indexing.py 1.51 KB
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#
# Copyright (C) 2012 INRA
# 
# This program 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.
# 
# This program 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 this program.  If not, see <http://www.gnu.org/licenses/>.
#

import os

from jflow.component import Component
from jflow.utils import split_and_rename_seq, get_file_base

from weaver.function import ShellFunction


class FormatDB (Component):
    
    def __init__(self):
        Component.__init__(self, is_dynamic=True)
    
    def define_parameters(self, input_fasta, protein=False, nb_seq_per_file=None):
        self.input_fasta = input_fasta
        self.protein = protein
        self.database = os.path.join(self.output_directory, os.path.basename(input_fasta))
    
    def run(self):
        # first make the symbolic link
        os.symlink(self.input_fasta, self.database)
        if self.protein: p = "T"
        else: p = "F"
        formatdb = ShellFunction(self.get_exec_path("formatdb") + " -p " + p + " -i $1 -n $2", cmd_format='{EXE} {IN} {OUT}')
        formatdb(inputs=self.input_fasta, outputs=self.database)