static GtOptionParser* gt_extractseq_option_parser_new(void *tool_arguments) { ExtractSeqArguments *arguments = tool_arguments; GtOptionParser *op; GtOption *frompos_option, *topos_option, *match_option, *width_option, *fastakeyfile_option; gt_assert(arguments); /* init */ op = gt_option_parser_new("[option ...] [sequence_file(s)] | fastaindex", "Extract sequences from given sequence file(s) or " "fastaindex."); /* -frompos */ frompos_option = gt_option_new_ulong_min(FROMPOS_OPTION_STR, "extract sequence from this position\n" "counting from 1 on", &arguments->frompos, 0, 1UL); gt_option_parser_add_option(op, frompos_option); /* -topos */ topos_option = gt_option_new_ulong_min(TOPOS_OPTION_STR, "extract sequence up to this position\n" "counting from 1 on", &arguments->topos, 0, 1UL); gt_option_parser_add_option(op, topos_option); /* -match */ match_option = gt_option_new_string("match", "extract all sequences whose " "description matches the given pattern.\n" "The given pattern must be a valid extended " "regular expression.", arguments->pattern, NULL); gt_option_parser_add_option(op, match_option); /* -keys */ fastakeyfile_option = gt_option_new_filename("keys", "extract substrings for keys " "in specified file", arguments->fastakeyfile); gt_option_parser_add_option(op, fastakeyfile_option); /* -width */ width_option = gt_option_new_ulong("width", "set output width for showing of " "sequences (0 disables formatting)", &arguments->width, 0); gt_option_parser_add_option(op, width_option); /* output file options */ gt_outputfile_register_options(op, &arguments->outfp, arguments->ofi); /* option implications */ gt_option_imply(frompos_option, topos_option); gt_option_imply(topos_option, frompos_option); /* option exclusions */ gt_option_exclude(frompos_option, match_option); gt_option_exclude(topos_option, match_option); gt_option_exclude(frompos_option, fastakeyfile_option); gt_option_exclude(match_option, fastakeyfile_option); gt_option_parser_set_comment_func(op, gt_gtdata_show_help, NULL); return op; }
static GtOptionParser *gt_tyr_mkindex_option_parser_new(void *tool_arguments) { GtOptionParser *op; GtOption *option, *optionminocc, *optionmaxocc, *optionpl, *optionstoreindex, *optionstorecounts, *optionscan, *optionesa; Tyr_mkindex_options *arguments = tool_arguments; op = gt_option_parser_new("[options] -esa suffixerator-index [options]", "Count and index k-mers in the given enhanced " "suffix array for a fixed value of k."); gt_option_parser_set_mailaddress(op,"<*****@*****.**>"); optionesa = gt_option_new_string("esa","specify suffixerator-index\n" "(mandatory option)", arguments->str_inputindex, NULL); gt_option_is_mandatory(optionesa); gt_option_parser_add_option(op, optionesa); option = gt_option_new_ulong("mersize", "Specify the mer size.", &arguments->mersize, 20UL); gt_option_parser_add_option(op, option); optionminocc = gt_option_new_ulong("minocc", "Specify the minimum occurrence number for " "the mers to output/index", &arguments->userdefinedminocc, 0); gt_option_parser_add_option(op, optionminocc); optionmaxocc = gt_option_new_ulong("maxocc", "Specify the maximum occurrence number for " "the mers to output/index", &arguments->userdefinedmaxocc, 0); gt_option_parser_add_option(op, optionmaxocc); optionpl = gt_option_new_uint_min("pl", "specify prefix length for bucket boundary construction\n" "recommendation: use without argument;\n" "then a reasonable prefix length is automatically determined", &arguments->userdefinedprefixlength, 0, 1U); gt_option_argument_is_optional(optionpl); gt_option_parser_add_option(op, optionpl); arguments->refoptionpl = gt_option_ref(optionpl); optionstoreindex = gt_option_new_string("indexname", "store the mers specified by options " "-maxocc and -minocc in an index", arguments->str_storeindex, NULL); gt_option_parser_add_option(op, optionstoreindex); optionstorecounts = gt_option_new_bool("counts", "store counts of the mers", &arguments->storecounts,false); gt_option_parser_add_option(op, optionstorecounts); option = gt_option_new_bool("test", "perform tests to verify program " "correctness", &arguments->performtest, false); gt_option_is_development_option(option); gt_option_parser_add_option(op, option); optionscan = gt_option_new_bool("scan", "read enhanced suffix array sequentially " "instead of mapping it to memory", &arguments->scanfile, false); gt_option_parser_add_option(op, optionscan); option = gt_option_new_verbose(&arguments->verbose); gt_option_parser_add_option(op, option); gt_option_imply(optionpl, optionstoreindex); gt_option_imply(optionstorecounts, optionstoreindex); gt_option_imply_either_2(optionstoreindex,optionminocc,optionmaxocc); return op; }
static GtOptionParser* gt_ltrdigest_option_parser_new(void *tool_arguments) { GtLTRdigestOptions *arguments = tool_arguments; GtOptionParser *op; GtOption *o, *ot, *oto; GtOption *oh, *oc, *oeval; static const char *cutoffs[] = {"NONE", "GA", "TC", NULL}; static GtRange pptlen_defaults = { 8UL, 30UL}, uboxlen_defaults = { 3UL, 30UL}, pbsalilen_defaults = {11UL, 30UL}, pbsoffsetlen_defaults = { 0UL, 5UL}, pbstrnaoffsetlen_defaults = { 0UL, 5UL}; gt_assert(arguments); /* init */ op = gt_option_parser_new("[option ...] gff3_file", "Identifies and annotates sequence features in LTR " "retrotransposon candidates."); /* Output files */ oto = gt_option_new_string("outfileprefix", "prefix for output files (e.g. 'foo' will create " "files called 'foo_*.csv' and 'foo_*.fas')\n" "Omit this option for GFF3 output only.", arguments->prefix, NULL); gt_option_parser_add_option(op, oto); gt_option_hide_default(oto); o = gt_option_new_bool("metadata", "output metadata (run conditions) to separate file", &arguments->print_metadata, true); gt_option_parser_add_option(op, o); gt_option_imply(o, oto); o = gt_option_new_uint("seqnamelen", "set maximal length of sequence names in FASTA headers" " (e.g. for clustalw or similar tools)", &arguments->seqnamelen, 20U); gt_option_parser_add_option(op, o); /* PPT search options */ o = gt_option_new_range("pptlen", "required PPT length range", &arguments->ppt_len, &pptlen_defaults); gt_option_parser_add_option(op, o); o = gt_option_new_range("uboxlen", "required U-box length range", &arguments->ubox_len, &uboxlen_defaults); gt_option_parser_add_option(op, o); o = gt_option_new_uint("uboxdist", "allowed U-box distance range from PPT", &arguments->max_ubox_dist, 0); gt_option_parser_add_option(op, o); o = gt_option_new_uint("pptradius", "radius around beginning of 3' LTR " "to search for PPT", &arguments->ppt_radius, 30U); gt_option_parser_add_option(op, o); o = gt_option_new_probability("pptrprob", "purine emission probability inside PPT", &arguments->ppt_purine_prob, PPT_PURINE_PROB); gt_option_parser_add_option(op, o); gt_option_is_extended_option(o); o = gt_option_new_probability("pptyprob", "pyrimidine emission probability inside PPT", &arguments->ppt_pyrimidine_prob, PPT_PYRIMIDINE_PROB); gt_option_parser_add_option(op, o); gt_option_is_extended_option(o); o = gt_option_new_probability("pptgprob", "background G emission probability outside PPT", &arguments->bkg_g_prob, BKG_G_PROB); gt_option_parser_add_option(op, o); gt_option_is_extended_option(o); o = gt_option_new_probability("pptcprob", "background C emission probability outside PPT", &arguments->bkg_c_prob, BKG_C_PROB); gt_option_parser_add_option(op, o); gt_option_is_extended_option(o); o = gt_option_new_probability("pptaprob", "background A emission probability outside PPT", &arguments->bkg_a_prob, BKG_A_PROB); gt_option_parser_add_option(op, o); gt_option_is_extended_option(o); o = gt_option_new_probability("ppttprob", "background T emission probability outside PPT", &arguments->bkg_t_prob, BKG_T_PROB); gt_option_parser_add_option(op, o); gt_option_is_extended_option(o); o = gt_option_new_probability("pptuprob", "U/T emission probability inside U-box", &arguments->ubox_u_prob, UBOX_U_PROB); gt_option_parser_add_option(op, o); gt_option_is_extended_option(o); /* PBS search options */ ot = gt_option_new_filename("trnas", "tRNA library in multiple FASTA format for PBS " "detection\n" "Omit this option to disable PBS search.", arguments->trna_lib); gt_option_parser_add_option(op, ot); gt_option_hide_default(ot); o = gt_option_new_range("pbsalilen", "required PBS/tRNA alignment length range", &arguments->alilen, &pbsalilen_defaults); gt_option_parser_add_option(op, o); gt_option_imply(o, ot); o = gt_option_new_range("pbsoffset", "allowed PBS offset from LTR boundary range", &arguments->offsetlen, &pbsoffsetlen_defaults); gt_option_parser_add_option(op, o); gt_option_imply(o, ot); o = gt_option_new_range("pbstrnaoffset", "allowed PBS/tRNA 3' end alignment offset range", &arguments->trnaoffsetlen, &pbstrnaoffsetlen_defaults); gt_option_parser_add_option(op, o); gt_option_imply(o, ot); o = gt_option_new_uint("pbsmaxedist", "maximal allowed PBS/tRNA alignment unit " "edit distance", &arguments->max_edist, 1U); gt_option_parser_add_option(op, o); gt_option_imply(o, ot); o = gt_option_new_uint("pbsradius", "radius around end of 5' LTR " "to search for PBS", &arguments->pbs_radius, 30U); gt_option_parser_add_option(op, o); gt_option_imply(o, ot); /* Protein domain search options */ oh = gt_option_new_filename_array("hmms", "profile HMM models for domain detection " "(separate by spaces, finish with --) in " "HMMER3 format\n" "Omit this option to disable pHMM search.", arguments->hmm_files); gt_option_parser_add_option(op, oh); oeval = gt_option_new_probability("pdomevalcutoff", "global E-value cutoff for pHMM search\n" "default 1E-6", &arguments->evalue_cutoff, 0.000001); gt_option_parser_add_option(op, oeval); gt_option_is_extended_option(oeval); gt_option_hide_default(oeval); gt_option_imply(oeval, oh); oc = gt_option_new_choice("pdomcutoff", "model-specific score cutoff\n" "choose from TC (trusted cutoff) | " "GA (gathering cutoff) | " "NONE (no cutoffs)", arguments->cutoffs, cutoffs[0], cutoffs); gt_option_parser_add_option(op, oc); gt_option_is_extended_option(oeval); gt_option_imply(oeval, oh); o = gt_option_new_bool("aliout", "output pHMM to amino acid sequence alignments", &arguments->write_alignments, false); gt_option_parser_add_option(op, o); gt_option_imply(o, oh); gt_option_imply(o, oto); o = gt_option_new_bool("aaout", "output amino acid sequences for protein domain " "hits", &arguments->write_aaseqs, false); gt_option_parser_add_option(op, o); gt_option_imply(o, oh); gt_option_imply(o, oto); o = gt_option_new_bool("allchains", "output features from all chains and unchained " "features, labeled with chain numbers", &arguments->output_all_chains, false); gt_option_parser_add_option(op, o); gt_option_imply(o, oh); o = gt_option_new_uint("maxgaplen", "maximal allowed gap size between fragments (in amino " "acids) when chaining pHMM hits for a protein domain", &arguments->chain_max_gap_length, 50U); gt_option_parser_add_option(op, o); gt_option_is_extended_option(o); gt_option_imply(o, oh); o = gt_option_new_ulong("threads", "DEPRECATED, only included for compatibility reasons!" " Use the -j parameter of the 'gt' call instead.", &arguments->nthreads, 0); gt_option_parser_add_option(op, o); gt_option_is_extended_option(o); /* Extended PBS options */ o = gt_option_new_int("pbsmatchscore", "match score for PBS/tRNA alignments", &arguments->ali_score_match, 5); gt_option_parser_add_option(op, o); gt_option_is_extended_option(o); gt_option_imply(o, ot); o = gt_option_new_int("pbsmismatchscore", "mismatch score for PBS/tRNA alignments", &arguments->ali_score_mismatch, -10); gt_option_parser_add_option(op, o); gt_option_is_extended_option(o); gt_option_imply(o, ot); o = gt_option_new_int("pbsinsertionscore", "insertion score for PBS/tRNA alignments", &arguments->ali_score_insertion, -20); gt_option_parser_add_option(op, o); gt_option_is_extended_option(o); gt_option_imply(o, ot); o = gt_option_new_int("pbsdeletionscore", "deletion score for PBS/tRNA alignments", &arguments->ali_score_deletion, -20); gt_option_parser_add_option(op, o); gt_option_is_extended_option(o); gt_option_imply(o, ot); /* verbosity */ o = gt_option_new_verbose(&arguments->verbose); gt_option_parser_add_option(op, o); /* output file options */ gt_output_file_info_register_options(arguments->ofi, op, &arguments->outfp); /* region mapping and sequence source options */ gt_seqid2file_register_options_ext(op, arguments->s2fi, false, false); return op; }