def dereplicate_seqs(seqs_fp, output_fp, min_size=2, uc_output=True): """Dereplicate FASTA sequences and remove singletons using VSEARCH Parameters ---------- seqs_fp : string filepath to FASTA sequence file output_fp : string file path to dereplicated sequences (FASTA format) min_size : integer, optional discard sequences with an abundance value smaller than integer uc_output: boolean, optional output the dereplication map in .uc format """ log_name = "%s.log" % splitext(output_fp)[0] vsearch_dereplicate_exact_seqs( fasta_filepath=seqs_fp, output_filepath=output_fp, output_uc=uc_output, minuniquesize=min_size, log_name=log_name)
def dereplicate_seqs(seqs_fp, output_fp, min_size=2): """Dereplicate FASTA sequences and remove singletons using VSEARCH Parameters ---------- seqs_fp : string filepath to FASTA sequence file output_fp : string filepath to dereplicated FASTA file min_size : integer discard sequences with an abundance value smaller than integer """ log_name = "%s.log" % splitext(output_fp)[0] vsearch_dereplicate_exact_seqs(fasta_filepath=seqs_fp, output_filepath=output_fp, minuniquesize=min_size, log_name=log_name)
def dereplicate_seqs(seqs_fp, output_fp, min_size=2, uc_output=True): """Dereplicate FASTA sequences and remove singletons using VSEARCH Parameters ---------- seqs_fp : string filepath to FASTA sequence file output_fp : string file path to dereplicated sequences (FASTA format) min_size : integer, optional discard sequences with an abundance value smaller than integer uc_output: boolean, optional output the dereplication map in .uc format """ log_name = "%s.log" % splitext(output_fp)[0] vsearch_dereplicate_exact_seqs(fasta_filepath=seqs_fp, output_filepath=output_fp, output_uc=uc_output, minuniquesize=min_size, log_name=log_name)
def dereplicate_seqs(seqs_fp, output_fp, min_size=2): """Dereplicate FASTA sequences and remove singletons using VSEARCH Parameters ---------- seqs_fp : string filepath to FASTA sequence file output_fp : string filepath to dereplicated FASTA file min_size : integer discard sequences with an abundance value smaller than integer """ log_name = "%s.log" % splitext(output_fp)[0] vsearch_dereplicate_exact_seqs( fasta_filepath=seqs_fp, output_filepath=output_fp, minuniquesize=min_size, log_name=log_name)