def main(args):
__location__ = os.path.realpath(
os.path.join(os.getcwd(), os.path.dirname(__file__)))
# additional argument checks
if not os.path.isdir(args.working_dir):
raise ValueError('Working directory not found')
args.working_dir = os.path.realpath(args.working_dir) + '/'
if os.path.isdir(args.working_dir + 'analysis/'):
shutil.rmtree(args.working_dir + 'analysis/')
options_dict = dict()
options_dict['wd_envs'] = hp.parse_output_path(args.working_dir + 'envs/')
options_dict['threads'] = args.threads_per_job
options_dict['ref_fasta'] = os.path.realpath(args.ref_fasta)
options_dict['reads_fastq'] = args.working_dir + 'all_reads.fastq'
options_dict['wd_analysis'] = hp.parse_output_path(args.working_dir +
'analysis/')
options_dict[
'wd_analysis_condas'] = __location__ + '/analysis_conda_files/'
options_dict['__location__'] = __location__
# --- create output directories
if os.path.isdir(options_dict['wd_analysis']):
shutil.rmtree(options_dict['wd_analysis'])
_ = hp.parse_output_path(options_dict['wd_analysis'] + 'quast')
_ = hp.parse_output_path(options_dict['wd_analysis'] + 'jellyfish')
_ = hp.parse_output_path(options_dict['wd_analysis'] + 'readset_analysis')
options_dict['wd_analysis_summary'] = hp.parse_output_path(
options_dict['wd_analysis'] + 'summary/')
options_dict[
'wd_assembler_results'] = args.working_dir + 'assembler_results/'
options_dict[
'wd_assemblies'] = args.working_dir + 'assembler_results/assemblies/'
assemblies_list = hp.parse_input_path(options_dict['wd_assemblies'],
pattern='*.fasta')
if len(assemblies_list) == 0:
raise ValueError('No succesful assemblies found to analyze!')
assemblies_names_list = [
os.path.splitext(os.path.basename(af))[0] for af in assemblies_list
]
options_dict['assemblies_string'] = ' '.join(assemblies_names_list)
with open(args.user_info, 'r') as f:
md_yaml = yaml.load(f)
md = Metadata(md_yaml)
md.write_publication_info(options_dict['wd_analysis_summary'] +
'publication_info.yaml')
# --- Quast ---
options_dict['quast_options'] = ''
if md.is_eukaryote:
options_dict['quast_options'] += '-e '
if args.gff_file:
options_dict['quast_options'] += '-G ' + os.path.abspath(
args.gff_file) + ' '
quast_output = ''
quast_output_cmd = ''
for anl in assemblies_names_list:
quast_output += (
',\n\t\t{anl}_fplot=\'{wd_analysis_summary}quast/{anl}.fplot\''
',\n\t\t{anl}_rplot=\'{wd_analysis_summary}quast/{anl}.rplot\''
).format(anl=anl,
wd_analysis_summary=options_dict['wd_analysis_summary'])
quast_output_cmd += (
'if [ -e contigs_reports/nucmer_output/{anl}.fplot ]; then ' # for quast <5.0.0
'cp contigs_reports/nucmer_output/{anl}.fplot {wd_analysis_summary}quast/.\n'
'cp contigs_reports/nucmer_output/{anl}.rplot {wd_analysis_summary}quast/.\n'
'fi\n').format(
anl=anl,
wd_analysis_summary=options_dict['wd_analysis_summary'])
quast_output_cmd += (
'if [ -e contigs_reports/all_alignments_{anl}.tsv ]; then ' # for quast =>5.0.0
'cp contigs_reports/all_alignments_{anl}.tsv {wd_analysis_summary}quast/.\n'
'fi\n').format(
anl=anl,
wd_analysis_summary=options_dict['wd_analysis_summary'])
options_dict['quast_output'] = quast_output
options_dict['quast_output_cmd'] = quast_output_cmd
# --- Construct snakemake file ---
sf_fn = args.working_dir + 'Snakefile_analysis_' + datetime.datetime.now(
).strftime('%Y%m%d%H%M%S')
with open(__location__ + '/Snakemake_analysis', 'r') as f:
sf = f.read()
sf = sf.format(**options_dict)
with open(sf_fn, 'w') as sf_handle:
sf_handle.write(sf)
sm_dict = {'use_conda': True}
if args.slurm_config is not None:
sm_dict['cluster'] = 'sbatch'
sm_dict['cluster_config'] = args.slurm_config
sm_dict['nodes'] = 5
snakemake.snakemake(sf_fn, **sm_dict)
