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_seqtransform_option_parser_new(void *tool_arguments)
{
SeqtransformArguments *arguments = tool_arguments;
GtOptionParser *op;
GtOption *o;
gt_assert(arguments);
op = gt_option_parser_new("[option ...] [sequence_file ...]",
"Perform simple transformations on the given "
"sequence file(s).");
/* -addstopaminos */
o = gt_option_new_bool("addstopaminos", "append stop amino acids ('"
GT_STOP_AMINO_CSTR"') to given protein sequences, if "
"not already present", &arguments->addstopaminos,
false);
gt_option_parser_add_option(op, o);
/* -width */
o = gt_option_new_width(&arguments->width);
gt_option_parser_add_option(op, o);
gt_output_file_info_register_options(arguments->ofi, op, &arguments->outfp);
return op;
}
static GtOptionParser* gt_seqfilter_option_parser_new(void *tool_arguments)
{
SeqFilterArguments *arguments = tool_arguments;
GtOption *option;
GtOptionParser *op;
gt_assert(arguments);
op = gt_option_parser_new("[option ...] [sequence_file ...]",
"Filter the given sequence file(s) and show the "
"results on stdout.");
/* -minlength */
option = gt_option_new_uword("minlength",
"set minimum length a sequence must "
"have to pass the filter", &arguments->minlength,
GT_UNDEF_UWORD);
gt_option_parser_add_option(op, option);
/* -maxlength */
option = gt_option_new_uword("maxlength", "set maximum length a sequence can "
"have to pass the filter", &arguments->maxlength,
GT_UNDEF_UWORD);
gt_option_parser_add_option(op, option);
/* -maxseqnum */
option = gt_option_new_uword("maxseqnum", "set the maximum number of "
"sequences which can pass the filter",
&arguments->maxseqnum, GT_UNDEF_UWORD);
gt_option_parser_add_option(op, option);
/* -sample */
option = gt_option_new_double_min_max("sample", "set a probability for each "
"sequence to pass the filter",
&arguments->sample_prob,
SEQFILTER_DEF_PROB,
SEQFILTER_MIN_PROB,
SEQFILTER_MAX_PROB);
gt_option_parser_add_option(op, option);
/* -step */
option = gt_option_new_uword_min("step", "only every 'step'-th sequence "
"passes the filter",
&arguments->step,
SEQFILTER_DEF_STEP,
SEQFILTER_MIN_STEP);
gt_option_parser_add_option(op, option);
/* -width */
option = gt_option_new_width(&arguments->width);
gt_option_parser_add_option(op, option);
gt_output_file_info_register_options(arguments->ofi, op, &arguments->outfp);
return op;
}
static GtOptionParser* gt_sequniq_option_parser_new(void *tool_arguments)
{
GtSequniqArguments *arguments = tool_arguments;
GtOptionParser *op;
GtOption *seqit_option, *verbose_option, *width_option, *rev_option,
*nofseqs_option;
gt_assert(arguments);
op = gt_option_parser_new("[option ...] sequence_file [...] ",
"Filter out repeated sequences in given "
"sequence files.");
/* -seqit */
seqit_option = gt_option_new_bool("seqit", "use sequence iterator",
&arguments->seqit, false);
gt_option_is_development_option(seqit_option);
gt_option_parser_add_option(op, seqit_option);
/* -nofseqs */
nofseqs_option = gt_option_new_uword("nofseqs", "number of sequences "
"(improves efficiency)\ndefault: unspecified",
&arguments->nofseqs, 0);
gt_option_is_development_option(nofseqs_option);
gt_option_hide_default(nofseqs_option);
gt_option_parser_add_option(op, nofseqs_option);
/* -rev */
rev_option = gt_option_new_bool("rev", "also filter out sequences whose "
"reverse complement is identical to a sequence already output",
&arguments->rev, false);
gt_option_parser_add_option(op, rev_option);
/* -v */
verbose_option = gt_option_new_verbose(&arguments->verbose);
gt_option_parser_add_option(op, verbose_option);
/* -width */
width_option = gt_option_new_width(&arguments->width);
gt_option_parser_add_option(op, width_option);
gt_output_file_info_register_options(arguments->ofi, op, &arguments->outfp);
/* option implications */
gt_option_imply(verbose_option, seqit_option);
gt_option_parser_set_comment_func(op, gt_gtdata_show_help, NULL);
gt_option_parser_set_min_args(op, 1U);
return op;
}
static GtOptionParser* gt_splitfasta_option_parser_new(void *tool_arguments)
{
SplitfastaArguments *arguments = tool_arguments;
GtOptionParser *op;
GtOption *targetsize_option, *splitdesc_option, *o, *numfiles_option;
gt_assert(arguments);
op = gt_option_parser_new("[option ...] fastafile","Split the supplied fasta "
"file.");
numfiles_option = gt_option_new_uint_min("numfiles",
"set the number of target files "
"",
&arguments->num_files, 0,
1);
gt_option_parser_add_option(op, numfiles_option);
targetsize_option = gt_option_new_ulong_min("targetsize",
"set the target file "
"size in MB",
&arguments->max_filesize_in_MB,
50, 1);
gt_option_parser_add_option(op, targetsize_option);
splitdesc_option = gt_option_new_string("splitdesc",
"put every fasta entry in "
"a separate file named by its "
"description in the given directory",
arguments->splitdesc, NULL);
gt_option_parser_add_option(op, splitdesc_option);
gt_option_exclude(targetsize_option, splitdesc_option);
gt_option_exclude(numfiles_option, splitdesc_option);
gt_option_exclude(numfiles_option, targetsize_option);
o = gt_option_new_width(&arguments->width);
gt_option_parser_add_option(op, o);
o = gt_option_new_bool(GT_FORCE_OPT_CSTR, "force writing to output file",
&arguments->force, false);
gt_option_parser_add_option(op, o);
gt_option_parser_set_min_max_args(op, 1, 1);
return op;
}
static GtOptionParser* gt_seqfilter_option_parser_new(void *tool_arguments)
{
SeqFilterArguments *arguments = tool_arguments;
GtOption *option;
GtOptionParser *op;
gt_assert(arguments);
op = gt_option_parser_new("[option ...] [sequence_file ...]",
"Filter the given sequence_file(s) and show the "
"results on stdout.");
/* -minlength */
option = gt_option_new_ulong("minlength",
"set minimum length a sequence must "
"have to pass the filter", &arguments->minlength,
GT_UNDEF_ULONG);
gt_option_parser_add_option(op, option);
/* -maxlength */
option = gt_option_new_ulong("maxlength", "set maximum length a sequence can "
"have to pass the filter", &arguments->maxlength,
GT_UNDEF_ULONG);
gt_option_parser_add_option(op, option);
/* -maxseqnum */
option = gt_option_new_ulong("maxseqnum", "set the maximum number of "
"sequences which can pass the filter",
&arguments->maxseqnum, GT_UNDEF_ULONG);
gt_option_parser_add_option(op, option);
/* -width */
option = gt_option_new_width(&arguments->width);
gt_option_parser_add_option(op, option);
gt_outputfile_register_options(op, &arguments->outfp, arguments->ofi);
return op;
}
static GtOptionParser* gt_seqmutate_option_parser_new(void *tool_arguments)
{
MutateArguments *arguments = tool_arguments;
GtOptionParser *op;
GtOption *o;
gt_assert(arguments);
op = gt_option_parser_new("[option ...] [sequence_file ...]",
"Mutate the sequences of the given sequence "
"file(s).");
/* -rate */
o = gt_option_new_uint_max("rate", "set the mutation rate", &arguments->rate,
1, 100);
gt_option_parser_add_option(op, o);
/* -width */
o = gt_option_new_width(&arguments->width);
gt_option_parser_add_option(op, o);
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_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_width(&arguments->width);
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_condenseq_extract_option_parser_new(void *tool_arguments)
{
GtCondenserExtractArguments *arguments = tool_arguments;
GtOptionParser *op;
GtOption *option,
*optionrange,
*optionseq,
*optionseqrange,
*optionmode;
static const char *modes[] = {"fasta", "concat", NULL};
gt_assert(arguments);
/* init */
op = gt_option_parser_new("[options] archive",
"Decompresses condenseq archive.");
/* -seq */
optionseq = gt_option_new_uword("seq",
"only extract sequence identified by its "
"number",
&arguments->seq, GT_UNDEF_UWORD);
gt_option_parser_add_option(op, optionseq);
/* -seqrange */
optionseqrange = gt_option_new_range("seqrange",
"only extract (inclusive) range of "
"consecutive sequences identified by "
"their zero based index numbers",
&arguments->seqrange, NULL);
gt_option_parser_add_option(op, optionseqrange);
gt_option_exclude(optionseq, optionseqrange);
/* -range */
optionrange = gt_option_new_range("range",
"only extract (inclusive) range of zero "
"based positions "
"(implies option -output concat)",
&arguments->range, NULL);
gt_option_parser_add_option(op, optionrange);
gt_option_exclude(optionseq, optionrange);
gt_option_exclude(optionseqrange, optionrange);
/* -output */
optionmode = gt_option_new_choice("output",
"specify output format "
"(choose from fasta|concat)",
arguments->mode,
modes[0],
modes);
gt_option_parser_add_option(op, optionmode);
gt_option_imply(optionrange, optionmode);
/* -sepchar */
option = gt_option_new_string("sepchar",
"specify character to print as SEPARATOR "
"(implies option -output concat",
arguments->sepchar, "|");
gt_option_parser_add_option(op, option);
gt_option_imply(option, optionmode);
arguments->sepchar_opt = gt_option_ref(option);
gt_output_file_info_register_options(arguments->ofi, op, &arguments->outfp);
/* -width */
option = gt_option_new_width(&arguments->width);
gt_option_parser_add_option(op, option);
/* -verbose */
option = gt_option_new_bool("verbose", "Print out verbose output to stderr.",
&arguments->verbose, false);
gt_option_parser_add_option(op, option);
return op;
}
static GtOptionParser* gt_gff3_option_parser_new(void *tool_arguments)
{
GFF3Arguments *arguments = tool_arguments;
GtOptionParser *op;
GtOption *sort_option, *load_option, *strict_option, *tidy_option,
*mergefeat_option, *addintrons_option, *offset_option,
*offsetfile_option, *setsource_option, *option;
gt_assert(arguments);
/* init */
op = gt_option_parser_new("[option ...] [GFF3_file ...]", "Parse, possibly "
"transform, and output GFF3 files.");
/* -sort */
sort_option = gt_option_new_bool("sort", "sort the GFF3 features (memory "
"consumption is proportional to the input "
"file size(s))",
&arguments->sort, false);
gt_option_parser_add_option(op, sort_option);
/* -strict */
strict_option = gt_option_new_bool("strict", "be very strict during GFF3 "
"parsing (stricter than the specification "
"requires)", &arguments->strict, false);
gt_option_is_development_option(strict_option);
gt_option_parser_add_option(op, strict_option);
/* -tidy */
tidy_option = gt_option_new_bool("tidy", "try to tidy the GFF3 files up "
"during parsing", &arguments->tidy, false);
gt_option_parser_add_option(op, tidy_option);
gt_option_exclude(strict_option, tidy_option);
/* -retainids */
option = gt_option_new_bool("retainids",
"when available, use the original IDs provided "
"in the source file\n"
"(memory consumption is proportional to the "
"input file size(s))", &arguments->retainids,
false);
gt_option_parser_add_option(op, option);
/* -checkids */
option = gt_option_new_bool("checkids",
"make sure the ID attributes are unique "
"within the scope of each GFF3_file, as required "
"by GFF3 specification\n"
"(memory consumption is proportional to the "
"input file size(s))", &arguments->checkids,
false);
gt_option_parser_add_option(op, option);
/* -addids */
option = gt_option_new_bool("addids", "add missing \""
GT_GFF_SEQUENCE_REGION"\" lines automatically",
&arguments->addids, true);
gt_option_parser_add_option(op, option);
/* -fixregionboundaries */
option = gt_option_new_bool("fixregionboundaries", "automatically adjust \""
GT_GFF_SEQUENCE_REGION"\" lines to contain all "
"their features (memory consumption is "
"proportional to the input file size(s))",
&arguments->fixboundaries, false);
gt_option_parser_add_option(op, option);
/* -mergefeat */
mergefeat_option = gt_option_new_bool("mergefeat",
"merge adjacent features of the same "
"type", &arguments->mergefeat, false);
gt_option_is_development_option(mergefeat_option);
gt_option_imply(mergefeat_option, sort_option);
gt_option_parser_add_option(op, mergefeat_option);
/* -load */
load_option = gt_option_new_bool("load", "load the GFF3 features into memory "
"(requires space proportional to the input "
"file size(s))",
&arguments->load, false);
gt_option_is_development_option(load_option);
gt_option_parser_add_option(op, load_option);
/* -addintrons */
addintrons_option = gt_option_new_bool("addintrons", "add intron features "
"between existing exon features",
&arguments->addintrons, false);
gt_option_parser_add_option(op, addintrons_option);
/* -offset */
offset_option = gt_option_new_word("offset", "transform all features by the "
"given offset", &arguments->offset,
GT_UNDEF_WORD);
gt_option_parser_add_option(op, offset_option);
/* -offsetfile */
offsetfile_option = gt_option_new_filename("offsetfile", "transform all "
"features by the offsets given in "
"file", arguments->offsetfile);
gt_option_parser_add_option(op, offsetfile_option);
gt_option_exclude(offset_option, offsetfile_option);
/* -setsource */
setsource_option = gt_option_new_string("setsource", "set the 'source' "
"value (2nd column) of each feature",
arguments->newsource, NULL);
gt_option_parser_add_option(op, setsource_option);
/* typecheck options */
gt_typecheck_info_register_options(arguments->tci, op);
/* -show */
option = gt_option_new_bool("show", "show GFF3 output", &arguments->show,
true);
gt_option_parser_add_option(op, option);
/* -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);
/* set comment function */
gt_option_parser_set_comment_func(op, gt_gtdata_show_help, NULL);
return op;
}
