static GtOptionParser* gt_extractfeat_option_parser_new(void *tool_arguments)
{
GtExtractFeatArguments *arguments = tool_arguments;
GtOptionParser *op;
GtOption *option;
gt_assert(arguments);
op = gt_option_parser_new("[option ...] [GFF3_file]",
"Extract features given in GFF3 file from "
"sequence file.");
/* -type */
option = gt_option_new_string("type", "set type of features to extract",
arguments->type, NULL);
gt_option_is_mandatory(option);
gt_option_parser_add_option(op, option);
/* -join */
option = gt_option_new_bool("join", "join feature sequences in the same "
"subgraph into a single one", &arguments->join,
false);
gt_option_parser_add_option(op, option);
/* -translate */
option = gt_option_new_bool("translate", "translate the features (of a DNA "
"sequence) into protein", &arguments->translate,
false);
gt_option_parser_add_option(op, option);
/* -seqid */
option = gt_option_new_bool("seqid", "add sequence ID of extracted features "
"to FASTA descriptions", &arguments->seqid,
false);
gt_option_parser_add_option(op, option);
/* -target */
option = gt_option_new_bool("target", "add target ID(s) of extracted "
"features to FASTA descriptions",
&arguments->target, false);
gt_option_parser_add_option(op, option);
/* -seqfile, -matchdesc, -usedesc and -regionmapping */
gt_seqid2file_register_options(op, arguments->s2fi);
/* -v */
option = gt_option_new_verbose(&arguments->verbose);
gt_option_parser_add_option(op, option);
/* -width */
option = gt_option_new_width(&arguments->width);
gt_option_parser_add_option(op, option);
/* output file options */
gt_output_file_info_register_options(arguments->ofi, op, &arguments->outfp);
gt_option_parser_set_comment_func(op, gt_gtdata_show_help, NULL);
gt_option_parser_set_max_args(op, 1);
return op;
}
static GtOptionParser* gt_splicesiteinfo_option_parser_new(void *tool_arguments)
{
SpliceSiteInfoArguments *arguments = tool_arguments;
GtOptionParser *op;
GtOption *option;
gt_assert(arguments);
op = gt_option_parser_new("[option ...] [GFF3_file ...]", "Show information "
"about splice sites given in GFF3 files.");
/* -seqfile, -matchdesc, -usedesc and -regionmapping */
gt_seqid2file_register_options(op, arguments->s2fi);
/* -addintrons */
option = gt_option_new_bool("addintrons", "add intron features between "
"existing exon features\n(before computing the "
"information to be shown)",
&arguments->addintrons, false);
gt_option_parser_add_option(op, option);
/* output file options */
gt_outputfile_register_options(op, &arguments->outfp, arguments->ofi);
gt_option_parser_set_comment_func(op, gt_gtdata_show_help, NULL);
return op;
}
static GtOptionParser* gt_cds_option_parser_new(void *tool_arguments)
{
CDSArguments *arguments = tool_arguments;
GtOptionParser *op;
GtOption *option;
gt_assert(arguments);
op = gt_option_parser_new("[option ...] [GFF3_file]",
"Add CDS (coding sequence) features to exon "
"features given in GFF3 file.");
/* -minorflen */
option = gt_option_new_uint_min("minorflen", "set the minimum length an open "
"reading frame (ORF) must have to be added "
"as a CDS feature (measured in amino acids)",
&arguments->minorflen, 64, 1);
gt_option_parser_add_option(op, option);
/* -startcodon */
option = gt_option_new_bool("startcodon", "require than an ORF must begin "
"with a start codon", &arguments->start_codon,
false);
gt_option_parser_add_option(op, option);
/* -finalstopcodon */
option = gt_option_new_bool("finalstopcodon", "require that the final ORF "
"must end with a stop codon",
&arguments->final_stop_codon, false);
gt_option_parser_add_option(op, option);
/* -genericstartcodons */
option = gt_option_new_bool("genericstartcodons", "use generic start codons",
&arguments->generic_start_codons, false);
gt_option_is_development_option(option);
gt_option_parser_add_option(op, option);
/* -seqfile, -matchdesc, -usedesc and -regionmapping */
gt_seqid2file_register_options(op, arguments->s2fi);
/* -v */
option = gt_option_new_verbose(&arguments->verbose);
gt_option_parser_add_option(op, option);
/* output file options */
gt_outputfile_register_options(op, &arguments->outfp, arguments->ofi);
gt_option_parser_set_comment_func(op, gt_gtdata_show_help, NULL);
gt_option_parser_set_max_args(op, 1);
return op;
}
static GtOptionParser* gt_speck_option_parser_new(void *tool_arguments)
{
GtOptionParser *op;
GtOption *option;
SpeccheckArguments *arguments = tool_arguments;
/* init */
op = gt_option_parser_new("[options] [GFF3_file ...]",
"Checks spec definition compliance in GFF3 input.");
option = gt_option_new_filename("specfile",
"file with specification definition",
arguments->specfile);
gt_option_parser_add_option(op, option);
gt_option_is_mandatory(option);
option = gt_option_new_bool("colored", "show colored output",
&arguments->colored, true);
gt_option_parser_add_option(op, option);
option = gt_option_new_bool("allexpects", "show results counted by "
"expectations instead of by nodes",
&arguments->allexpects, false);
gt_option_parser_add_option(op, option);
option = gt_option_new_bool("provideindex", "provide feature index in "
"specfile namespace (requires O(n) memory for n "
"input features)",
&arguments->provideindex, false);
gt_option_parser_add_option(op, option);
option = gt_option_new_bool("sort", "sort input before checking (requires "
"O(n) memory for n input features)",
&arguments->sort, false);
gt_option_parser_add_option(op, option);
option = gt_option_new_bool("failhard", "stop processing and report runtime "
"errors instead of recording them in the results",
&arguments->fail_hard, false);
gt_option_parser_add_option(op, option);
option = gt_option_new_verbose(&arguments->verbose);
gt_option_parser_add_option(op, option);
gt_seqid2file_register_options(op, arguments->s2fi);
gt_output_file_info_register_options(arguments->ofi, op, &arguments->outfp);
return op;
}
static GtOptionParser* gt_inlineseq_add_option_parser_new(void *tool_arguments)
{
GtOptionParser *op;
GT_UNUSED GtOption *option;
InlineseqAddArguments *arguments = tool_arguments;
/* init */
op = gt_option_parser_new("[options] [GFF3_file ...]",
"Adds inline sequences from external source to "
"GFF3 input.");
gt_seqid2file_register_options(op, arguments->s2fi);
gt_output_file_info_register_options(arguments->ofi, op, &arguments->outfp);
return op;
}
