premirnaplot 0.4

python3+ premiRNA-plot.py [INPUTS] … [OPTIONS] …

Pre-miRNA-plot is a program for generating multiple custom images of miRNA precursors based on RNAfold and RNAplot. It allows you to highlight the miRNA location within the precursor and obtain general and practical information about your data, so you can filter it or use it in publications.

The program accepts tab-separated text files containing possibly 4 columns:

1. Sequence ID (optional): Some sort of annotation or ID

   information about the sequence (e.g. ‘ath-miR-171’ or ‘seq1’);

2. Precursor sequence: The pre-miRNA sequence.

3. miRNA1 sequence: One of the miRNAs sequences.

4. miRNA2 sequence (optional): The other miRNA sequence.

File format examples:

pre-miRNA | miRNA1 | miRNA2 |

>>>>>>>>>>>>>>>>>>>>>> OR <<<<<<<<<<<<<<<<<<<<<<<

ID | pre-miRNA | miRNA1 | miRNA2 |

There is no problem if you don’t have both miRNAs sequences; you can inform just one and the program will work just fine.

Checkout our github repository for more details on how to use the program: https://github.com/igrorp/pre-miRNA-plot

Parameters:

-i, --input

(str …)

Inform the names of/paths to the files that you want to use.

-a, --annot

(str) –> (T or F)

Informs if you have some sort of sequence ID, such as a miRNA family annotation (e.g.’ath-miRNA-171’, ‘seq1’), necessarily on the first column, so that the generated image files can be named according to that ID.

Default = F (False)

-s, --style

(int) –> (between 1 and 5)

The style of created images. Check the repository to see how they look like.

Default = 3

-c, --color

(str str) OR (int int int int int int)

You can choose which colors to paint the miRNA sequence within the precursor. Always provide the 5p and 3p colors, respectively. You can choose the predefined color names blue, red, green, purple, pink, yellow, cyan, white, black and orange; or you can inform the RGB codes of the colors you want.

Ex: ‘-c blue green’ for blue 5p and green 3p Ex: ‘-c 255 255 0 153 0 204’ for yellow 5p and purple 3p Default = green and red

-t, --threads

(int)

Choose the number of allowed processors (CPUs) to be used.

Default = 1

-f, --formats

(str) –> (svg or pdf)

Choose the output format of the images. Choose between PDF and SVG.

Default = svg

-o, --outdir

(str)

The output name of directory created containing all the generated data.

Default = premirnaplot

If you have any comments, complaints, doubts or suggestions, please contact our main responsible for this project at igorpaim8@gmail.com or create an issue in out github repository https://github.com/igrorp/pre-miRNA-plot/issues.

Have a nice work and let’s keep making science evolve!