def search(sphmm_directory, prot_family_name, cohort_name, nucl_seq_directory,
prot_seq_directory, seq_fmt, pair_fmt, r1_file_suffix,
r2_file_suffix, max_dist, min_samples, min_reads_bin, min_abund_bin,
hmm_search_directory, blastn_search_directory,
blast_db_directory_map_file, output_directory, cpu):
logging.basicConfig(filename=os.path.join(output_directory, 'metabgc.log'),
level=logging.INFO)
logging.info('Invoking MetaBGC search...')
click.echo('Invoking MetaBGC search...')
t0 = time()
ident_reads_file = mbgcidentify(sphmm_directory, cohort_name,
nucl_seq_directory, prot_seq_directory,
seq_fmt, pair_fmt, r1_file_suffix,
r2_file_suffix, prot_family_name,
hmm_search_directory, output_directory,
cpu)
abund_file, abund_wide_table = mbgcquantify(
ident_reads_file, prot_family_name, cohort_name, nucl_seq_directory,
seq_fmt, pair_fmt, r1_file_suffix, r2_file_suffix,
blast_db_directory_map_file, blastn_search_directory, output_directory,
cpu)
summary_file, cluster_file = mbgccluster(abund_file, abund_wide_table,
ident_reads_file, max_dist,
min_samples, min_reads_bin,
min_abund_bin, cpu)
click.echo('Cluster summary file: ' + summary_file)
click.echo('Cluster detail file: ' + cluster_file)
logging.info('Cluster summary file: ' + summary_file)
logging.info('Cluster detail file: ' + cluster_file)
t1 = time() - t0
logging.info("Time elapsed: " + str(t1))
logging.info("MetaBGC search complete...")
click.echo("MetaBGC search complete...")
def quantify(identify_fasta, prot_family_name, cohort_name, nucl_seq_directory,
seq_fmt, pair_fmt, r1_file_suffix, r2_file_suffix,
blastn_search_directory, output_directory, cpu):
click.echo('Invoking MetaBGC Quantify...')
abund_file = mbgcquantify(identify_fasta, prot_family_name, cohort_name,
nucl_seq_directory, seq_fmt, pair_fmt,
r1_file_suffix, r2_file_suffix,
blastn_search_directory, output_directory, cpu)
print('Reads abundance file: ' + abund_file)
def search(sphmm_directory, prot_family_name, cohort_name, nucl_seq_directory,
prot_seq_directory, seq_fmt, pair_fmt, r1_file_suffix,
r2_file_suffix, max_dist, min_samples, hmm_search_directory,
blastn_search_directory, output_directory, cpu):
click.echo('Invoking MetaBGC search...')
ident_reads_file = mbgcidentify(sphmm_directory, cohort_name,
nucl_seq_directory, prot_seq_directory,
seq_fmt, pair_fmt, r1_file_suffix,
r2_file_suffix, prot_family_name,
hmm_search_directory, output_directory,
cpu)
abund_file = mbgcquantify(ident_reads_file, prot_family_name, cohort_name,
nucl_seq_directory, seq_fmt, pair_fmt,
r1_file_suffix, r2_file_suffix,
blastn_search_directory, output_directory, cpu)
cluster_file = mbgccluster(abund_file, max_dist, min_samples, cpu)
print('Clustered file: ' + cluster_file)