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#!/bin/bash
source ~/miniconda3/etc/profile.d/conda.sh
conda activate tangram-env
################## TANGRAM ##########################
##------------------------------------------------##
## 4 ST test pairs
##------------------------------------------------##
# # Adult mouse brain stereo-seq (celltype_pred)
# python scripts/tangram_script.py --st_path /goofys/Samples/Stereo_seq/Mouse_brain/SS200000141TL_B5_pruned_inplace.h5ad --sc_path /goofys/Samples/sc_reference/mouse_brain_L5_csr.h5ad -a cell_subclass --annotation_st celltype_pred
# # Mouse brain 16.5 stereo-seq (sim anno)
# python scripts/tangram_script.py --st_path /goofys/Samples/Stereo_seq/E16.5_E1S3_cell_bin_whole_brain_noborderct_unlog1p_pruned_inplace.h5ad --sc_path /goofys/Samples/sc_reference/mouse_brain_L5_csr.h5ad -a cell_subclass --annotation_st "sim anno"
# # Mouse brain visium 40K cells
# python scripts/tangram_script.py --st_path /goofys/Samples/10X/mouse_brain_visium_cell2location_pruned_inplace.h5ad --sc_path /goofys/projects/SSI/datasets/mouse_brain_visium_cell2location/visium_mouse_brain_cell2location_sc_unlog1p_pruned_inplace.h5ad -a annotation_1
# # Mouse kidney 43636x31053
# python scripts/tangram_script.py --st_path /goofys/Samples/slide_seq/cellxgene_kidney_slide_seq_v2/Puck_191223_19_corr_pruned_inplace.h5ad --sc_path /goofys/Samples/sc_reference/mouse_kidney/GSE157079_P0_adult.h5ad -a clusters --annotation_st author_cell_type
##------------------------------------------------##
## Mouse kidney - synthetic TANGRAM
##------------------------------------------------##
# python scripts/tangram_script.py --st_path /goofys/Samples/sc_reference/mouse_kidney/GSE157079_P0_adult.h5ad --sc_path /goofys/Samples/sc_reference/mouse_kidney/GSE157079_P0_adult.h5ad -a clusters --annotation_st clusters
# python scripts/tangram_script.py --st_path /goofys/Samples/sc_reference/mouse_kidney/GSE157079_P0_adult_0.05.h5ad --sc_path /goofys/Samples/sc_reference/mouse_kidney/GSE157079_P0_adult.h5ad -a clusters --annotation_st clusters
# python scripts/tangram_script.py --st_path /goofys/Samples/sc_reference/mouse_kidney/GSE157079_P0_adult_0.1.h5ad --sc_path /goofys/Samples/sc_reference/mouse_kidney/GSE157079_P0_adult.h5ad -a clusters --annotation_st clusters
# python scripts/tangram_script.py --st_path /goofys/Samples/sc_reference/mouse_kidney/GSE157079_P0_adult_0.2.h5ad --sc_path /goofys/Samples/sc_reference/mouse_kidney/GSE157079_P0_adult.h5ad -a clusters --annotation_st clusters
# python scripts/tangram_script.py --st_path /goofys/Samples/sc_reference/mouse_kidney/GSE157079_P0_adult_0.3.h5ad --sc_path /goofys/Samples/sc_reference/mouse_kidney/GSE157079_P0_adult.h5ad -a clusters --annotation_st clusters
# python scripts/tangram_script.py --st_path /goofys/Samples/sc_reference/mouse_kidney/GSE157079_P0_adult_0.5.h5ad --sc_path /goofys/Samples/sc_reference/mouse_kidney/GSE157079_P0_adult.h5ad -a clusters --annotation_st clusters
# python scripts/tangram_script.py --st_path /goofys/Samples/sc_reference/mouse_kidney/GSE157079_P0_adult_0.6.h5ad --sc_path /goofys/Samples/sc_reference/mouse_kidney/GSE157079_P0_adult.h5ad -a clusters --annotation_st clusters
# python scripts/tangram_script.py --st_path /goofys/Samples/sc_reference/mouse_kidney/GSE157079_P0_adult_0.7.h5ad --sc_path /goofys/Samples/sc_reference/mouse_kidney/GSE157079_P0_adult.h5ad -a clusters --annotation_st clusters
# python scripts/tangram_script.py --st_path /goofys/Samples/sc_reference/mouse_kidney/GSE157079_P0_adult_0.8.h5ad --sc_path /goofys/Samples/sc_reference/mouse_kidney/GSE157079_P0_adult.h5ad -a clusters --annotation_st clusters
# python scripts/tangram_script.py --st_path /goofys/Samples/sc_reference/mouse_kidney/GSE157079_P0_adult_0.9.h5ad --sc_path /goofys/Samples/sc_reference/mouse_kidney/GSE157079_P0_adult.h5ad -a clusters --annotation_st clusters
##------------------------------------------------##
## visium mouse brain subsampled - TANGRAM
##------------------------------------------------##
#python scripts/tangram_script.py --st_path /goofys/projects/SSI/datasets/mouse_brain_visium_cell2location/synthetic_sc.h5ad --sc_path /goofys/projects/SSI/datasets/mouse_brain_visium_cell2location/synthetic_sc.h5ad -a annotation_1 --annotation_st annotation_1
# python scripts/tangram_script.py --st_path /goofys/projects/SSI/datasets/mouse_brain_visium_cell2location/synthetic_sc_0.05.h5ad --sc_path /goofys/projects/SSI/datasets/mouse_brain_visium_cell2location/synthetic_sc.h5ad -a annotation_1 --annotation_st annotation_1
# python scripts/tangram_script.py --st_path /goofys/projects/SSI/datasets/mouse_brain_visium_cell2location/synthetic_sc_0.1.h5ad --sc_path /goofys/projects/SSI/datasets/mouse_brain_visium_cell2location/synthetic_sc.h5ad -a annotation_1 --annotation_st annotation_1
# python scripts/tangram_script.py --st_path /goofys/projects/SSI/datasets/mouse_brain_visium_cell2location/synthetic_sc_0.2.h5ad --sc_path /goofys/projects/SSI/datasets/mouse_brain_visium_cell2location/synthetic_sc.h5ad -a annotation_1 --annotation_st annotation_1
# python scripts/tangram_script.py --st_path /goofys/projects/SSI/datasets/mouse_brain_visium_cell2location/synthetic_sc_0.3.h5ad --sc_path /goofys/projects/SSI/datasets/mouse_brain_visium_cell2location/synthetic_sc.h5ad -a annotation_1 --annotation_st annotation_1
# python scripts/tangram_script.py --st_path /goofys/projects/SSI/datasets/mouse_brain_visium_cell2location/synthetic_sc_0.4.h5ad --sc_path /goofys/projects/SSI/datasets/mouse_brain_visium_cell2location/synthetic_sc.h5ad -a annotation_1 --annotation_st annotation_1
# python scripts/tangram_script.py --st_path /goofys/projects/SSI/datasets/mouse_brain_visium_cell2location/synthetic_sc_0.5.h5ad --sc_path /goofys/projects/SSI/datasets/mouse_brain_visium_cell2location/synthetic_sc.h5ad -a annotation_1 --annotation_st annotation_1
# python scripts/tangram_script.py --st_path /goofys/projects/SSI/datasets/mouse_brain_visium_cell2location/synthetic_sc_0.6.h5ad --sc_path /goofys/projects/SSI/datasets/mouse_brain_visium_cell2location/synthetic_sc.h5ad -a annotation_1 --annotation_st annotation_1
# python scripts/tangram_script.py --st_path /goofys/projects/SSI/datasets/mouse_brain_visium_cell2location/synthetic_sc_0.7.h5ad --sc_path /goofys/projects/SSI/datasets/mouse_brain_visium_cell2location/synthetic_sc.h5ad -a annotation_1 --annotation_st annotation_1
# python scripts/tangram_script.py --st_path /goofys/projects/SSI/datasets/mouse_brain_visium_cell2location/synthetic_sc_0.8.h5ad --sc_path /goofys/projects/SSI/datasets/mouse_brain_visium_cell2location/synthetic_sc.h5ad -a annotation_1 --annotation_st annotation_1
# python scripts/tangram_script.py --st_path /goofys/projects/SSI/datasets/mouse_brain_visium_cell2location/synthetic_sc_0.9.h5ad --sc_path /goofys/projects/SSI/datasets/mouse_brain_visium_cell2location/synthetic_sc.h5ad -a annotation_1 --annotation_st annotation_1
##------------------------------------------------##
## snRNA cell atlas - TANGRAM
##------------------------------------------------##
python scripts/tangram_script.py --st_path /goofys/Samples/sc_reference/single_nucleus_cell_atlas/GTEX-1HSMQ-5005.h5ad --sc_path /goofys/Samples/sc_reference/single_nucleus_cell_atlas/GTEX-1HSMQ-5005.h5ad -a "Cell types level 2" --annotation_st "Cell types level 2"
echo ************************* 0.05
python scripts/tangram_script.py --st_path /goofys/Samples/sc_reference/single_nucleus_cell_atlas/GTEX-1HSMQ-5005_0.05.h5ad --sc_path /goofys/Samples/sc_reference/single_nucleus_cell_atlas/GTEX-1HSMQ-5005.h5ad -a "Cell types level 2" --annotation_st "Cell types level 2"
echo ************************* 0.1
python scripts/tangram_script.py --st_path /goofys/Samples/sc_reference/single_nucleus_cell_atlas/GTEX-1HSMQ-5005_0.1.h5ad --sc_path /goofys/Samples/sc_reference/single_nucleus_cell_atlas/GTEX-1HSMQ-5005.h5ad -a "Cell types level 2" --annotation_st "Cell types level 2"
echo ************************* 0.2
python scripts/tangram_script.py --st_path /goofys/Samples/sc_reference/single_nucleus_cell_atlas/GTEX-1HSMQ-5005_0.2.h5ad --sc_path /goofys/Samples/sc_reference/single_nucleus_cell_atlas/GTEX-1HSMQ-5005.h5ad -a "Cell types level 2" --annotation_st "Cell types level 2"
echo ************************* 0.3
python scripts/tangram_script.py --st_path /goofys/Samples/sc_reference/single_nucleus_cell_atlas/GTEX-1HSMQ-5005_0.3.h5ad --sc_path /goofys/Samples/sc_reference/single_nucleus_cell_atlas/GTEX-1HSMQ-5005.h5ad -a "Cell types level 2" --annotation_st "Cell types level 2"
echo ************************* 0.4
python scripts/tangram_script.py --st_path /goofys/Samples/sc_reference/single_nucleus_cell_atlas/GTEX-1HSMQ-5005_0.4.h5ad --sc_path /goofys/Samples/sc_reference/single_nucleus_cell_atlas/GTEX-1HSMQ-5005.h5ad -a "Cell types level 2" --annotation_st "Cell types level 2"
echo ************************* 0.5
python scripts/tangram_script.py --st_path /goofys/Samples/sc_reference/single_nucleus_cell_atlas/GTEX-1HSMQ-5005_0.5.h5ad --sc_path /goofys/Samples/sc_reference/single_nucleus_cell_atlas/GTEX-1HSMQ-5005.h5ad -a "Cell types level 2" --annotation_st "Cell types level 2"
echo ************************* 0.6
python scripts/tangram_script.py --st_path /goofys/Samples/sc_reference/single_nucleus_cell_atlas/GTEX-1HSMQ-5005_0.6.h5ad --sc_path /goofys/Samples/sc_reference/single_nucleus_cell_atlas/GTEX-1HSMQ-5005.h5ad -a "Cell types level 2" --annotation_st "Cell types level 2"
echo ************************* 0.7
python scripts/tangram_script.py --st_path /goofys/Samples/sc_reference/single_nucleus_cell_atlas/GTEX-1HSMQ-5005_0.7.h5ad --sc_path /goofys/Samples/sc_reference/single_nucleus_cell_atlas/GTEX-1HSMQ-5005.h5ad -a "Cell types level 2" --annotation_st "Cell types level 2"
echo ************************* 0.8
python scripts/tangram_script.py --st_path /goofys/Samples/sc_reference/single_nucleus_cell_atlas/GTEX-1HSMQ-5005_0.8.h5ad --sc_path /goofys/Samples/sc_reference/single_nucleus_cell_atlas/GTEX-1HSMQ-5005.h5ad -a "Cell types level 2" --annotation_st "Cell types level 2"
echo ************************* 0.9
python scripts/tangram_script.py --st_path /goofys/Samples/sc_reference/single_nucleus_cell_atlas/GTEX-1HSMQ-5005_0.9.h5ad --sc_path /goofys/Samples/sc_reference/single_nucleus_cell_atlas/GTEX-1HSMQ-5005.h5ad -a "Cell types level 2" --annotation_st "Cell types level 2"