padaligner

import os, sys

scriptdir = sys.path[0]

if os.path.basename(scriptdir).startswith('bin'):
	sys.path.append( os.path.dirname(scriptdir) )
else:
	pass

from satelib.alignment import Alignment, SequenceDataset

argc = len(sys.argv)
if argc == 4:
	datatype, seqfn, outp = sys.argv[1:]
	second_inp = None
elif argc == 5:
	datatype, seqfn, second_inp, outp = sys.argv[1:]
else:
	sys.exit("Expecting DNA|PROTEIN <input1> [input2] <output>")

datatype = datatype.upper()
if datatype not in ["DNA", "PROTEIN"]:
	raise Exception("Expecting the datatype to by DNA or PROTEIN\n")

sd = SequenceDataset()
try:
	fileobj = open(seqfn, 'rU')
	sd.read(fileobj, file_format='FASTA', datatype=datatype)
	alignment = sd.relabel_for_sate(make_names_safe=False)
except Exception, x:
	raise Exception("Error reading file:\n%s\n" % str(x))

if second_inp:
	sd = SequenceDataset()
	try:
		fileobj = open(second_inp, 'rU')
		sd.read(fileobj, file_format='FASTA', datatype=datatype)
		alignment2 = sd.relabel_for_sate(make_names_safe=False)
	except Exception, x:
		raise Exception("Error reading file:\n%s\n" % str(x))
else:
	alignment2  = {}

for k in alignment2.keys():
	if k in alignment:
		sys.exit("Taxon %s was found in both alignments" % k)
alignment.update(alignment2)
max_len = 0
x = []
for k, v in alignment.iteritems():
	gapless_v = ''.join(v.split('-'))
	max_len = max(max_len, len(gapless_v))
	x.append((k, gapless_v))

o = open(outp, 'w')
for el in x:
	k, v = el
	num_gaps = int(max_len - len(v))
	gaps = '-'*num_gaps
	o.write('>%s\n%s%s\n' % (k, v, gaps))
o.close()