Package: ipanemap
IPANEMAPIntegrative Probing Analysis of Nucleic Acids Empowered by Multiple Accessibility Profiles.IPANEMAP is a software for predicting stable RNA secondary structures compatible from multiple chemical probing (SHAPE, DMS, Enzymatic...)  reactivities profiles. From one or several input sequences, along with several reactivity profiles, it computes and outputs one or several secondary structures, corresponding to the conformers best supported by experimental data and thermodynamics.Installing IPANEMAPIPANEMAP consists in a set of Python 2.7+ scripts, and requires the prior installation, and accessibility from the command line, of the followingdependencies:ViennaRNApackage, version posterior to 2.0,downloadable from the TBIscikit-learn,version 0.2 for Python 2.7+scipyandnumpy.On a standardpythoninstallation, all dependencies except for theViennaRNApackage can be solved usingpip:pip install cython scipy numpy sklearnExecuting IPANEMAPOnce all dependencies are satisfied, IPANEMAP can be invoked through:python2.7 IPANEMAP.py [--RNA rnafile.fa] [--cond c1 c2 ...]The method will run with a configuration specified withinIPANEMAP.cfg, optionally overriding the RNA using the--RNAcommand-line option, and the  list of conditions with the--condoption (see below for more details).Input filesReactivity/soft constraints file formatIPANEMAP expects to find reactivities for a condition{Cond}in  a file{SoftConstraintsDir}/{RNA}{Cond}.txt, where{RNA}is the name of the chosen RNA (ie the name of the input FASTA file, minus its extension), and{SoftConstraintsDir}is the general folder where reactivities are located.The content of a reactivity file is simply a list of position/value pairs providing a reactivity for each position.
Values are expected to be loosely normalized, and fall in the [0,1] interval (except for a few outliers), with negative numbers mainly indicating missing values.Example:1	0.568309
  2	0.179692
  3	-999
  4	0.568389
       ....Hard constraints file formatHard constraints allow to force predictions to be consistent with prior partial knowledge. They should be expressed in a file{HardConstraintsDir}/{RNA}{Cond}.txtin classic FASTA/DBN format (see example below), consisting of sequence/constraint mask in extended dot-bracket notation supported by theVienna package syntax.Example: The following file content> Some RNA
  CCCAAAUGGG
  (x(....)x)indicates that two base pairs, corresponding to matching parentheses(and), should always be respected by the models.
Positions associated withxwill be forced to remain unpaired, but positions associated with a dot.are not constrained in the folding.
More complex constraints are available, as described in theVienna package documentation.OutputsBasic outputIPANEMAP typically produces many messages during execution, to keep the user informed of its progress.
However, only the final (Pareto) structural models are output to the standard output, meaning that, after runningpython2.7 IPANEMAP.py > output.dattheoutput.datfile will only consist of the final models.Example:For an input sequenceGGGAAACCCAAAGGGAAACCC, and probing profile assigning high accessibilities toAs, running the above command will lead to the production of a fileoutput.dat, having contentStructure                 dG   #SupportingConditions     BoltzmannProbability
(((...)))...(((...)))   -4.3                       1       0.5735037115553154where each line represents a cluster, and consists of:Secondary structure model (centroid of the cluster)Free-energy, as recomputed usingRNAeval;Number of supporting conditions;Accumulated Boltzmann probability across conditions (aka stability in the companion manuscript), as computed usingRNAeval.In this example, a unique probing condition implies a single model, but multiple structures may be produced in a multi-probing setting.ConfigurationMost configuration options are set by modifying the content of theIPANEMAP.cfgfile.Main optionsRNA: Specifies a path (relative to the working directory) to a FASTA file where the nucleotide sequence of the main RNA of interest can be found. Note that the filename is important, as it will be used as a base name for the other input files.Example:RNA: fasta_files/didymium.fawill process the sequence found in the file, anddidymiumwill be used as thebase nameof reactivities/hard contraints files (seeConditionsoption)SoftConstraintsDirandHardConstraintsDir: Sets thedirectoriesused by IPANEMAP to locate soft (reactivities) and hard constraints files (if available)Conditions: Can be used to specify the list of probing conditions used for the prediction. Should be set to a comma-separated list of conditions, i.e. the names of reactivity profiles/experiments to be considered for structure predictionFor an RNA having base name{RNA}, and a condition name{Cond}, IPANEMAP will attempt to locate files named{SoftConstraintsDir}/{RNA}{Cond}.txtand{HardConstraintsDir}/{RNA}{Cond}.txt. If none of these files is found, the method will rely on a purely thermodynamic sampling.Example:Given a configuration[Input] 
  RNA: fasta_files/5sRNA.fa
  SoftConstraintsDir: soft
  HardConstraintsDir: hard
  Conditions: DMSMG,NMIA
  ...the method will attempt to locate, and use for the sampling phase of the method, two files5sRNADMSMG.txtand5sRNANMIA.txtin each of thesoftandharddirectories.Sampling optionsDoSampling: If set totrue, IPANEMAP will always re-generate a representative structural sample (even if one can already be found)NumStructures: Number of structures per condition, generated to approximate the pseudo-Boltzmann ensembleTemperature: Temperature (in Celsius) used for the samplingmandb: Slope and intercept used in thereactivity to pseudo-energyconversion (see Deigan et al, PNAS 2009)Misc optionsWorkingDir: Main output directory for temp files, and final results of the analysis. Directory  will be created if non-existent.LogFile: Name of file gathering the accumulated log. File will be created if non-existent.Visualization optionsIPANEMAP currently relies on VARNA to produceDrawModels: If set totrue, uses VARNA to draw the final, Pareto-optimal, secondary structure models.DrawCentroids: If set totrue, uses VARNA to draw the centroids associated with all of the clusters.ShowProbing:  If set totrue, uses the reactivities ofthe first probing condition(as specified to thecondoption, orConditionssection of the config file) to annotate the secondary structure drawings.How to...How do I perform apure thermodynamic/constraints-free prediction?Simply make sure that no constraint file named{RNA}{Cond}.txtis found in either{SoftConstraintsDir}or{HardConstraintsDir}, and IPANEMAP will default to a purely thermodynamic sampling (you may safely ignore the warning).Example:Executing the commandpython2.7 IPANEMAP.py --RNA rna.fa --cond thermowithnofile namedrnathermo.txtin either of the constraints directories will run a pure thermodynamic prediction.How do I specify a different sequence for some specific condition?This need arises when minor variants of the original sequence have been probed (eg Mutate-and-Map protocols), and must be used for the sampling.When available, hard constraint files already specify a sequence, which is used instead of the main FASTA file for the sampling.Example:For an RNA filemyRNA.faand a condition name ofSHAPE, the sequence found in a{HardConstraintsDir}/myRNASHAPE.txtfile, will be used for the sampling instead of the one found inmyRNA.fa.For reactivity/SHAPE data files, if a FASTA file named{RNA}{Cond}.fais found in either of the condition directories, then its sequence will be used instead of the main FASTA file.Example:For an RNArib.faand a condition name1M7, the sequence found at{SoftConstraintsDir}/rib1M7.fawill be used for the sampling instead of the one found inrib.fa.CitationPlease cite:
A. Saaidi, D. Allouche, M. Regnier, B. Sargueil, Y.Ponty. IPANEMAP: Integrative Probing Analysis of Nucleic Acids Empowered by Multiple Accessibility Profiles, NAR(2020),link