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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 string
from sys import stderr as STDERR
from re import search
from six.moves import map
from six.moves import range
def read_paml (source, obj=None, header_delimiter="\t", fix_duplicates=True):
""" Reads a collection of sequences econded in PAML format... that is, something between PHYLIP and fasta
3 6
seq1
ATGATG
seq2
ATGATG
seq3
ATGATG
or
3 6
>seq1
ATGATG
>seq2
ATGATG
>seq3
ATGATG
or
>seq1
ATGATG
>seq2
ATGATG
>seq3
ATGATG
"""
if obj is None:
from ..coretype import seqgroup
SC = seqgroup.SeqGroup()
else:
SC = obj
names = set([])
seq_id = -1
# Prepares handle from which read sequences
if os.path.isfile(source):
_source = open(source, "r")
else:
_source = iter(source.split("\n"))
seq_name = None
num_seq = 0
len_seq = 0
in_seq = False
for line in _source:
line = line.strip()
if line.startswith('#') or not line:
continue
if line.startswith('// end of file'):
break
# Reads seq number
elif line.startswith('>') or ((num_seq and len_seq) and not in_seq):
fasta = line.startswith('>')
line = line.replace('>','')
# Checks if previous name had seq
if seq_id>-1 and SC.id2seq[seq_id] == "":
raise Exception("No sequence found for "+seq_name)
seq_id += 1
# Takes header info
seq_header_fields = [_f.strip() for _f in line.split(header_delimiter)]
in_seq = True
if (not fasta) and ' ' in seq_header_fields[0].strip():
seq_header_fields = seq_header_fields[0].split(' ')[0]
seq_header_fields = [seq_header_fields]
SC.id2seq[seq_id] = line.split(' ')[-1].strip().replace(' ', '')
if len_seq:
if len(SC.id2seq[seq_id]) == len_seq:
in_seq=False
elif len(SC.id2seq[seq_id]) > len_seq:
raise Exception("Error reading sequences: Wrong sequence length.\n"+line)
else:
SC.id2seq[seq_id] = ""
seq_name = seq_header_fields[0]
# Checks for duplicated seq names
if fix_duplicates and seq_name in names:
tag = str(len([k for k in list(SC.name2id.keys()) if k.endswith(seq_name)]))
old_name = seq_name
seq_name = tag+"_"+seq_name
print("Duplicated entry [%s] was renamed to [%s]" %(old_name, seq_name), file=STDERR)
# stores seq_name
SC.id2name[seq_id] = seq_name
SC.name2id[seq_name] = seq_id
SC.id2comment[seq_id] = seq_header_fields[1:]
names.add(seq_name)
else:
if seq_name is None:
if search ('^[0-9]+ *[0-9]+ *[A-Z]*', line):
try:
num_seq, len_seq = line.strip().split()
except ValueError:
num_seq, len_seq, _ = line.strip().split()
num_seq = int(num_seq)
len_seq = int(len_seq)
continue
if line.startswith('\n'):
continue
raise Exception("Error reading sequences: Wrong format.\n"+line)
elif in_seq:
# removes all white spaces in line
s = line.strip().replace(" ","")
# append to seq_string
SC.id2seq[seq_id] += s
if len_seq:
if len(SC.id2seq[seq_id]) == len_seq:
in_seq=False
elif len(SC.id2seq[seq_id]) > len_seq:
raise Exception("Error reading sequences: Wrong sequence length.\n"+line)
if seq_name and SC.id2seq[seq_id] == "":
print(seq_name,"has no sequence", file=STDERR)
return None
# Everything ok
return SC
def write_paml(sequences, outfile = None, seqwidth = 80):
"""
Writes a SeqGroup python object using PAML format.
sequences are ordered, because PAML labels tree according to this.
"""
text = ' %d %d\n' % (len (sequences), len (sequences.get_entries()[0][1]))
text += '\n'.join(["%s\n%s" %( "\t".join([name]+comment), _seq2str(seq)) for
name, seq, comment in sorted(sequences)])
if outfile is not None:
OUT = open(outfile,"w")
OUT.write(text)
OUT.close()
else:
return text
def _seq2str(seq, seqwidth = 80):
sequence = ""
for i in range(0,len(seq),seqwidth):
sequence+= seq[i:i+seqwidth] + "\n"
return sequence
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