"""

Main execution of the program in the proper order

input: argv from arg parser

"""

utils.check_dependencies(check_run=argv.check,

verbose=argv.verbose)

input_file = argv.input_file

if argv.run_name is False:

basename = os.path.basename(input_file)

run_name = os.path.splitext(basename)[0]

else:

run_name = argv.run_name

tmp_dir = os.path.join(os.getcwd(), 'intermediate_outputs_'+run_name)

try:

os.makedirs(tmp_dir)

except OSError:

if os.path.exists(tmp_dir):

warnings.warn('\n\nintermediate output dir: {0} exists '

'overwriting contents\n'.format(tmp_dir))

else:

raise OSError('Error creating intermediate '

'output dir: {0}'.format(tmp_dir))

rename_mappings, formatted_fasta_fp = utils.format_fasta(input_file,

tmp_dir,

verbose=argv.verbose)

mature_seqs_fp, \

accessions_with_sig_pep, \

full_sequences_with_sigpep_fp = utils.signalp(formatted_fasta_fp,

tmp_dir,

rename_mappings,

run_name,

trans=argv.trans,

verbose=argv.verbose)

if argv.trans:

utils.detect_and_output_transporters(formatted_fasta_fp,

rename_mappings,

tmp_dir,

run_name,

mature_seqs=mature_seqs_fp,

verbose=argv.verbose,

tm_threshold=argv.trans)

accesions_no_tm_in_mature_seq = utils.tmhmm(mature_seqs_fp,

verbose=argv.verbose)

secreted_accessions = utils.targetp(full_sequences_with_sigpep_fp,

plant=False,

verbose=argv.verbose)

extracellular_accessions = utils.wolfpsort(formatted_fasta_fp,

verbose=argv.verbose)

if argv.permissive:

conservative_flag = False

else:

conservative_flag = True

secretome_accessions = utils.secretome(accessions_with_sig_pep,

accesions_no_tm_in_mature_seq,

secreted_accessions,

extracellular_accessions,

conservative=conservative_flag,

verbose=argv.verbose)

utils.generate_output(formatted_fasta_fp,

secretome_accessions,

rename_mappings,

run_name,

conservative=conservative_flag,

verbose=argv.verbose)

if not argv.nocleanup: