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; }