Source code for hylite.bowtie2_wrapper

#!/usr/bin/env python3

#    (c) Copyright 2013-2018 Murray Cox, Wandrille Duchemin, Pierre-Yves Dupont.
#
#
#    This file is part of HyLiTE.
#
#    HyLiTE is a free software: you can redistribute it and/or modify
#    it under the terms of the GNU General Public License version 3 as published by
#    the Free Software Foundation.
#
#    HyLiTE 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 HyLiTE.  If not, see <http://www.gnu.org/licenses/>


#===============================#
# author: Wandrille Duchemin    #
#         Murray Cox            #
# last modified: 9 January 2018 #
#===============================#


from .Parameters import Parameters
from .Generic_wrapper import Generic_wrapper #import os too
import sys


class bowtie2_wrapper(Generic_wrapper):
    '''This class is a wrapper for bowtie2 inheriting from Generic_wrapper

    Attributes:
        - commandline (str): commandline used
    '''
    def __init__(self):
        '''Wrapper for bowtie2
        It takes no arguments
        '''
        param = Parameters()
        Generic_wrapper.__init__(self, param.get_param('BOWTIE2_PATH'), {'build_index':param.get_param('BOWTIE2_NAME_BUILD'),'align':param.get_param('BOWTIE2_NAME_ALIGN')},\
        {'base':param.get_param('BOWTIE2_OPTION_BASE'),'unpaired':param.get_param('BOWTIE2_OPTION_UNPAIRED'),'paired1':param.get_param('BOWTIE2_OPTION_PAIRED_1'),'paired2':param.get_param('BOWTIE2_OPTION_PAIRED_2'),\
         'mismatch':param.get_param('BOWTIE2_OPTION_MISMATCH'),\
         'out':param.get_param('BOWTIE2_OPTION_OUT'), 'phred64':param.get_param('BOWTIE2_OPTION_PHRED64'), 'thread':param.get_param('BOWTIE2_OPTION_THREAD'),\
         'build_ref':param.get_param('BOWTIE2_BUILD_OPTION_REF'), 'build_out':param.get_param('BOWTIE2_BUILD_OPTION_OUT')\
         })
        #this should provide a flexible framework. if an option change, just modify the according variable in params.py
        #should you wish to add a new option, add an option to the params.py and add it to the options dictionnary
        return

    def build_index(self, reffile, outname):
        '''Function used to build the .bt2 index from a reffile fasta file

        Args:
             - reffile (str): a reference file name (file is fasta)
             - outname (str): the name of the .bt2 base to create
        '''

        basename = 'build_index'
        order = ['build_ref', 'build_out']
        options_value = {'build_ref':reffile,'build_out':outname}
        self.commandline = self.build_command_line(basename, options_value, order)

        if Parameters().get_param('VERBOSE'):
            self.print_command_line()

        p=self.run()
        if Parameters().get_param('VERBOSE'):
            sys.stdout.write(p.stdout.read().decode('utf8')+'\n')
            sys.stderr.write(p.stderr.read().decode('utf8')+'\n')
        else: # have to read it to execute the code
            p.stdout.read().decode('utf8')
            p.stderr.read().decode('utf8')

        return

    def mappe_versus(self, base, lfile, paired, mismatch, thread, quality64, outfile):
        '''Function used to map reads against a base using bowtie2.

        Args:
             - base (str): the name of the .bt2 base
             - lfile (list): a list of the name of the file containing the reads
             - paired (bool): a boolean set to True of the data are paired end reads
             - mismatch (bool): a boolean set to True of you want to allow mismatch in the seed
             - thread(int): an int specifying the number of thread to use (1 is authorized)
             - quality64 (bool): a boolean set to True if the quality of the reads is in phred64 format
             - outfile (str): a string specifying the name of the .sam out file to write
        '''
        basename = 'align'
        option_value = dict()
        order=list()
        if max(1, thread)>1:
            option_value['thread']=str(thread)
            order.append('thread')
        if quality64 is True:
            option_value['phred64']=True
            order.append('phred64')
        if mismatch is True:
            option_value['mismatch']=True
            order.append('mismatch')
        option_value['base'] = base
        order.append('base')
        if paired is True:
            option_value['paired1']=lfile[0]
            option_value['paired2']=lfile[1]
            order.append('paired1')
            order.append('paired2')
        else:
            option_value['unpaired']=lfile[0]
            order.append('unpaired')
        option_value['out'] = outfile
        order.append('out')

        self.commandline = self.build_command_line(basename, option_value, order)


        if Parameters().get_param('VERBOSE'):
            self.print_command_line()

        p=self.run()
        if Parameters().get_param('VERBOSE'):
            sys.stdout.write(p.stdout.read().decode('utf8')+'\n')
            sys.stderr.write(p.stderr.read().decode('utf8')+'\n')
        else: # have to read it to execute the code
            p.stdout.read().decode('utf8')
            p.stderr.read().decode('utf8')

        return