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mutarna's Introduction

MutARNA: mutational analysis and visualization for short and long span interactions of RNAs

Setup

conda env create -f conda-env-MutaRNA.yml -n MutaRNA
source activate MutaRNA

Usage

usage: MutaRNA-plot.py [-h] --fasta-wildtype FASTA_WILDTYPE --SNP-tag SNP_TAG
                       [--out-dir OUT_DIR] [--no-global-fold]
                       [--no-local-fold] [--local-W LOCAL_W]
                       [--local-L LOCAL_L] [--global-maxL GLOBAL_MAXL]
                       [--no-SNP-score] [--enable-long-range]
                       [--enable-global-fold]

MutaRNA-plot predict and plot local and global base-pair probabilities of
wildtype and mutant RNAs Sample call: "python bin/MutaRNA-plot.py --fasta-
wildtype data/sample0.fa --SNP-tag G3C --out-dir tmp --no-global-fold"

optional arguments:
  -h, --help            show this help message and exit
  --fasta-wildtype FASTA_WILDTYPE
                        Input sequence wildtype in fasta format
  --SNP-tag SNP_TAG     SNP tag e.g. "C3G" for mutation at position 3 from C
                        to G
  --out-dir OUT_DIR     path the output directory. The directory must already
                        exist.
  --no-global-fold      Do not run (semi-)global fold (semi: max-window
                        1000nt)
  --no-local-fold       Do not run local fold
  --local-W LOCAL_W     Window length for local fold
  --local-L LOCAL_L     Max base-pair interaction span for local fold
  --global-maxL GLOBAL_MAXL
                        Maximum interaction span of global length.
  --no-SNP-score        Do not run SNP structure abberation scores with RNAsnp
                        and remuRNA
  --enable-long-range   predict and plot long-range interactions of wildtype
                        and mutant RNAs using IntaRNA
  --enable-global-fold  enable global fold

Example call

python bin/MutaRNA-plot.py --fasta-wildtype data/sample0.fa --SNP-tag G3C --out-dir ./results/

Output

Outputs are stored under the current directory (by default) or the specified path via --out-dir option.

Local

The results under the local/ directory contain the visualization of base-pairing probabilities as computed by RNAplfold under different conditions. The plots are generated in two file formats (.png and svg).

- `RNA-WILD-circos`: The base pair probabilities of the wild type in circular Circos form. 
- `RNA-MUTANT-circos`: The base pair probabilities of the mutant in circular Circos form. 
- `RNA-MUTANT-removed-circos`: The weakened base-pairing potentials in the form of probability difference between WT and mutant.
- `RNA-MUTANT-introduced-circos`: The increased base-pairings potentials in the form of probability difference between mutant and WT.
- `RNA-WT-MUT-dotplot`: The base pair probabilities of the wild type (upper right) and mutant (lower left) in dotplot-style matrix format heatmap plots.
- `RNA-REMOVED-INTRODUCED-dotplot`: The weakened base-pairing potentials in the form of probability difference between WT and mutant (upper right). The increased base-pairings potentials in the form of probability difference between mutant and WT (lower left).
- `RNA_lunp-ECG` The position-wise unpaired probability, also know as accessibility, of wild type, mutant and their difference.

Global

The results under the global/ directory contain the visualization of base-pairing probabilities as computed by RNAplfold. Similar to the local mode but allowing for large base-pair span over the sequence length in a single window. under different conditions. The plots are generated in two file formats (.png and svg).

Predicted structural impact of the mutation:
- remuRNA.csv : prediction scores by remuRNA. remuRNA score (H(WT||MUT))is the relative entropy between the ensemble of structures in wild type versus mutant RNA. The score reflects the changes in the global structure of the RNA.
- RNAsnp.csv : prediction scores by RNAsnp. RNAsnp scores are generated in two modes (-m 1, -m 2) of (semi-)global and local folding and based on the two metrics of base-pairing distance (d_max) in both modes and correlation coefficient (r_min). RNAsnp further computes the significance of score in term of p-values against a pre-computed table of sequence with similar features.

mutarna's People

Contributors

Stargazers

Watchers

Forkers

backofenlab martin-raden

mutarna's Issues

Possible 1b shift in circos annotation

The annotation seems to be 1 base shifted. Here upstream neighbor C must be annotated not the G

And:

Unique data and file folder on tmp path for dot2circ

The dot2circ temporary results must be located under the dynamic tmp location:

$ ls dot2circ/
dot.ps
data

accessibility plots : differential diff plotting

green = wt accessibility
orange = mt accessibility
blue= max( 0 , wt - mt ) : accessibility increased
red = max( 0 , mt -wt ) : accessibility decreased

circos : title slightly rotated to the left

title layout not horizontal

remuRNA output col order (SNP not first)

SNP should be first column...

accessibility plot

title: remove "(wt)"
legend order: wt (top), mt, delta (bottom)

position ticks in circplots

.. to better map location and base pairing

heatmaps tweaks

vertical + horizontal red line at mutation position

generate and store RNAfold mfe structure plots

to visualize also mfe within webserver

plot title wrong!

in the diff-dot-plots titles you write Pr(wt)-Pr(mt) but in the box you annotate delta > 0 : weakend and delta < 0 : increased

but if Pr(wt) > Pr(mt), ie. weaker, delta >0 according to your formula..

so either the title is wrong or the in-box-text ..

@mmiladi please correct

heatmap tweaks

ticks only every 10
vertical x-tick label (at the bottom?)
50%alpha gray lines every 50nt

Annotate mutation on dotplot and ECG

Annotate mutation on dotplot with two horizontal and vertical dashed lines
Annotate mutation on ECG with one vertical dashed line

--temperature parameter

acc plot tweaks

red mutation line = dashed (as in heatmap)
ticks only every 10 (not at every x)
gray background lines only every 10 (at ticks); instead of leaving it out every 10

Report RNAsnp warnings

RNAsnp reports a warning if p-values are not available for the provided sequence length. These errors must be reported to the user.

Report of a form:

'SNP', 'H(wt||mu)', 'MFE(mu)', 'MFE(wt)', 'dMFE']
-m 1 
ERROR: RNASNP returned warning for: /scratch/rna/bisge001/RNA_results/CARNA-result/MutaRNA_4348332/input_rna.fa message is:Warnings: The input sequence length 55 is less than twice the size of chosen flanking size 200. Thus, the reporting p-value is not accurate. Please refer to the README file for more details.
SNP	w	Slen	GC	interval	d_max	p-value	interval	r_min	p-value
C7G	200	55	0.2182	2-51	0.0014	0.9048	4-53	0.9929	0.8692

full collaborator rights for martin in this repo... :)

document arc plot R scripts

short docu on main README
dedicated README.MD file in bin folder

color coding in differential circos plots

weaking plot: make edges blue
increase plot: make edges red

indel support ?

could be done by inserting dummy N chars at the deleted or inserted positions for plotting
the "extended" sequences should NOT be used as RNAplfold input, since they are causing problems with the minimal and maximal base pair span

Empty impact range diff matrix throws an exception

In the procedure to get the ideal impact range in the zoomed mode, a fixed minimum probability is assigned. This causes a problem once all the probability differences are below the set threshold.

Do these the zoomed range list get empty:
https://github.com/mmiladi/MutaRNA/blob/master/bin/MutaRNA-plot.py#L129

Now the question is how to deal with this case:

Should the the probability threshold be dynamically lowered (e.g. by 1/10) until the list is not empty?
Should we report the full figure instead?

ping @martin-raden

Rename WILD to WILDTYPE in Circos plots

support for input of multiple mutations (batch mode)

generate files per mutation
generate one table for remuRNA/rnaSNP covering values for all mutations

new option '--idxPos0' (default=1) to guide indexing

defines the in/out index of the first sequence position
if negative; ignore 0 from indexing
use this information to map mutation encoding to sequence position

(similar to IntaRNA --t/qIdxPos0)

allows to study same mutation (encoding) within different sequence context lengths

Min threshold for circos and rchie plots

The probability cutoff thresholds used for arc plots and circos/dot plots are different.
http://rna.informatik.uni-freiburg.de/MutaRNA/Result.jsp?toolName=MutaRNA&jobID=6777765

It could confuse the users.

Installation issue: PackagesNotFoundError

Hi. I'm trying to install MutaRNA but I'm getting PackagesNotFoundError error.

git clone https://github.com/mmiladi/MutaRNA.git
cd MutaRNA
conda env create -f conda-env-MutaRNA.yml -n MutaRNA

Channels:
 - conda-forge
 - bioconda
 - defaults
 - r
 - conda
Platform: linux-64
Collecting package metadata (repodata.json): done
Solving environment: failed

PackagesNotFoundError: The following packages are not available from current channels:

  - gcc_impl_linux-64==7.3.0=habb00fd_2
  - gdk-pixbuf==2.36.12=haf2c3b9_1004
  - gxx_impl_linux-64==7.3.0=hdf63c60_2

Current channels:

  - https://conda.anaconda.org/conda-forge/linux-64
  - https://conda.anaconda.org/bioconda/linux-64
  - https://repo.anaconda.com/pkgs/main/linux-64
  - https://repo.anaconda.com/pkgs/r/linux-64
  - https://conda.anaconda.org/r/linux-64
  - https://conda.anaconda.org/conda/linux-64

To search for alternate channels that may provide the conda package you're
looking for, navigate to

    https://anaconda.org

and use the search bar at the top of the page.