extract FASTA information from GFF files

python gff_to_fasta.py --input_folder gff_files_generated/ --output_folder extracted_fasta

process FASTA files with prediction tools

python run_minced.py --input_folder extracted_fasta --output_folder minced_gff --update_gff gff_files_with_crispr_pred

python run_crt.py --input_folder extracted_fasta --output_folder crt_gff --update_gff gff_files_with_crispr_pred

python run_crt.py --input_folder extracted_fasta --output_folder crt_gff --update_gff gff_files_generated --output_gff gff_files_with_crispr_pred

gff_files_generated --output_gff gff_files_with_crispr_pred

python run_crt.py --input_folder extracted_fasta --output_folder crt_gff

export PATH="/opt/homebrew/opt/openjdk/bin:$PATH"

java -cp CRT1.2-CLI.jar crt extracted_fasta/GCA_000013345.1_ASM1334v1_genomic.fasta test123

run crisprcasfinder on AIME, transfer json to output_json/

python reformat_cplus.py --input_folder output_json --output_folder gff_files_cplus

combine

python combine_gff.py
--gff_folders gff_files_generated
--extra_gff_folders crt_gff
--output_folder merged_gff
--log DEBUG

python summarize_crisprs.py --input_folder output_json --output_file summary_table.csv python summarize_crisprs.py --input_folder output_json --output_file summary_table3.csv --kmer_sizes 4 5

python predict_crispr.py
--summary_table summary_table.csv
--metadata_table limited.csv
--model random_forest
--test_size 0.2
--output_folder model_output

python predict_crispr.py
--summary_table summary_table.csv
--metadata_table limited.csv
--model linear
--test_size 0.2
--output_folder model_output

python predict_crispr.py
--summary_table summary_table.csv
--metadata_table limited.csv
--taxa_table taxa.csv
--model linear
--test_size 0.2
--target_variable average_crispr_length
--output_folder model_output

python predict_crispr.py
--summary_table summary_table.csv
--metadata_table limited.csv
--taxa_table taxa.csv
--model linear
--test_size 0.2
--output_folder model_output
--target_variable percent_plus_orientation

python summarize_crisprs.py --input_folder output_json --output_file summary_table2.csv

python predict_crispr.py
--summary_table summary_table2.csv
--metadata_table limited.csv
--taxa_table taxa.csv
--model linear
--test_size 0.1
--output_folder model_output
--target_variable num_crispr_arrays

python plot_kmer.py
--summary_table summary_table3.csv
--metadata_table limited.csv
--taxa_table taxa.csv
--output_folder kmer_plots2

python summarize_crisprs.py --input_folder output_json --output_file summary_table3.csv --kmer_sizes 4 5

python summarize_crisprs.py --input_folder output_json --output_file summary_table_k6.csv --kmer_sizes 5 6

python plot_kmer.py
--summary_table summary_table5.csv
--metadata_table limited.csv
--taxa_table taxa.csv
--output_folder kmer_plots5

python summarize_crisprs.py --input_folder output_json --output_file summary_table_k62.csv --kmer_sizes 6

Summary table created: summary_table_k6.csv

python plot_kmer.py
--summary_table summary_table_k62.csv
--metadata_table limited.csv
--taxa_table taxa.csv
--kmer_sizes 6
--output_folder kmer_plots_k62
--tsne_perplexity 5

python plot_tree.py --summary_table summary_table_k62.csv --metadata_table limited.csv --taxa_table taxa.csv --output_folder output_trees --kmer_sizes 6

python summarize_crisprs.py --input_folder output_json --output_file summary_table_k4.csv --kmer_sizes 4

python plot_kmer.py
--summary_table summary_table_k4.csv
--metadata_table limited.csv
--taxa_table taxa.csv
--kmer_sizes 4
--output_folder kmer_plots_k4_3
--tsne_perplexity 100

python combine_gff.py
--gff_folders gff_files_generated
--extra_gff_folders crt_gff gff_files_cplus
--output_folder merged_gff3
--log DEBUG

python summarize_crisprs.py --input_folder output_json_1k --output_file summary_table_new.csv --kmer_sizes 4

python plot_kmer.py
--summary_table summary_table_new.csv
--metadata_table limited.csv
--taxa_table taxa.csv
--kmer_sizes 4
--output_folder kmer_plots_new
--tsne_perplexity 10

python summarize_crisprs.py --input_folder output_json_1k --output_file summary_table_new_xx.csv --kmer_sizes 4

python plot_kmer.py
--summary_table summary_table_new_x5.csv
--metadata_table limited.csv
--taxa_table taxa.csv
--kmer_sizes 4
--output_folder kmer_plots_new5
--tsne_perplexity 5

python plot_kmer.py
--summary_table summary_table_new_x5.csv
--metadata_table limited.csv
--taxa_table taxa.csv
--kmer_sizes 2
--output_folder kmer_plots_new8
--tsne_perplexity 20