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