# Path: ssbio/protein/sequence/utils/fasta.py
# def write_fasta_file(seq_records, outname, outdir=None, outext='.faa', force_rerun=False):
# def write_fasta_file_from_dict(indict, outname, outdir=None, outext='.faa', force_rerun=False):
# def write_seq_as_temp_fasta(seq):
# def load_fasta_file(filename):
# def load_fasta_file_as_dict_of_seqs(filename):
# def load_fasta_file_as_dict_of_seqrecords(filename):
# def fasta_files_equal(seq_file1, seq_file2):


import getpass
import logging
import os
import os.path as op
from ssbio.protein.sequence.utils import fasta as fasta
            additional_options += '-GO true '
        self.additional_options = additional_options

        if not java_home:
            self.java_home = '${JAVA_HOME}'
        else:
            self.java_home = java_home

        if not job_scheduler_header:
            self.job_scheduler_header = ''
        else:
            self.job_scheduler_header = job_scheduler_header

        if runtype == 'local' or runtype == 'torque':
            self.prep_script_local(itasser_loc=itasser_path,
                                   itlib_loc=itlib_path)

        if runtype == 'slurm':
            self.prep_script_slurm(itasser_loc=itasser_path,
                                   itlib_loc=itlib_path)

    def prep_folder(self, seq):
        """Take in a sequence string and prepares the folder for the I-TASSER run."""
        itasser_dir = op.join(self.root_dir, self.id)

        if not op.exists(itasser_dir):
            os.makedirs(itasser_dir)

        tmp = {self.id: seq}


# Path: ssbio/protein/sequence/utils/fasta.py
# def write_fasta_file(seq_records, outname, outdir=None, outext='.faa', force_rerun=False):
# def write_fasta_file_from_dict(indict, outname, outdir=None, outext='.faa', force_rerun=False):
# def write_seq_as_temp_fasta(seq):
# def load_fasta_file(filename):
# def load_fasta_file_as_dict_of_seqs(filename):
# def load_fasta_file_as_dict_of_seqrecords(filename):
# def fasta_files_equal(seq_file1, seq_file2):


# Path: ssbio/protein/structure/homology/itasser/itasserprep.py
import getpass
import logging
import os
import os.path as op
from ssbio.protein.sequence.utils import fasta as fasta

            additional_options += '-GO true '
        self.additional_options = additional_options

        if not java_home:
            self.java_home = '${JAVA_HOME}'
        else:
            self.java_home = java_home

        if not job_scheduler_header:
            self.job_scheduler_header = ''
        else:
            self.job_scheduler_header = job_scheduler_header

        if runtype == 'local' or runtype == 'torque':
            self.prep_script_local(itasser_loc=itasser_path,
                                   itlib_loc=itlib_path)

        if runtype == 'slurm':
            self.prep_script_slurm(itasser_loc=itasser_path,
                                   itlib_loc=itlib_path)

    def prep_folder(self, seq):
        """Take in a sequence string and prepares the folder for the I-TASSER run."""
        itasser_dir = op.join(self.root_dir, self.id)

        if not op.exists(itasser_dir):
            os.makedirs(itasser_dir)

        tmp = {self.id: seq}


        fasta.write_fasta_file_from_dict(indict=tmp,