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from __future__ import absolute_import
from __future__ import print_function
# #START_LICENSE###########################################################
#
#
# This file is part of the Environment for Tree Exploration program
# (ETE). http://etetoolkit.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 (2008-2015).
#
# 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 may be available in the documentation.
#
# More info at http://etetoolkit.org. Contact: huerta@embl.de
#
#
# #END_LICENSE#############################################################
import os
import re
from sys import stderr as STDERR
import six
from six.moves import range
def read_phylip(source, interleaved=True, obj=None,
relaxed=False, fix_duplicates=True):
if obj is None:
from ..coretype import SeqGroup
SG = SeqGroup()
else:
SG = obj
# Prepares handle from which read sequences
if os.path.isfile(source):
if source.endswith('.gz'):
import gzip
_source = gzip.open(source)
else:
_source = open(source, "r")
else:
_source = iter(source.split("\n"))
nchar, ntax = None, None
counter = 0
id_counter = 0
for line in _source:
line = line.strip("\n")
# Passes comments and blank lines
if not line or line[0] == "#":
continue
# Reads head
if not nchar or not ntax:
m = re.match("^\s*(\d+)\s+(\d+)",line)
if m:
ntax = int (m.groups()[0])
nchar = int (m.groups()[1])
else:
raise Exception("A first line with the alignment dimension is required")
# Reads sequences
else:
if not interleaved:
# Reads names and sequences
if SG.id2name.get(id_counter, None) is None:
if relaxed:
m = re.match("^([^ ]+)(.+)", line)
else:
m = re.match("^(.{10})(.+)", line)
if m:
name = m.groups()[0].strip()
if fix_duplicates and name in SG.name2id:
tag = str(len([k for k in list(SG.name2id.keys()) \
if k.endswith(name)]))
old_name = name
# Tag is in the beginning to avoid being
# cut it by the 10 chars limit
name = tag+"_"+name
print("Duplicated entry [%s] was renamed to [%s]" %\
(old_name, name), file=STDERR)
SG.id2name[id_counter] = name
SG.name2id[name] = id_counter
SG.id2seq[id_counter] = ""
line = m.groups()[1]
else:
raise Exception("Wrong phylip sequencial format.")
SG.id2seq[id_counter] += re.sub("\s","", line)
if len(SG.id2seq[id_counter]) == nchar:
id_counter += 1
name = None
elif len(SG.id2seq[id_counter]) > nchar:
raise Exception("Unexpected length of sequence [%s] [%s]." %(name,SG.id2seq[id_counter]))
else:
if len(SG)<ntax:
if relaxed:
m = re.match("^([^ ]+)(.+)", line)
else:
m = re.match("^(.{10})(.+)",line)
if m:
name = m.groups()[0].strip()
seq = re.sub("\s","",m.groups()[1])
SG.id2seq[id_counter] = seq
SG.id2name[id_counter] = name
if fix_duplicates and name in SG.name2id:
tag = str(len([k for k in list(SG.name2id.keys()) \
if k.endswith(name)]))
old_name = name
name = tag+"_"+name
print("Duplicated entry [%s] was renamed to [%s]" %\
(old_name, name), file=STDERR)
SG.name2id[name] = id_counter
id_counter += 1
else:
raise Exception("Unexpected number of sequences.")
else:
seq = re.sub("\s", "", line)
if id_counter == len(SG):
id_counter = 0
SG.id2seq[id_counter] += seq
id_counter += 1
if len(SG) != ntax:
raise Exception("Unexpected number of sequences.")
# Check lenght of all seqs
for i in list(SG.id2seq.keys()):
if len(SG.id2seq[i]) != nchar:
raise Exception("Unexpected lenght of sequence [%s]" %SG.id2name[i])
return SG
def write_phylip(aln, outfile=None, interleaved=True, relaxed=False):
width = 60
seq_visited = set([])
show_name_warning = False
lenghts = set((len(seq) for seq in list(aln.id2seq.values())))
if len(lenghts) >1:
raise Exception("Phylip format requires sequences of equal lenght.")
seqlength = lenghts.pop()
if not relaxed:
name_fix = 10
else:
name_fix = max([len(name) for name in list(aln.id2name.values())])
alg_lines = []
alg_text = " %d %d" %(len(aln), seqlength)
alg_lines.append(alg_text)
if interleaved:
visited = set([])
for i in range(0, seqlength, width):
for j in six.iterkeys(aln.id2name): #xrange(len(aln)):
name = aln.id2name[j]
if not relaxed and len(name)>name_fix:
name = name[:name_fix]
show_name_warning = True
seq = aln.id2seq[j][i:i+width]
if j not in visited:
name_str = "%s " %name.ljust(name_fix)
visited.add(j)
else:
name_str = "".ljust(name_fix+3)
seq_str = ' '.join([seq[k:k+10] for k in range(0, len(seq), 10)])
line_str = "%s%s" %(name_str, seq_str)
alg_lines.append(line_str)
alg_lines.append("")
else:
for name, seq, comments in aln.iter_entries():
if not relaxed and len(name)>10:
name = name[:name_fix]
show_name_warning = True
line_str = "%s %s\n%s" %\
(name.ljust(name_fix), seq[0:width-name_fix-3], '\n'.join([seq[k:k+width] \
for k in range(width-name_fix-3, len(seq), width)]))
alg_lines.append(line_str)
alg_lines.append("")
if show_name_warning:
print("Warning! Some sequence names were cut to 10 characters!!", file=STDERR)
alg_text = '\n'.join(alg_lines)
if outfile is not None:
OUT = open(outfile, "w")
OUT.write(alg_text)
OUT.close()
else:
return alg_text
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