def process(args, raw_hud_lines):
"""
@param args: user options from the web or cmdline
@param hud_lines: raw lines of a .hud file
@return: results in convenient text form
"""
out = StringIO()
names, data = hud.decode(raw_hud_lines)
# normalize the names of the isolates
if args.clean_isolates:
names = [Carbone.clean_isolate_element(x) for x in names]
# get the pcs
C_full = np.array(data, dtype=float)
pcs = eigenpop.get_scaled_eigenvectors(C_full, args.diploid_and_biallelic)
# check for sufficient number of eigenvectors
if len(pcs) < args.npcs:
msg_a = 'the number of requested principal components '
msg_b = 'must be no more than the number of OTUs'
raise ValueError(msg_a + msg_b)
# create the R frame
headers = ['otu'] + ['pc%d' % (i+1) for i in range(args.npcs)]
print >> out, '\t'.join(headers)
for i, name in enumerate(names):
typed_row = [name] + [pcs[j][i] for j in range(args.npcs)]
if args.add_indices:
typed_row = [i+1] + typed_row
row = [str(x) for x in typed_row]
print >> out, '\t'.join(row)
return out.getvalue()
def process(args, raw_hud_lines):
"""
@param args: user options from the web or cmdline
@param hud_lines: raw lines of a .hud file
@return: results in convenient text form
"""
out = StringIO()
names, data = hud.decode(raw_hud_lines)
# normalize the names of the isolates
if args.clean_isolates:
names = [Carbone.clean_isolate_element(x) for x in names]
# get the pcs
C_full = np.array(data, dtype=float)
pcs = eigenpop.get_scaled_eigenvectors(C_full, args.diploid_and_biallelic)
# check for sufficient number of eigenvectors
if len(pcs) < args.npcs:
msg_a = 'the number of requested principal components '
msg_b = 'must be no more than the number of OTUs'
raise ValueError(msg_a + msg_b)
# create the R frame
headers = ['otu'] + ['pc%d' % (i + 1) for i in range(args.npcs)]
print >> out, '\t'.join(headers)
for i, name in enumerate(names):
typed_row = [name] + [pcs[j][i] for j in range(args.npcs)]
if args.add_indices:
typed_row = [i + 1] + typed_row
row = [str(x) for x in typed_row]
print >> out, '\t'.join(row)
return out.getvalue()
