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))