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update_git.sh
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#!/bin/bash
#MIT License
#
#Copyright (c) 2023 Pierre Michel Joubert
#
#Permission is hereby granted, free of charge, to any person obtaining a copy
#of this software and associated documentation files (the "Software"), to deal
#in the Software without restriction, including without limitation the rights
#to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
#copies of the Software, and to permit persons to whom the Software is
#furnished to do so, subject to the following conditions:
#
#The above copyright notice and this permission notice shall be included in all
#copies or substantial portions of the Software.
#
#THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
#IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
#FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
#AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
#LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
#OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
#SOFTWARE.
## this script simply updates code by copying them over from the submodules, only for the author's use for maintaining the code repo
git submodule update --remote KVK-lab-scripts
git submodule update --remote pav_project_local
SLURM_SCRIPTS=KVK-lab-scripts/slurm
BASH_SCRIPTS=KVK-lab-scripts/bash
PYTHON_SCRIPTS=KVK-lab-scripts/python
WHEAT_BLAST_ANALYSIS_DIR=pav_project_local/pav_newest_wheat_blast_all
RICE_BLAST_ANALYSIS_DIR=pav_project_local/pav_newest_gladieux_only_fungap
CROSS_HOST_ANALYSIS_DIR=pav_project_local/cross_host_comparisons
## gc_content
TARGET_DIR=gc_content/rice_blast/
if [ -d $TARGET_DIR ]; then rm -r $TARGET_DIR; fi && mkdir -p $TARGET_DIR
cp ${SLURM_SCRIPTS}/gc_content_per_gene.slurm $TARGET_DIR
cp ${PYTHON_SCRIPTS}/generate_gc_table_per_genome.py $TARGET_DIR
TARGET_DIR=gc_content/wheat_blast/
if [ -d $TARGET_DIR ]; then rm -r $TARGET_DIR; fi && mkdir -p $TARGET_DIR
cp ${SLURM_SCRIPTS}/gc_content_per_gene_wheat_blast.slurm $TARGET_DIR
cp ${PYTHON_SCRIPTS}/generate_gc_table_per_genome.py $TARGET_DIR
## call_pav_orthogroups
TARGET_DIR=call_pav_orthogroups/rice_blast/
if [ -d $TARGET_DIR ]; then rm -r $TARGET_DIR; fi && mkdir -p $TARGET_DIR
cp $RICE_BLAST_ANALYSIS_DIR/pipeline_methods/pav_w_tree_climbing.Rmd $TARGET_DIR
TARGET_DIR=call_pav_orthogroups/wheat_blast/
if [ -d $TARGET_DIR ]; then rm -r $TARGET_DIR; fi && mkdir -p $TARGET_DIR
cp $WHEAT_BLAST_ANALYSIS_DIR/pipeline_methods/pav_w_tree_climbing.Rmd $TARGET_DIR
## deletion_calling
TARGET_DIR=deletion_calling/rice_blast/
if [ -d $TARGET_DIR ]; then rm -r $TARGET_DIR; fi && mkdir -p $TARGET_DIR
cp $SLURM_SCRIPTS/sv_callers_PJ.slurm $TARGET_DIR
cp $SLURM_SCRIPTS/download_sra_and_map.slurm $TARGET_DIR
cp $BASH_SCRIPTS/run_delly.sh $TARGET_DIR
cp $BASH_SCRIPTS/run_lumpy.sh $TARGET_DIR
cp $BASH_SCRIPTS/run_manta.sh $TARGET_DIR
cp $BASH_SCRIPTS/run_wham.sh $TARGET_DIR
TARGET_DIR=deletion_calling/wheat_blast/
if [ -d $TARGET_DIR ]; then rm -r $TARGET_DIR; fi && mkdir -p $TARGET_DIR
cp $SLURM_SCRIPTS/sv_callers_wheat.slurm $TARGET_DIR
cp $SLURM_SCRIPTS/download_sra_and_map.slurm $TARGET_DIR
cp $BASH_SCRIPTS/run_delly.sh $TARGET_DIR
cp $BASH_SCRIPTS/run_lumpy.sh $TARGET_DIR
cp $BASH_SCRIPTS/run_manta.sh $TARGET_DIR
cp $BASH_SCRIPTS/run_wham.sh $TARGET_DIR
## deletion sizes
TARGET_DIR=deletion_sizes/
if [ -d $TARGET_DIR ]; then rm -r $TARGET_DIR; fi && mkdir -p $TARGET_DIR
cp $CROSS_HOST_ANALYSIS_DIR/cross_host_pav_differences/deletion_size.Rmd $TARGET_DIR
## pav counts
TARGET_DIR=pav_counts_comparison/
if [ -d $TARGET_DIR ]; then rm -r $TARGET_DIR; fi && mkdir -p $TARGET_DIR
cp $CROSS_HOST_ANALYSIS_DIR/cross_host_pav_differences/pav_counts.Rmd $TARGET_DIR
## pav density
TARGET_DIR=pav_gene_density/
if [ -d $TARGET_DIR ]; then rm -r $TARGET_DIR; fi && mkdir -p $TARGET_DIR
cp $CROSS_HOST_ANALYSIS_DIR/cross_host_pav_differences/cross_host_deletion_distance_plots.Rmd $TARGET_DIR
TARGET_DIR=pav_gene_density/rice_blast
if [ -d $TARGET_DIR ]; then rm -r $TARGET_DIR; fi && mkdir -p $TARGET_DIR
cp $RICE_BLAST_ANALYSIS_DIR/deletion_statistics/deletion_distance.Rmd $TARGET_DIR
TARGET_DIR=pav_gene_density/wheat_blast
if [ -d $TARGET_DIR ]; then rm -r $TARGET_DIR; fi && mkdir -p $TARGET_DIR
cp $WHEAT_BLAST_ANALYSIS_DIR/deletion_statistics/deletion_distance.Rmd $TARGET_DIR
## deletion_other_params
TARGET_DIR=deletion_other_params/rice_blast/
if [ -d $TARGET_DIR ]; then rm -r $TARGET_DIR; fi && mkdir -p $TARGET_DIR
cp $SLURM_SCRIPTS/gather_data_all_svs_rice_blast.slurm $TARGET_DIR
cp $BASH_SCRIPTS/average_coverage_files.sh $TARGET_DIR
cp $CROSS_HOST_ANALYSIS_DIR/del_param_dsns/del_params_dsns.Rmd $TARGET_DIR
TARGET_DIR=deletion_other_params/wheat_blast/
if [ -d $TARGET_DIR ]; then rm -r $TARGET_DIR; fi && mkdir -p $TARGET_DIR
cp $SLURM_SCRIPTS/gather_data_all_svs_wheat.slurm $TARGET_DIR
cp $BASH_SCRIPTS/average_coverage_files.sh $TARGET_DIR
cp $CROSS_HOST_ANALYSIS_DIR/del_param_dsns/del_params_dsns.Rmd $TARGET_DIR
## deletion_te_gene_density
TARGET_DIR=deletion_te_gene_density/rice_blast/
if [ -d $TARGET_DIR ]; then rm -r $TARGET_DIR; fi && mkdir -p $TARGET_DIR
cp $BASH_SCRIPTS/plot_profiler.sh $TARGET_DIR
cp $SLURM_SCRIPTS/plot_profiler_all_svs_rice_blast.slurm $TARGET_DIR
cp $CROSS_HOST_ANALYSIS_DIR/sv_profile_plots/profile_plots.Rmd $TARGET_DIR
TARGET_DIR=deletion_te_gene_density/wheat_blast/
if [ -d $TARGET_DIR ]; then rm -r $TARGET_DIR; fi && mkdir -p $TARGET_DIR
cp $BASH_SCRIPTS/plot_profiler.sh $TARGET_DIR
cp $SLURM_SCRIPTS/plot_profiler_all_svs_wheat_blast.slurm $TARGET_DIR
cp $CROSS_HOST_ANALYSIS_DIR/sv_profile_plots/profile_plots.Rmd $TARGET_DIR
## effector_annotation
TARGET_DIR=effector_annotation/
if [ -d $TARGET_DIR ]; then rm -r $TARGET_DIR; fi && mkdir -p $TARGET_DIR
cp $BASH_SCRIPTS/effector_predictor.sh $TARGET_DIR
cp $CROSS_HOST_ANALYSIS_DIR/other_params/compare_param_distributions.Rmd $TARGET_DIR
cp $RICE_BLAST_ANALYSIS_DIR/pipeline_methods/get_effector_og_list.ipynb $TARGET_DIR
## ngs_data_signal
TARGET_DIR=ngs_data_signal/
if [ -d $TARGET_DIR ]; then rm -r $TARGET_DIR; fi && mkdir -p $TARGET_DIR
cp $CROSS_HOST_ANALYSIS_DIR/other_params/compare_param_distributions.Rmd $TARGET_DIR
TARGET_DIR=ngs_data_signal/rice_blast/
if [ -d $TARGET_DIR ]; then rm -r $TARGET_DIR; fi && mkdir -p $TARGET_DIR
cp $SLURM_SCRIPTS/expression_guy11.slurm $TARGET_DIR
cp $SLURM_SCRIPTS/histone_marks_guy11.slurm $TARGET_DIR
cp $SLURM_SCRIPTS/methylation_guy11.slurm $TARGET_DIR
cp $RICE_BLAST_ANALYSIS_DIR/random_forest/transfer_info_from_guy11.ipynb $TARGET_DIR
cp $SLURM_SCRIPTS/eccdnas_guy11.slurm $TARGET_DIR
TARGET_DIR=ngs_data_signal/wheat_blast/
if [ -d $TARGET_DIR ]; then rm -r $TARGET_DIR; fi && mkdir -p $TARGET_DIR
cp $SLURM_SCRIPTS/expression_b71.slurm $TARGET_DIR
cp $WHEAT_BLAST_ANALYSIS_DIR/random_forest/transer_info_from_b71.ipynb $TARGET_DIR
## orthogroup_pca
TARGET_DIR=orthogroup_pca/
if [ -d $TARGET_DIR ]; then rm -r $TARGET_DIR; fi && mkdir -p $TARGET_DIR
cp $RICE_BLAST_ANALYSIS_DIR/lineage_differentiating_pavs/pca_heat_map_phylogeny/pav_pca.Rmd $TARGET_DIR
## pfam_go_annotation
TARGET_DIR=pfam_go_annotation/
if [ -d $TARGET_DIR ]; then rm -r $TARGET_DIR; fi && mkdir -p $TARGET_DIR
cp $SLURM_SCRIPTS/pfam_scan_per_proteome.slurm $TARGET_DIR
cp $SLURM_SCRIPTS/pannzer_single_core.slurm $TARGET_DIR
cp $CROSS_HOST_ANALYSIS_DIR/other_params/compare_param_distributions.Rmd $TARGET_DIR
## pfam_go_enrichment
TARGET_DIR=pfam_nlr_go_enrichment/
if [ -d $TARGET_DIR ]; then rm -r $TARGET_DIR; fi && mkdir -p $TARGET_DIR
cp $RICE_BLAST_ANALYSIS_DIR/lineage_differentiating_pavs/pfam_enrichment/pfam_enrichment_plot.Rmd $TARGET_DIR
cp $RICE_BLAST_ANALYSIS_DIR/lineage_differentiating_pavs/pfam_enrichment/pfam_nlr_enrichment.ipynb $TARGET_DIR
cp $RICE_BLAST_ANALYSIS_DIR/lineage_differentiating_pavs/go_enrichment/assign_go_to_ogs_all_ogs.ipynb $TARGET_DIR
cp $RICE_BLAST_ANALYSIS_DIR/lineage_differentiating_pavs/go_enrichment/go_enrichment.Rmd $TARGET_DIR
## phylogenies
TARGET_DIR=phylogenies/
if [ -d $TARGET_DIR ]; then rm -r $TARGET_DIR; fi && mkdir -p $TARGET_DIR
cp $SLURM_SCRIPTS/get_sco_msa.slurm $TARGET_DIR
cp $PYTHON_SCRIPTS/concatenate_msas.py $TARGET_DIR
cp $SLURM_SCRIPTS/fasttree_scos.slurm $TARGET_DIR
TARGET_DIR=phylogenies/rice_blast/
if [ -d $TARGET_DIR ]; then rm -r $TARGET_DIR; fi && mkdir -p $TARGET_DIR
cp $RICE_BLAST_ANALYSIS_DIR/pipeline_methods/plot_phylogeny.Rmd $TARGET_DIR
TARGET_DIR=phylogenies/wheat_blast/
if [ -d $TARGET_DIR ]; then rm -r $TARGET_DIR; fi && mkdir -p $TARGET_DIR
cp $WHEAT_BLAST_ANALYSIS_DIR/pipeline_methods/plot_phylogeny.Rmd $TARGET_DIR
## random forest model importances
TARGET_DIR=random_forest_model_importances
if [ -d $TARGET_DIR ]; then rm -r $TARGET_DIR; fi && mkdir -p $TARGET_DIR
cp $SLURM_SCRIPTS/launch_rf_importances_parallel.slurm $TARGET_DIR
cp $PYTHON_SCRIPTS/rf_importances_parallel.py $TARGET_DIR
cp $PYTHON_SCRIPTS/average_importances_results.py $TARGET_DIR
cp $CROSS_HOST_ANALYSIS_DIR/importances/importances_plots.Rmd $TARGET_DIR
## random_forest_models
TARGET_DIR=random_forest_models
if [ -d $TARGET_DIR ]; then rm -r $TARGET_DIR; fi && mkdir -p $TARGET_DIR
cp $SLURM_SCRIPTS/launch_rf_parallel_single_host.slurm $TARGET_DIR
cp $PYTHON_SCRIPTS/rf_perf_test_parallel.py $TARGET_DIR
cp $PYTHON_SCRIPTS/average_rf_results.py $TARGET_DIR
cp $CROSS_HOST_ANALYSIS_DIR/confusion_matrices/confusion_matrix.Rmd $TARGET_DIR
TARGET_DIR=random_forest_models/rice_blast
if [ -d $TARGET_DIR ]; then rm -r $TARGET_DIR; fi && mkdir -p $TARGET_DIR
cp $RICE_BLAST_ANALYSIS_DIR/random_forest/get_per_gene_info.Rmd $TARGET_DIR
TARGET_DIR=random_forest_models/wheat_blast
if [ -d $TARGET_DIR ]; then rm -r $TARGET_DIR; fi && mkdir -p $TARGET_DIR
cp $WHEAT_BLAST_ANALYSIS_DIR/random_forest/get_per_gene_info.Rmd $TARGET_DIR
## random forest cross host
TARGET_DIR=random_forest_models_cross_host_test
if [ -d $TARGET_DIR ]; then rm -r $TARGET_DIR; fi && mkdir -p $TARGET_DIR
cp $SLURM_SCRIPTS/launch_rf_parallel_cross_host.slurm $TARGET_DIR
cp $PYTHON_SCRIPTS/rf_perf_test_cross_host.py $TARGET_DIR
cp $PYTHON_SCRIPTS/average_rf_results.py $TARGET_DIR
cp $CROSS_HOST_ANALYSIS_DIR/confusion_matrices/confusion_matrix.Rmd $TARGET_DIR
## random forest incorrect predictions heatmap
TARGET_DIR=random_forest_incorrect_preds
if [ -d $TARGET_DIR ]; then rm -r $TARGET_DIR; fi && mkdir -p $TARGET_DIR
cp $CROSS_HOST_ANALYSIS_DIR/model_errors/wrong_preds_heatmap.Rmd $TARGET_DIR
cp $SLURM_SCRIPTS/rf_cross_host_output_predictions.slurm $TARGET_DIR
cp $PYTHON_SCRIPTS/rf_perf_test_cross_host_output_preds.py $TARGET_DIR
TARGET_DIR=random_forest_incorrect_preds/rice_blast
if [ -d $TARGET_DIR ]; then rm -r $TARGET_DIR; fi && mkdir -p $TARGET_DIR
cp $RICE_BLAST_ANALYSIS_DIR/deletion_statistics/deletion_distance.Rmd $TARGET_DIR
TARGET_DIR=random_forest_incorrect_preds/wheat_blast
if [ -d $TARGET_DIR ]; then rm -r $TARGET_DIR; fi && mkdir -p $TARGET_DIR
cp $WHEAT_BLAST_ANALYSIS_DIR/deletion_statistics/deletion_distance.Rmd $TARGET_DIR
## random_forest_variable_dependence
TARGET_DIR=random_forest_variable_dependence
if [ -d $TARGET_DIR ]; then rm -r $TARGET_DIR; fi && mkdir -p $TARGET_DIR
cp $RICE_BLAST_ANALYSIS_DIR/random_forest/dependency_matrix/cor_matrices.Rmd $TARGET_DIR
cp $RICE_BLAST_ANALYSIS_DIR/random_forest/dependency_matrix/dependence_heatmaps.Rmd $TARGET_DIR
cp $SLURM_SCRIPTS/generate_dependence_matrix.slurm $TARGET_DIR
cp $PYTHON_SCRIPTS/output_train_test.py $TARGET_DIR
cp $PYTHON_SCRIPTS/dependencies_per_column.py $TARGET_DIR
## te gene distance
TARGET_DIR=te_gene_distance
if [ -d $TARGET_DIR ]; then rm -r $TARGET_DIR; fi && mkdir -p $TARGET_DIR
cp $CROSS_HOST_ANALYSIS_DIR/distance/cross_host_pav_distance_plots.Rmd $TARGET_DIR
TARGET_DIR=te_gene_distance/rice_blast
if [ -d $TARGET_DIR ]; then rm -r $TARGET_DIR; fi && mkdir -p $TARGET_DIR
cp $RICE_BLAST_ANALYSIS_DIR/distance/pav_distances.Rmd $TARGET_DIR
TARGET_DIR=te_gene_distance/wheat_blast
if [ -d $TARGET_DIR ]; then rm -r $TARGET_DIR; fi && mkdir -p $TARGET_DIR
cp $WHEAT_BLAST_ANALYSIS_DIR/distance/pav_distances.Rmd $TARGET_DIR
## validate missing orthogroups
TARGET_DIR=validate_missing_orthogroups/
if [ -d $TARGET_DIR ]; then rm -r $TARGET_DIR; fi && mkdir -p $TARGET_DIR
cp $BASH_SCRIPTS/tblastn_validation_launch_script.sh $TARGET_DIR
cp $BASH_SCRIPTS/tblastn_validation.sh $TARGET_DIR
cp $PYTHON_SCRIPTS/make_single_file_from_og_dir.py $TARGET_DIR
cp $PYTHON_SCRIPTS/parse_tblastn_hits.py $TARGET_DIR
cp $PYTHON_SCRIPTS/parse_blastp_hits.py $TARGET_DIR
TARGET_DIR=validate_missing_orthogroups/rice_blast
if [ -d $TARGET_DIR ]; then rm -r $TARGET_DIR; fi && mkdir -p $TARGET_DIR
cp $RICE_BLAST_ANALYSIS_DIR/pipeline_methods/print_pav_for_validation.Rmd $TARGET_DIR
TARGET_DIR=validate_missing_orthogroups/wheat_blast
if [ -d $TARGET_DIR ]; then rm -r $TARGET_DIR; fi && mkdir -p $TARGET_DIR
cp $WHEAT_BLAST_ANALYSIS_DIR/pipeline_methods/print_pav_for_validation.Rmd $TARGET_DIR
## genome stats
TARGET_DIR=genome_stats
if [ -d $TARGET_DIR ]; then rm -r $TARGET_DIR; fi && mkdir -p $TARGET_DIR
cp $SLURM_SCRIPTS/generate_assembly_stats_tables.slurm $TARGET_DIR
## fungap
TARGET_DIR=genome_annotation
if [ -d $TARGET_DIR ]; then rm -r $TARGET_DIR; fi && mkdir -p $TARGET_DIR
cp $SLURM_SCRIPTS/run_fungap.slurm $TARGET_DIR
cp $SLURM_SCRIPTS/process_fungap_out.slurm $TARGET_DIR
cp $BASH_SCRIPTS/fungap_launcher.sh $TARGET_DIR
cp $PYTHON_SCRIPTS/process_gffs_for_orthofinder.py $TARGET_DIR
cp $PYTHON_SCRIPTS/process_protein_sequences_for_orthofinder.py $TARGET_DIR
## orthogrouping
TARGET_DIR=orthogrouping
if [ -d $TARGET_DIR ]; then rm -r $TARGET_DIR; fi && mkdir -p $TARGET_DIR
cp $BASH_SCRIPTS/launch_orthofinder_blast.sh $TARGET_DIR
cp $SLURM_SCRIPTS/orthofinder_blast.slurm $TARGET_DIR
cp $SLURM_SCRIPTS/full_orthofinder_run.slurm $TARGET_DIR
## te annotation
TARGET_DIR=te_annotation/rice_blast
if [ -d $TARGET_DIR ]; then rm -r $TARGET_DIR; fi && mkdir -p $TARGET_DIR
cp $SLURM_SCRIPTS/repeatmasker_rice_blast.slurm $TARGET_DIR
TARGET_DIR=te_annotation/wheat_blast
if [ -d $TARGET_DIR ]; then rm -r $TARGET_DIR; fi && mkdir -p $TARGET_DIR
cp $SLURM_SCRIPTS/repeatmasker_wheat_blast.slurm $TARGET_DIR
## gather stats
TARGET_DIR=feature_statistical_comparisons
if [ -d $TARGET_DIR ]; then rm -r $TARGET_DIR; fi && mkdir -p $TARGET_DIR
cp $CROSS_HOST_ANALYSIS_DIR/distances_param_stats/distances_stats.Rmd $TARGET_DIR
cp $CROSS_HOST_ANALYSIS_DIR/distances_param_stats/param_categorical_stats_table.Rmd $TARGET_DIR
cp $CROSS_HOST_ANALYSIS_DIR/distances_param_stats/param_dsns_stats_table.Rmd $TARGET_DIR
cp $CROSS_HOST_ANALYSIS_DIR/distances_param_stats/genomic_deletion_param_dsns_stats_table.Rmd $TARGET_DIR