def invoke_check_fasta_gff(): """ Parse command-line options then invoke :py:func:`riboviz.check_fasta_gff.check_fasta_gff`. """ print(provenance.write_provenance_to_str(__file__)) options = parse_command_line_options() fasta = options.fasta gff = options.gff check_fasta_gff.check_fasta_gff(fasta, gff)
def invoke_subsample_bioseqfile(): """ Parse command-line options then invoke :py:func:`riboviz.subsample_bioseqfile.subsample_bioseqfile`. """ print(provenance.write_provenance_to_str(__file__)) options = parse_command_line_options() input_file = options.input_file output_file = options.output_file file_type = options.file_type prob = options.prob verbose = options.verbose subsample_bioseqfile.subsample_bioseqfile(input_file, prob, output_file, file_type, verbose)
def invoke_count_reads(): """ Parse command-line options then invoke :py:func:`riboviz.count_reads.count_reads`. """ print(provenance.write_provenance_to_str(__file__)) options = parse_command_line_options() config_file = options.config_file input_dir = options.input_dir tmp_dir = options.tmp_dir output_dir = options.output_dir reads_file = options.reads_file count_reads.count_reads(config_file, input_dir, tmp_dir, output_dir, reads_file)
def invoke_trim_5p_mismatch(): """ Parse command-line options then invoke :py:func:`riboviz.trim_5p_mismatch.trim_5p_mismatch_file`. """ print(provenance.write_provenance_to_str(__file__)) options = parse_command_line_options() sam_file_in = options.sam_file_in sam_file_out = options.sam_file_out fivep_remove = options.fivep_remove max_mismatches = options.max_mismatches summary_file = options.summary_file trim_5p_mismatch.trim_5p_mismatch_file(sam_file_in, sam_file_out, fivep_remove, max_mismatches, summary_file)
def invoke_demultiplex_fastq(): """ Parse command-line options then invoke :py:func:`riboviz.demultiplex_fastq.demultiplex`. """ print(provenance.write_provenance_to_str(__file__)) options = parse_command_line_options() sample_sheet_file = options.sample_sheet_file read1_file = options.read1_file read2_file = options.read2_file mismatches = options.mismatches out_dir = options.out_dir delimiter = options.delimiter demultiplex_fastq.demultiplex(sample_sheet_file, read1_file, read2_file, mismatches, out_dir, delimiter)
def invoke_get_cds_codons(): """ Parse command-line options then invoke :py:func:`riboviz.get_cds_codons.get_cds_codons_file`. """ print(provenance.write_provenance_to_str(__file__)) options = parse_command_line_options() fasta = options.fasta gff = options.gff cds_codons = options.cds_codons exclude_stop_codons = options.exclude_stop_codons cds_feature_format = options.cds_feature_format use_feature_name = options.use_feature_name try: get_cds_codons.get_cds_codons_file(fasta, gff, cds_codons, exclude_stop_codons, cds_feature_format, use_feature_name) except FastaIndexingError as e: print("{}: {}".format(type(e).__name__, e)) except FileNotFoundError as e: print("{}: {}".format(type(e).__name__, e)) except ValueError as e: print("{}: {}".format(type(e).__name__, e))