Scripts in this repository served to calculate and nalyse SIDD in comparison with evolutionary changes
- select_genomes.ipynb - based refseq summary downloads ecoli genomes matching requierements calculate Mash for them and select 100 genomes to achive even distribution over mash downloaded genomes are added to ecoli_genomes folder calculated MaSH is stored in mash_k12_vs_ecoli.tsv 100 chosen genomes are written down in sampled.csv as refseq entries
- calc_sidd.py - runs nocoRNAc program to calculate SIDD and saves it in chosen folder
- calculate_single_sidd.sh - runs job for calculating SIDD of single genome
- calculate_sidd.slurm - runs multiple jobs to calculate SIDD for all listed genomes
- peaks.py - calculates peak density based on SIDD profile form .sidd file and saves it in .pik format as file with intigeres one under another
- peaks.slurm - runs peak.py for multiple SIDD profiles
- blast.sh - runs megablast, requieres prepared database calc_fragments_params.py - divides aligments into fragments and calculate their properties to save them in 'aligned_pairs_1000bp_params.txt'
- calc_genomes_aligmnet_params.py - sumas all aligments of same genomes and calculates their parameters
- shorten_file.py - shortens file with floats one after another to 1.5 10^7 so they can be loaded into artemis user plots. File is saved with "short" sufix
- shorten_many_files.py - shortens all files in directory with given prefix to 1.5 10^7 lines so they can be loaded into artemis user plots. Files are saved with "short" sufix
- plot_aligned_pairs.py - creates 2d or 3d plot based of shosen parameters from file "aligned_pairs_1000bp_params.txt" based on all found aligned pairs
- plot_pairs_hist.py - creates set of histograms based on chosen parameters from file "aligned_pairs_1000bp_params.txt". Data for each histogram can be chosen based on one or two prameters
- find_pairs.ipynb - loads "aligned_pairs_1000bp_params.txt" and searches for pairs fulfiling given criteria. Can also plot SIDD of found fragments.