source: branches/help/GDE/SATIVA/sativa/epac/ete2/seqgroup.py

__VERSION__="ete2-2.2rev1026" 
# -*- coding: utf-8 -*-
# #START_LICENSE###########################################################
#  !!!!This is a hacked version by Jiajie Zhang!!!!!
#  !!!!The internally used sequence id is exposed!!!!!
#
# This file is part of the Environment for Tree Exploration program
# (ETE).  http://ete.cgenomics.org
#  
# ETE is free software: you can redistribute it and/or modify it
# under the terms of the GNU General Public License as published by
# the Free Software Foundation, either version 3 of the License, or
# (at your option) any later version.
#  
# ETE is distributed in the hope that it will be useful, but WITHOUT
# ANY WARRANTY; without even the implied warranty of MERCHANTABILITY
# or FITNESS FOR A PARTICULAR PURPOSE.  See the GNU General Public
# License for more details.
#  
# You should have received a copy of the GNU General Public License
# along with ETE.  If not, see <http://www.gnu.org/licenses/>.
#
# 
#                     ABOUT THE ETE PACKAGE
#                     =====================
# 
# ETE is distributed under the GPL copyleft license (2008-2011).  
#
# If you make use of ETE in published work, please cite:
#
# Jaime Huerta-Cepas, Joaquin Dopazo and Toni Gabaldon.
# ETE: a python Environment for Tree Exploration. Jaime BMC
# Bioinformatics 2010,:24doi:10.1186/1471-2105-11-24
#
# Note that extra references to the specific methods implemented in 
# the toolkit are available in the documentation. 
# 
# More info at http://ete.cgenomics.org
#
# 
# #END_LICENSE#############################################################

"""
The 'seqgroup' module provides methods and classes to operate with
Multiple Sequence Files, including Multiple Sequence Alignments.

Currently, Fasta, Phylip sequencial and Phylip interleaved formats are
supported.
"""

from fasta import read_fasta, write_fasta, write_fasta_internal
from paml import read_paml, write_paml
from phylip import read_phylip, write_phylip

__all__ = ["SeqGroup"]

class SeqGroup(object):
    """
    SeqGroup class can be used to store a set of sequences (aligned
    or not).


    :argument sequences: Path to the file containing the sequences or,
        alternatively, the text string containing the same
        information.

    :argument fasta format: the format in which sequences are
        encoded. Current supported formats are: ``fasta``, ``phylip``
        (phylip sequencial) and ``iphylip`` (phylip
        interleaved). Phylip format forces sequence names to a maximum
        of 10 chars. To avoid this effect, you can use the relaxed
        phylip format: ``phylip_relaxed`` and ``iphylip_relaxed``.

    ::

     msf = ">seq1\\nAAAAAAAAAAA\\n>seq2\\nTTTTTTTTTTTTT\\n"
     seqs = SeqGroup(msf, format="fasta")
     print seqs.get_seq("seq1")
     """

    def __len__(self):
        return len(self.id2seq)

    def __contains__(self, item):
        return item in self.name2id

    def __str__(self):
        return write_fasta(self)

    def __iter__(self):
        return self.iter_entries()

    def __init__(self, sequences=None , format="fasta", fix_duplicates=True, **kwargs):
        self.parsers = {
            "fasta": [read_fasta, write_fasta, {}],
            "fasta_internal": [read_fasta, write_fasta_internal, {}],
            "phylip": [read_phylip, write_phylip, {"interleaved":False, "relaxed":False}],
            "iphylip": [read_phylip, write_phylip, {"interleaved":True, "relaxed":False}],
            "phylip_relaxed": [read_phylip, write_phylip, {"interleaved":False, "relaxed":True}],
            "iphylip_relaxed": [read_phylip, write_phylip, {"interleaved":True, "relaxed":True}],
            "paml"   : [read_paml  , write_paml  , kwargs                   ]
            }

        self.id2name = {}
        self.name2id = {}
        self.id2comment= {}
        self.id2seq = {}

        if sequences is not None:
            format = format.lower()
            if format in self.parsers:
                read = self.parsers[format][0]
                args = self.parsers[format][2]
                read(sequences, obj=self, fix_duplicates=fix_duplicates, **args)
            else:
                raise ValueError, "Unsupported format: [%s]" %format

    def __repr__(self):
        return "SeqGroup (%s)" %hex(self.__hash__())

    def write(self, format="fasta", outfile=None):
        """ Returns the text representation of the sequences in the
        supplied given format (default=FASTA). If "oufile" argument is
        used, the result is written into the given path."""

        format = format.lower()
        if format in self.parsers:
            write = self.parsers[format][1]
            args = self.parsers[format][2]
            return write(self, outfile, **args)
        else:
            raise ValueError, "Unsupported format: [%s]" %format

    def iter_entries(self):
        """ Returns an iterator over all sequences in the
        collection. Each item is a tuple with the sequence name,
        sequence, and sequence comments """
        for i, seq in self.id2seq.iteritems():
            yield self.id2name[i], seq, self.id2comment.get(i, []), i

    def get_seq(self, name):
        """ Returns the sequence associated to a given entry name."""
        return self.id2seq[self.name2id[name]]
        
    def get_seqbyid(self, iid):
        return self.id2seq[iid]
    
    def get_comment(self, name):
        return self.id2comment[self.name2id[name]]
        
    def get_name(self, sid):
        return self.id2name[sid]

    def get_entries(self):
        """ Returns the list of entries currently stored."""
        keys = self.id2seq.keys()
        seqs = self.id2seq.values()
        comments = [self.id2comment.get(x, []) for x in  keys]
        names = map(lambda x: self.id2name[x], keys)
        return zip(names, seqs, comments)

    def set_seq(self, name, seq, comments = None):
        """Updates or adds a sequence """
        if comments is None:
            comments = []
        name = name.strip()
        seq = seq.replace(" ", "")
        seq = seq.replace("\t", "")
        seq = seq.replace("\n", "")
        seq = seq.replace("\r", "")
        seqid = self.name2id.get(name, max([0]+self.name2id.values())+1)
        self.name2id[name] = seqid
        self.id2name[seqid] = name
        self.id2comment[seqid] = comments
        self.id2seq[seqid] = seq

    def add_name_prefix(self, prefix):
        for sid in self.id2name.iterkeys():
            old_name = self.id2name[sid]
            new_name = prefix + old_name
            self.name2id[new_name] = self.name2id.pop(old_name)
            self.id2name[sid] = new_name

    def has_seq(self, name):
        return (name in self.name2id)