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#! /usr/bin/env python
##############################################################################
## DendroPy Phylogenetic Computing Library.
##
## Copyright 2010-2015 Jeet Sukumaran and Mark T. Holder.
## All rights reserved.
##
## See "LICENSE.rst" for terms and conditions of usage.
##
## If you use this work or any portion thereof in published work,
## please cite it as:
##
## Sukumaran, J. and M. T. Holder. 2010. DendroPy: a Python library
## for phylogenetic computing. Bioinformatics 26: 1569-1571.
##
##############################################################################
"""
Implementation of FASTA-format data reader.
"""
from dendropy.dataio import ioservice
from dendropy.utility.error import DataParseError
from dendropy.utility import deprecate
class FastaReader(ioservice.DataReader):
"Encapsulates loading and parsing of a FASTA format file."
def __init__(self, **kwargs):
"""
Keyword Arguments
-----------------
data_type: str
When reading into a |DataSet| object, the type of data must be
specified: "dna", "rna", "protein", "restriction", "infinite",
"standard", or "continuous".
default_state_alphabet: |StateAlphabet| instance
A |StateAlphabet| object to be used to manage the alphabet of the
characters (|StandardCharacterMatrix| **only**).
"""
ioservice.DataReader.__init__(self)
self.data_type = kwargs.pop("data_type", None)
self.default_state_alphabet = kwargs.pop("default_state_alphabet", None)
if self.default_state_alphabet is not None:
if self.data_type is None:
self.data_type = "standard"
elif self.data_type != "standard":
raise ValueError("Cannot specify 'default_state_alphabet' with data type of '{}'".format(self.data_type))
self.check_for_unused_keyword_arguments(kwargs)
def _read(self,
stream,
taxon_namespace_factory=None,
tree_list_factory=None,
char_matrix_factory=None,
state_alphabet_factory=None,
global_annotations_target=None):
taxon_namespace = taxon_namespace_factory(label=None)
if self.data_type is None:
raise TypeError("Data type must be specified for this schema")
if self.data_type == "standard" and self.default_state_alphabet is not None:
char_matrix = char_matrix_factory(
self.data_type,
label=None,
taxon_namespace=taxon_namespace,
default_state_alphabet=self.default_state_alphabet,
)
else:
char_matrix = char_matrix_factory(
self.data_type,
label=None,
taxon_namespace=taxon_namespace)
symbol_state_map = char_matrix.default_state_alphabet.full_symbol_state_map
curr_vec = None
curr_taxon = None
for line_index, line in enumerate(stream):
s = line.strip()
if not s:
continue
if s.startswith('>'):
name = s[1:].strip()
curr_taxon = taxon_namespace.require_taxon(label=name)
if curr_taxon in char_matrix:
raise DataParseError(message="FASTA error: Repeated sequence name ('{}') found".format(name), line_num=line_index + 1, stream=stream)
if curr_vec is not None and len(curr_vec) == 0:
raise DataParseError(message="FASTA error: Expected sequence, but found another sequence name ('{}')".format(name), line_num=line_index + 1, stream=stream)
curr_vec = char_matrix[curr_taxon]
elif curr_vec is None:
raise DataParseError(message="FASTA error: Expecting a lines starting with > before sequences", line_num=line_index + 1, stream=stream)
else:
states = []
for col_ind, c in enumerate(s):
c = c.strip()
if not c:
continue
try:
state = symbol_state_map[c]
except KeyError:
raise DataParseError(message="Unrecognized sequence symbol '{}'".format(c), line_num=line_index + 1, col_num=col_ind + 1, stream=stream)
states.append(state)
curr_vec.extend(states)
product = self.Product(
taxon_namespaces=None,
tree_lists=None,
char_matrices=[char_matrix])
return product
class DnaFastaReader(FastaReader):
def __init__(self, **kwargs):
deprecate.dendropy_deprecation_warning(
preamble="Deprecated since DendroPy 4:",
old_construct="d = dendropy.CharacterMatrix.get_from_path(schema='dnafasta', ...)\nd = dendropy.DataSet.get_from_path(schema='dnafasta', ...)",
new_construct="d = dendropy.DnaCharacterMatrix.get(path=..., schema='fasta', ...)\nd = dendropy.DataSet.get(path=..., schema='fasta', data_type='dna', ...)",
stacklevel=7)
# raise TypeError("'dnafasta' is no longer a supported schema: use 'schema=\"fasta\"' with the 'DnaCharacterMatrix.get()' method instead or 'schema=\"fasta\"' and 'data_type=\"dna\" with the 'DataSet.get()' or 'DataSet.read()' methods")
kwargs["data_type"] = "dna"
FastaReader.__init__(self, **kwargs)
class RnaFastaReader(FastaReader):
def __init__(self, **kwargs):
deprecate.dendropy_deprecation_warning(
preamble="Deprecated since DendroPy 4:",
old_construct="d = dendropy.CharacterMatrix.get_from_path(schema='rnafasta', ...)\nd = dendropy.DataSet.get_from_path(schema='rnafasta', ...)",
new_construct="d = dendropy.RnaCharacterMatrix.get(path=..., schema='fasta', ...)\nd = dendropy.DataSet.get(path=..., schema='fasta', data_type='rna', ...)",
stacklevel=7)
# raise TypeError("'rnafasta' is no longer a supported schema: use 'schema=\"fasta\"' with the 'RnaCharacterMatrix.get()' method instead or 'schema=\"fasta\"' and 'data_type=\"dna\" with the 'DataSet.get()' or 'DataSet.read()' methods")
kwargs["data_type"] = "rna"
FastaReader.__init__(self, **kwargs)
class ProteinFastaReader(FastaReader):
def __init__(self, **kwargs):
deprecate.dendropy_deprecation_warning(
preamble="Deprecated since DendroPy 4:",
old_construct="d = dendropy.CharacterMatrix.get_from_path(schema='proteinfasta', ...)\nd = dendropy.DataSet.get_from_path(schema='proteinfasta', ...)",
new_construct="d = dendropy.ProteinCharacterMatrix.get(path=..., schema='fasta', ...)\nd = dendropy.DataSet.get(path=..., schema='fasta', data_type='protein', ...)",
stacklevel=7)
# raise TypeError("'proteinfasta' is no longer a supported schema: use 'schema=\"fasta\"' with the 'ProteinCharacterMatrix.get()' method instead or 'schema=\"fasta\"' and 'data_type=\"dna\" with the 'DataSet.get()' or 'DataSet.read()' methods")
kwargs["data_type"] = "protein"
FastaReader.__init__(self, **kwargs)
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