annotate corebio/seq_io/nexus_io.py @ 9:f3462128e87c

Minor alterations to the galaxy interface with some better examples and error messages added.

#!/usr/bin/env python

# Copyright 2005 Gavin E. Crooks <[e-mail]>
# Copyright 2005-2006 The Regents of the University of California.
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"""Read the sequence data from a nexus file.

This IO code only gives read access to the sequence data.

Reference:
'NEXUS: An extensible file format for systematic information'
Maddison, Swofford, Maddison. 1997. Syst. Biol. 46(4):590-621
"""

from corebio.seq import Seq, SeqList, Alphabet
from corebio.seq_io._nexus import Nexus, safename





names = ( 'nexus', 'paup')
extensions = ('nex', 'nexus', 'paup', 'nxs')

def iterseq(fin, alphabet=None):
    """Iterate over the sequences in the file."""
    # Default implementation
    return iter(read(fin, alphabet) )


def read(fin, alphabet=None):          
    """ Extract sequence data from a nexus file."""
    n = Nexus(fin)
    
    seqs = []
    for taxon in n.taxlabels:   
        name = safename(taxon)
        r = n.matrix[taxon]
        if alphabet is None  :
            s = Seq(r, name = name, alphabet=r.alphabet)
        else :
            s = Seq(r, name = name, alphabet=alphabet )
        seqs.append(s)

    if len(seqs) == 0 :
        # Something went terrible wrong.
        raise ValueError("Cannot parse file")
        
    return SeqList(seqs)