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#!/usr/bin/env python
__author__ = "Gavin Huttley"
__copyright__ = "Copyright 2007-2012, The Cogent Project"
__credits__ = ["Gavin Huttley"]
__license__ = "GPL"
__version__ = "1.5.3"
__maintainer__ = "Gavin Huttley"
__email__ = "gavin.huttley@anu.edu.au"
__status__ = "Production"
def nexus_from_alignment(aln, seq_type, interleave_len=50):
"""returns a nexus formatted string
Arguments:
- seq_type: dna, rna, or protein
- interleave_len: the line width"""
if aln.isRagged():
raise ValueError, "Sequences in alignment are not all the same " +\
"length. Cannot generate NEXUS format."
num_seq = len(aln.Seqs)
if not aln or not num_seq:
return ""
aln_len = aln.SeqLen
nexus_out = ["#NEXUS\n\nbegin data;"]
nexus_out.append(" dimensions ntax=%d nchar=%d;" % (num_seq,
aln_len))
nexus_out.append(" format datatype=%s interleave=yes missing=? " % \
seq_type + "gap=-;")
nexus_out.append(" matrix")
cur_ix = 0
while cur_ix < aln_len:
nexus_out.extend([" %s %s" % (x, y[cur_ix:cur_ix + \
interleave_len]) for x, y in aln.NamedSeqs.items()])
nexus_out.append("")
cur_ix += interleave_len
nexus_out.append(" ;\nend;")
return '\n'.join(nexus_out)
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