# Name of your program
package "RNAsubopt" # don't use package if you're using automake
purpose "calculate suboptimal secondary structures of RNAs"
#usage "RNAsubopt [options]\n"

# Version of your program
#version "2.0"   # don't use version if you're using automake


# command line options passed to gengetopt
args "--file-name=RNAsubopt_cmdl --include-getopt --default-optional --func-name=RNAsubopt_cmdline_parser --arg-struct-name=RNAsubopt_args_info"


description "Reads RNA sequences from stdin and (in the default -e mode) calculates all suboptimal secondary\
 structures within a user defined energy range above the minimum free energy (mfe). It prints the suboptimal\
 structures in dot-bracket notation followed by the energy in kcal/mol to stdout. Be careful, the number of\
 structures returned grows exponentially with both sequence length and energy range.\n\nAlternatively, when\
 used with the -p option, RNAsubopt produces Boltzmann weighted samples of secondary structures.\n"

# Options

option  "verbose" v
"Be verbose.\n"
details="Lower the log level setting such that even INFO messages are passed through.\n\n"
flag
off


section "I/O Options"
sectiondesc="Command line options for input and output (pre-)processing\n\n"

option  "infile"  i
"Read a file instead of reading from stdin.\n"
details="The default behavior of RNAsubopt is to read input from stdin. Using this parameter\
 the user can specify an input file name where data is read from.\n\n"
string
typestr="filename"
optional

option  "outfile" o
"Print output to file instead of stdout.\n"
details="This option may be used to write all output to output files rather than printing\
 to stdout. The default filename is \"RNAsubopt_output.sub\" if no FASTA header precedes\
 the input sequences and the --auto-id feature is inactive. Otherwise, output files with\
 the scheme \"prefix.sub\" are generated, where the \"prefix\" is taken from the sequence\
 id. The user may specify a single output file name for all data generated from the input\
 by supplying an optional string as argument to this parameter. In case a file with the same\
 filename already exists, any output of the program will be appended to it.\
 Note: Any special characters in the filename will be replaced by the filename delimiter,\
 hence there is no way to pass an entire directory path through this option yet.\
 (See also the \"--filename-delim\" parameter)\n\n"
string
typestr="filename"
argoptional
optional

option  "noconv"  -
"Do not automatically substitute nucleotide \"T\" with \"U\".\n\n"
flag
off

option  "auto-id"  -
"Automatically generate an ID for each sequence.\n"
details="The default mode of RNAsubopt is to automatically determine an ID from the input sequence\
 data if the input file format allows to do that. Sequence IDs are usually given in the FASTA\
 header of input sequences. If this flag is active, RNAsubopt ignores any IDs retrieved from the\
 input and automatically generates an ID for each sequence. This ID consists of a prefix and an\
 increasing number. This flag can also be used to add a FASTA header to the output even if\
 the input has none.\n\n"
flag
off

option  "id-prefix" -
"Prefix for automatically generated IDs (as used in output file names).\n"
details="If this parameter is set, each sequences' FASTA id will be prefixed\
 with the provided string. FASTA ids then take the form \">prefix_xxxx\" where\
 xxxx is the sequence number. Note: Setting this parameter implies --auto-id.\n\n"
string
typestr="STRING"
default="sequence"
optional

option  "id-delim" -
"Change the delimiter between prefix and increasing number for automatically generated IDs (as used in output file names).\n"
details="This parameter can be used to change the default delimiter \"_\" between\
 the prefix string and the increasing number for automatically generated ID.\n\n"
string
typestr="CHAR"
default="_"
optional
hidden

option  "id-digits"  -
"Specify the number of digits of the counter in automatically generated alignment IDs.\n"
details="When alignments IDs are automatically generated, they receive an increasing number, starting\
 with 1. This number will always be left-padded by leading zeros, such that the number takes up a\
 certain width. Using this parameter, the width can be specified to the users need. We allow\
 numbers in the range [1:18]. This option implies --auto-id.\n\n"
int
default="4"
optional
hidden

option  "id-start"  -
"Specify the first number in automatically generated IDs.\n"
details="When sequence IDs are automatically generated, they receive an increasing number,\
 usually starting with 1. Using this parameter, the first number can be specified to the users\
 requirements. Note: negative numbers are not allowed.\nNote: Setting this parameter implies\
 to ignore any IDs retrieved from the input data, i.e. it activates the --auto-id flag.\n\n"
long
default="1"
optional
hidden

option  "filename-delim" -
"Change the delimiting character used in sanitized filenames.\n"
details="This parameter can be used to change the delimiting character used while\
 sanitizing filenames, i.e. replacing invalid characters. Note, that the default\
 delimiter ALWAYS is the first character of the \"ID delimiter\" as supplied through\
 the --id-delim option. If the delimiter is a whitespace character or empty, invalid\
 characters will be simply removed rather than substituted.\
 Currently, we regard the following characters as illegal for use in filenames:\
 backslash '\', slash '/', question mark '?', percent sign '%', asterisk '*', colon ':',\
 pipe symbol '|', double quote '\"', triangular brackets '<' and '>'.\n\n"
string
typestr="CHAR"
default="ID-delimiter"
optional
hidden

option  "filename-full" -
"Use full FASTA header to create filenames.\n"
details="This parameter can be used to deactivate the default behavior of limiting\
 output filenames to the first word of the sequence ID. Consider the following example:\
 An input with FASTA header '>NM_0001 Homo Sapiens some gene' usually produces output\
 files with the prefix \"NM_0001\" without the additional data available in the FASTA\
 header, e.g. \"NM_0001.sub\". With this flag set, no truncation of the output filenames\
 is performed, i.e. output filenames receive the full FASTA header data as prefixes. Note,\
 however, that invalid characters (such as whitespace) will be substituted by a delimiting\
 character or simply removed, (see also the parameter option --filename-delim).\n\n"
flag
off
hidden


option  "log-level" -
"Set log level threshold.\n"
details="By default, any log messages are filtered such that only warnings (level 2) or errors (level 3)\
 are printed. This setting allows for specifying the log level threshold, where higher values result in\
 fewer information. Log-level 5 turns off all messages, even errors and other critical information.\n\n"
int
typestr="level"
default="2"
hidden


option  "log-file" -
"Print log messages to a file instead of stderr.\n"
string
typestr="filename"
default="RNAsubopt.log"
argoptional
hidden


option  "log-time" -
"Include time stamp in log messages.\n\n"
flag
off
hidden


option  "log-call" -
"Include file and line of log calling function.\n\n"
flag
off
hidden


section "Algorithms"
sectiondesc="Select the algorithms which should be applied to the given RNA sequence(s).\n\n"

option  "deltaEnergy" e
"Compute suboptimal structures with energy in a certain range of the optimum (kcal/mol).\n"
details="Default is calculation of mfe structure only.\n\n"
float
typestr="range"
optional

option  "deltaEnergyPost" -
"Only print structures with energy within range of the mfe after post reevaluation of energies.\n"
details="Useful in conjunction with -logML, -d1 or -d3: while the -e option specifies the range\
 before energies are re-evaluated, this option specifies the maximum energy after re-evaluation.\n\n"
float
typestr="range"
optional
hidden

option  "sorted"  s
"Sort the suboptimal structures by energy and lexicographical order.\n"
details="Structures are first sorted by energy in ascending order. Within groups of the same\
 energy, structures are then sorted in ascending in lexicographical order of their dot-bracket\
 notation. See the --en-only flag to deactivate this second step. Note that sorting is done in\
 memory, thus it can easily lead to exhaution of RAM! This is especially true if the number of\
 structures produced becomes large or the RNA sequence is rather long. In such cases better use\
 an external sort method, such as UNIX \"sort\".\n\n"
flag
off

option  "en-only" -
"Only sort structures by free energy.\n"
details="In combination with --sorted, this flag deactivates the second sorting criteria and\
 sorts structures solely by their free energy instead of additionally sorting by lexicographic\
 order in each energy band. This might save some time during the sorting process in situations\
 where lexicographic order is not required.\n\n"
dependon="sorted"
flag
off
hidden

option "stochBT"  p
"Randomly draw structures according to their probability in the Boltzmann ensemble.\n"
details="Instead of producing all suboptimals in an energy range, produce a random sample of suboptimal structures,\
 drawn with probabilities equal to their Boltzmann weights via stochastic backtracking in the partition\
 function. The -e and -p options are mutually exclusive.\n\n"
int
typestr="number"
optional

option  "stochBT_en"      -
"Same as \"--stochBT\" but also print free energies and probabilities of the backtraced structures.\n\n"
int
typestr="number"
optional
hidden

option    "random-seed"  -
"Set the seed for the random number generator\n\n"
int
optional
hidden


option  "betaScale" -
"Set the scaling of the Boltzmann factors.\n"
details="The argument provided with this option is used to scale the thermodynamic temperature\
 in the Boltzmann factors independently from the temperature of the individual loop energy contributions.\
 The Boltzmann factors then become 'exp(- dG/(kT*betaScale))' where 'k' is the Boltzmann constant, 'dG'\
 the free energy contribution of the state and 'T' the absolute temperature.\n\n"
double
default="1."
optional
dependon="stochBT"
hidden

option "nonRedundant" N
"Enable non-redundant sampling strategy.\n\n"
flag
off

option  "pfScale" S
"In the calculation of the pf use scale*mfe as an estimate for the ensemble free energy (used to avoid\
 overflows).\n"
details="The default is 1.07, useful values are 1.0 to 1.2. Occasionally needed for long sequences.\n\n"
double
default="1.07"
optional
hidden

option  "circ"    c
"Assume a circular (instead of linear) RNA molecule.\n\n"
flag
off

option  "dos" D
"Compute density of states instead of secondary structures.\n"
details="This option enables the evaluation of the number of secondary structures in certain energy bands around\
 the MFE.\n\n"
flag
off

option  "zuker" z
"Compute Zuker suboptimals instead of all suboptimal structures within an energy band around the MFE.\n\n"
flag
off

option  "gquad" g
"Incoorporate G-Quadruplex formation.\n"
details="No support of G-quadruplex prediction for stochastic backtracking and Zuker-style suboptimals yet).\n\n"
flag
off


section "Structure Constraints"
sectiondesc="Command line options to interact with the structure constraints feature of this program\n\n"

option  "maxBPspan" -
"Set the maximum base pair span.\n\n"
int
default="-1"
optional

option  "constraint"  C
"Calculate structures subject to constraints.\n"
details="The program reads first the\
 sequence, then a string containing constraints on the structure encoded with the symbols:\n\n'.' (no constraint\
 for this base)\n\n'|' (the corresponding base has to be paired\n\n'x' (the base is unpaired)\n\n'<' (base i is paired with\
 a base j>i)\n\n'>' (base i is paired with a base j<i)\n\nand matching brackets '(' ')' (base i pairs base j)\n\nWith the\
 exception of '|', constraints will disallow all pairs conflicting with the constraint. This is usually\
 sufficient to enforce the constraint, but occasionally a base may stay unpaired in spite of constraints. PF\
 folding ignores constraints of type '|'.\n\n"
string
typestr="filename"
default = ""
argoptional

option  "batch"   -
"Use constraints for multiple sequences.\n"
details="Usually, constraints provided from input file only apply to a single input sequence. Therefore,\
 RNAsubopt will stop its computation and quit after the first input sequence was processed. Using this\
 switch, RNAsubopt processes multiple input sequences and applies the same provided constraints to each of them.\n\n"
flag
off
dependon="constraint"
hidden

option  "canonicalBPonly" -
"Remove non-canonical base pairs from the structure constraint.\n\n"
flag
off
dependon="constraint"
hidden

option  "enforceConstraint" -
"Enforce base pairs given by round brackets '(' ')' in structure constraint.\n\n"
flag
off
dependon="constraint"


option  "commands"   -
"Read additional commands from file\n"
details="Commands include hard and soft constraints, but also structure motifs in hairpin and internal\
 loops that need to be treeted differently. Furthermore, commands can be set for unstructured and structured\
 domains.\n\n"
string
typestr="filename"
optional
hidden


section "Experimental Structure Probing Data"
sectiondesc="The following arguments and siwtches control various implementations that allow for\
 guiding the structure prediction with the help of additional (experimental) RNA structure probing\
 data, such as SHAPE, DMS, etc.\n\n"


option  "sp-data"   -
"Read structure probing data from an input file and guide the predictions accordingly. Must precede\
 the strategy, i.e. a data file must be specified before the corresponding --sp-strategy option!\n\n"
details="This option and its argument only specifies the file name with the (reactivity)\
 data. What kind of data the file contains and how the data is actually used during the\
 predictions can be specified by the --sp-strategy and --sp-preprocess options.\n\n"
string
typestr="filename"
multiple
optional


option  "sp-strategy" -
"Select the strategy how the probing data is used to guide the structure predictions.\n\n"
details="The following strategies (methods) are available to convert structure probing data into\
 pseudo energy contributions:\n\n\
 'D': Deigan et al 2009 strategy.\n\n\
 Here, probing data is converted into pseudo energy terms\
 using a linear model. The derived energies are then applied for every nucleotide involved in a\
 stacked pair. The default slope and intercept variables of the linear model are 'm=1.8' and\
 'b=-0.6', respectively. To change these parameters, e.g. to 'm=1.9' and 'b=-0.7', use a parameter\
 string like this: --sp-strategy=\"Dm1.9b-0.7\". Note the precedence of 'm' over 'b'. You may also\
 provide only one of the two variables like: --sp-strategy=\"Dm1.9\" or --sp-strategy=\"Db-0.7\".\n\n\
 'E': Eddy 2014 strategy.\n\n\
 This strategy distinguishes two structural states (classes) for each base, paired and unpaired.\
 Based on a list of prior distributions for each of the classes, the posterior probability for\
 observing a probing reactivity of a base is estimated and then converted into a respective\
 pseudo energy contribution. Thermodynamic temperature T is taken from the model settings as\
 specified by --temp but can be changed to any other value, either in degrees Celcius ('c' or 't')\
 or Kelvin ('k'). Use one of the following parameter strings to change the temperature to 25 degree\
 Celcius: --sp-strategy=\"Ec=25\" or --sp-strategy=\"Ek=298.15\".\
 By default, built-in prior distributions are used with this strategy. This can be changed if\
 the user passes additional probing data files via the --sp-data option and then selects the\
 prior distribution specifier ('P') as strategy (see below).\n\n\
 'P': Use probing data as prior distribution for Eddy 2014 strategy.\n\n\
 This indicates that the most recent probing data file actually contains a prior distribution\
 of probing data for a particular structure class, i.e. unpaired or paired bases. The prior\
 distribution then replaces the default priors in the Eddy 2014 ('E') strategy. Use the lower\
 case characters 'u' and 'p' to indicate which class, unpaired or paired, the prior distribution\
 represents, e.g. --sp-strategy=\"Pp\" will be interpreted as prior distribution for paired\
 nucleotides.\nNote, that this option must follow after the --sp-strategy=\"E\" and before\
 any further --sp-strategy options that do not specify other prior distributions!\n\n\
 'Z': Zarringhalam et al 2012 strategy.\n\n\
 Here, the probing data is first converted into pairing probabilities and aberration from the\
 observed pairing probabilities will be penalized during the folding recursion. The magnitude of\
 the penalties can affected by adjusting the factor beta (e.g. --sp-strategy=\"Zb0.8\").\n\n\
 'W': Apply a given vector of perturbation energies to unpaired nucleotides according to Washietl et al 2012.\
 Perturbation vectors can be calculated by using RNApvmin.\n\n"
string
typestr="strategy"
dependon="sp-data"
multiple
default="D"
optional


option  "sp-preprocess"  -
"Select a method to pre-process the structure probing data before it undergoes conversion by a strategy.\n\n"
string
typestr="method"
dependon="sp-data"
multiple
default="I"
optional
hidden


option  "shape" -
"Use SHAPE reactivity data to guide structure predictions.\n\n"
string
typestr="filename"
optional

option  "shapeMethod" -
"Select SHAPE reactivity data incorporation strategy.\n\n"
details="The following methods can be used to convert SHAPE reactivities into pseudo energy contributions.\n\n\
 'D': Convert by using the linear equation according to Deigan et al 2009. Derived pseudo energy terms\
 will be applied for every nucleotide involved in a stacked pair. This method is recognized by a capital\
 'D' in the provided parameter, i.e.: --shapeMethod=\"D\" is the default setting. The slope 'm' and the\
 intercept 'b' can be set to a non-default value if necessary, otherwise m=1.8 and b=-0.6. To alter these\
 parameters, e.g. m=1.9 and b=-0.7, use a parameter string like this: --shapeMethod=\"Dm1.9b-0.7\". You\
 may also provide only one of the two parameters like: --shapeMethod=\"Dm1.9\" or --shapeMethod=\"Db-0.7\".\n\n\
 'Z': Convert SHAPE reactivities to pseudo energies according to Zarringhalam et al 2012.\
 SHAPE reactivities will be converted to pairing probabilities by using linear mapping.\
 Aberration from the observed pairing probabilities will be penalized during the folding recursion.\
 The magnitude of the penalties can affected by adjusting the factor beta\
 (e.g. --shapeMethod=\"Zb0.8\").\n\n\
 'W': Apply a given vector of perturbation energies to unpaired nucleotides according to Washietl et al 2012.\
 Perturbation vectors can be calculated by using RNApvmin.\n\n"
string
typestr="method"
dependon="shape"
default="D"
optional
hidden

option  "shapeConversion" -
"Select method for SHAPE reactivity conversion.\n\n"
details="This parameter is useful when dealing with the SHAPE incorporation according to Zarringhalam et al. \
The following methods can be used to convert SHAPE reactivities into the probability for a certain nucleotide to be unpaired.\n
'M': Use linear mapping according to Zarringhalam et al.
'C': Use a cutoff-approach to divide into paired and unpaired nucleotides (e.g. \"C0.25\")
'S': Skip the normalizing step since the input data already represents probabilities for being unpaired rather than raw reactivity values
'L': Use a linear model to convert the reactivity into a probability for being unpaired (e.g. \"Ls0.68i0.2\" to use a slope of 0.68 and an intercept of 0.2)
'O': Use a linear model to convert the log of the reactivity into a probability for being unpaired (e.g. \"Os1.6i-2.29\" to use a slope of 1.6 and an intercept of -2.29)\n\n"
string
typestr="method"
default="O"
optional
hidden


section "Energy Parameters"
sectiondesc="Energy parameter sets can be adapted or loaded from user-provided input files\n\n"

option  "temp"  T
"Rescale energy parameters to a temperature of temp C. Default is 37C.\n\n"
double
default="37.0"
optional

option  "paramFile" P
"Read energy parameters from paramfile, instead of using the default parameter set.\n"
details="Different sets of energy parameters for RNA and DNA should accompany your distribution.\nSee the\
 RNAlib documentation for details on the file format. The placeholder file name 'DNA' can be used\
 to load DNA parameters without the need to actually specify any input file.\n\n"
string
typestr="paramfile"
optional

option  "noTetra" 4
"Do not include special tabulated stabilizing energies for tri-, tetra- and hexaloop hairpins.\n"
details="Mostly for testing.\n\n"
flag
off
hidden

option  "salt" -
"Set salt concentration in molar (M). Default is 1.021M.\n\n"
double
optional

option  "modifications" m
"Allow for modified bases within the RNA sequence string.\n"
details="Treat modified bases within the RNA sequence differently, i.e. use corresponding\
 energy corrections and/or pairing partner rules if available. For that, the modified bases\
 in the input sequence must be marked by their corresponding one-letter code. If no additional\
 arguments are supplied, all available corrections are performed. Otherwise, the user may\
 limit the modifications to a particular subset of modifications, resp. one-letter codes,\
 e.g. -mP6 will only correct for pseudouridine and m6A bases.\n\
 Currently supported one-letter codes and energy corrections are:\n\n\
 '7': 7-deaza-adenonsine (7DA)\n\n\
 'I': Inosine\n\n\
 '6': N6-methyladenosine (m6A)\n\n\
 'P': Pseudouridine\n\n\
 '9': Purine (a.k.a. nebularine)\n\n\
 'D': Dihydrouridine\n\n"
string
argoptional
default="7I6P9D"

option  "mod-file"  -
"Use additional modified base data from JSON file.\n\n"
string
multiple
optional


section "Model Details"
sectiondesc="Tweak the energy model and pairing rules additionally using the following parameters\n\n"

option  "dangles" d
"How to treat \"dangling end\" energies for bases adjacent to helices in free ends and multi-loops.\n"
details="\nWith -d1 only unpaired bases can participate in at most one dangling end. With -d2 this\
 check is ignored, dangling energies will be added for the bases adjacent to a helix on both sides in\
 any case; this is the default for mfe and partition function folding (-p).\nThe option -d0 ignores\
 dangling ends altogether (mostly for debugging).\nWith -d3 mfe folding will allow coaxial stacking\
 of adjacent helices in multi-loops. At the moment the implementation will not allow coaxial stacking\
 of the two enclosed pairs in a loop of degree 3 and works only for mfe folding.\n\nNote that with\
 -d1 and -d3 only the MFE computations will be using this setting while partition function uses\
 -d2 setting, i.e. dangling ends will be treated differently.\n\n"
int
default="2"
optional

option  "noLP"  -
"Produce structures without lonely pairs (helices of length 1).\n"
details="For partition function folding this only disallows pairs that can only occur isolated. Other\
 pairs may still occasionally occur as helices of length 1.\n\n"
flag
off

option  "noGU"  -
"Do not allow GU pairs.\n\n"
flag
off
hidden

option  "noClosingGU" -
"Do not allow GU pairs at the end of helices.\n\n"
flag
off
hidden

option  "logML" -
"Recompute energies of structures using a logarithmic energy function for multi-loops before output."
details="This option does not effect structure generation, only the energies that are printed out.\
 Since logML lowers energies somewhat, some structures may be missing.\n"
flag
off

option  "nsp" -
"Allow other pairs in addition to the usual AU,GC,and GU pairs.\n"
details="Its argument is a comma separated list of additionally allowed pairs. If the\
 first character is a \"-\" then AB will imply that AB and BA are allowed pairs, e.g.\
 --nsp=\"-GA\"  will allow GA and AG pairs. Nonstandard pairs are given 0 stacking\
 energy.\n\n"
string
optional
hidden

option  "energyModel" -
"Set energy model.\n"
details="Rarely used option to fold sequences from the artificial ABCD... alphabet, where\
 A pairs B, C-D etc.  Use the energy parameters for GC (--energyModel 1) or AU (--energyModel 2) pairs.\n\n"
int
optional
hidden

option  "helical-rise"  -
"Set the helical rise of the helix in units of Angstrom.\n"
details="Use with caution! This value will be re-set automatically to 3.4 in case DNA\
 parameters are loaded via -P DNA and no further value is provided.\n\n"
float
optional
default="2.8"
hidden

option  "backbone-length"  -
"Set the average backbone length for looped regions in units of Angstrom.\n"
details="Use with caution! This value will be re-set automatically to 6.76 in case DNA\
 parameters are loaded via -P DNA and no further value is provided.\n\n"
float
optional
default="6.0"
hidden


text    "\nIf in doubt our program is right, nature is at fault.\nComments should be sent to\
 rna@tbi.univie.ac.at.\n\n"
