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 cluster(table, table_wide, identify_fasta, max_dist, min_samples, min_reads_bin, min_abund_bin, cpu): click.echo('Invoking MetaBGC Cluster...') summary_file, cluster_file = mbgccluster(table, table_wide, identify_fasta, 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)
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)
def cluster(table, max_dist, min_samples, cpu): click.echo('Invoking MetaBGC Cluster...') cluster_file = mbgccluster(table, max_dist, min_samples, cpu) print('Clustered file: ' + cluster_file)
def cluster(table, table_wide, identify_fasta, max_dist, min_samples, min_reads_bin, min_abund_bin, cpu): click.echo('Invoking MetaBGC Cluster...') cluster_file = mbgccluster(table, table_wide, identify_fasta, max_dist, min_samples, min_reads_bin, min_abund_bin, cpu) print('Clustered file: ' + cluster_file)