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# -*- coding: utf-8 -*-
########################################################################################
# #
# Author: Bertrand Néron #
# Organization:'Biological Software and Databases' Group, Institut Pasteur, Paris. #
# Distributed under GPLv2 Licence. Please refer to the COPYING.LIB document. #
# #
########################################################################################
import os
from logging import getLogger
f_log = getLogger(__name__)
from Mobyle.MobyleError import MobyleError , UnSupportedFormatError
from Mobyle.Converter.DataConverter import DataConverter
from Bio import AlignIO
class stockholm_phyml(DataConverter):
def __init__(self, path):
super( stockholm_phyml , self ).__init__( path )
self.program_name = 'Stockholm2Phylip-relaxed'
def detect(self, dataFileName):
#we lay on squizz to detect the format file
return None, None
def detectedFormat(self):
#we lay on squizz to detect the format file
return []
def convert(self, dataFileName , outputFormat , inputFormat = None):
outputFormat = outputFormat.lower()
assert outputFormat == 'phylip-relaxed'
if inputFormat is None:
raise UnSupportedFormatError("the input format must be specify" )
inputFormat = inputFormat.lower()
if inputFormat != 'stockholm':
raise UnSupportedFormatError("support only stockholm as input, provide " + str(inputFormat))
with open(dataFileName) as data_input:
#read allow only one multiple alignment
#for more msa (after bootstarp) use parse
#but for now squiz manage only one msa perfile
try:
align = AlignIO.read(data_input, 'stockholm')
except Exception, err:
f_log.error( "failed to read stockholm alignment", exc_info= True)
raise UnSupportedFormatError( "the conversion from stockholm to phylip-relaxed failed")
outFileName = os.path.splitext( dataFileName )[0] + "." + outputFormat
with open(outFileName, 'w') as output:
try:
AlignIO.write(align, output , 'phylip-relaxed')
except Exception, err:
f_log.error( "failed to write phylip-relaxed alignment", exc_info= True)
raise UnSupportedFormatError( "the convertion from stockholm to phylip-relaxed failed")
return outFileName
def convertedFormat(self):
return [('STOCKHOLM', 'PHYLIP-RELAXED')]
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