + string.join(args['species'], ",") + "\n")
for i in range(len(args['species'])):
s1 = args['species'][i]
fwm.write(s1)
for j in range(len(args['species'])):
if i == j:
fwm.write(",1")
continue
s2 = args['species'][j]
v1, v2 = [], []
for did in hash.keys():
v1.append(species2counts[s1].get(did, 0))
v2.append(species2counts[s2].get(did, 0))
cor, p = stats.correlate(v1, v2)
fwm.write("," + str(cor))
#print string.join([s1, s2, str(cor), str(p)], "\t")#
fwm.write("\n")
fwm.close()
