monimaanam/Modomics_Decoder

Annotates modomics RNA sequences for easy viewing of RNA modifications and nucleotide positions.

Installation

git clone https://github.com/monimaanam/Modomics_Decoder

Modomics_Decoder.py

This script will take any copied unicode Modomics RNA sequence (from: https://genesilico.pl/modomics/sequences/) and annotate each modified position for easy viewing. Enter an RNA unicode sequence of interest (e.g., GGGGCUAU...) when prompted or through the CLI. A second prompt can be called to display all nucleotide positions enumerated, highlighting modified base positions.

Command Line Interface

USAGE: 
    python Modomics_Decoder.py
    python Modomics_Decoder.py --input <rna_sequence> --all
    python Modomics_Decoder.py -i <rna_sequence> -a > output_filename.txt
          
FLAGS: (optional)
    none             If flags are excluded, the script will prompt for inputs. 
    -h --help:       Displays the help menu (usage, flags, arguments). 
    -i --input:      Input RNA sequence as argument. RNA sequences must be in MODOMICS code. 
    -a --all:        Displays both the modifications table and the sequence positions list. 
    -t --table:      Displays the modifications table.
    -l --list:       Displays the enumerated sequence position list.
    -v --version:    Displays the current version (Version 1.1). 

Example Output

UNICODE Sequence: GGGGCUAUAGCUCAGCDGGGAGAGCGCCUGCUUVGCACGCAGGAG7UCUGCGGTPCGAUCCCGCAUAGCUCCACCA

position: 45 | symbol: 7 | short names: ['m7G', 'pm7G']
position: 16 | symbol: D | short names: ['pD', 'D']
position: 54 | symbol: P | short names: ['Y', 'pY']
position: 53 | symbol: T | short names: ['m5U', 'pm5U']
position: 33 | symbol: V | short names: ['pcmo5U', 'cmo5U']

View all positions? (Yes / No) Yes

(0, 'G')
(1, 'G')
(2, 'G')
(3, 'G')
(4, 'C')
(5, 'U')
(6, 'A')
(7, 'U')
(8, 'A')
(9, 'G')
(10, 'C')
(11, 'U')
(12, 'C')
(13, 'A')
(14, 'G')
(15, 'C')
(16, 'D') * mod
(17, 'G')
(18, 'G')
(19, 'G')
(20, 'A')
(21, 'G')
(22, 'A')
(23, 'G')
(24, 'C')
(25, 'G')
(26, 'C')
(27, 'C')
(28, 'U')
(29, 'G')
(30, 'C')
(31, 'U')
(32, 'U')
(33, 'V') * mod
(34, 'G')
(35, 'C')
(36, 'A')
(37, 'C')
(38, 'G')
(39, 'C')
(40, 'A')
(41, 'G')
(42, 'G')
(43, 'A')
(44, 'G')
(45, '7') * mod
(46, 'U')
(47, 'C')
(48, 'U')
(49, 'G')
(50, 'C')
(51, 'G')
(52, 'G')
(53, 'T') * mod
(54, 'P') * mod
(55, 'C')
(56, 'G')
(57, 'A')
(58, 'U')
(59, 'C')
(60, 'C')
(61, 'C')
(62, 'G')
(63, 'C')
(64, 'A')
(65, 'U')
(66, 'A')
(67, 'G')
(68, 'C')
(69, 'U')
(70, 'C')
(71, 'C')
(72, 'A')
(73, 'C')
(74, 'C')
(75, 'A')