Mercurial > repos > ebi-gxa > seurat_select_integration_features

annotate get_test_data.sh @ 0:699c0ca328f2 draft default tip

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planemo upload commit 0264c359f1d638bbbbab515a3502231f679cdcf6
author ebi-gxa
date Sat, 02 Mar 2024 10:40:57 +0000
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1 #!/usr/bin/env bash
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2
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3 BASENAME_FILE='E-MTAB-6077-3k_features_90_cells'
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5 MTX_LINK='https://drive.google.com/uc?export=download&id=1-1ejn7scP80xsbrG0FtWzsozjg0hhc23'
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6 RDS_LINK='https://drive.google.com/uc?export=download&id=1KW_GX6xznSUpWRWUykpNaSbAhyClf7_n'
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7 NORM_LINK='https://drive.google.com/uc?export=download&id=1mvo3ENkBvEAOyWG6ejApzQTPDLX5yBKU'
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8 FVG_LINK='https://drive.google.com/uc?export=download&id=13Fhruuj-vEEo1WM138ahtAYqfHc7LsaZ'
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9 SCALED_LINK='https://drive.google.com/uc?export=download&id=18TK8us235LWNajarWDBAtASUXMYAxvw0'
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10 PCA_LINK='https://drive.google.com/uc?export=download&id=1gf3BTB4dygDsom1TzjsBfgZnZepcoG5c'
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11 NEIGHBOURS_LINK='https://drive.google.com/uc?export=download&id=1N2lHoKRBZ7pmAYGfghLWB9KUrLA5WoNX'
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12 CLUSTERS_LINK='https://drive.google.com/uc?export=download&id=1HWxZWHbNUNo4z__9PhhL_CJOLzec_ETa'
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13 TSNE_LINK='https://drive.google.com/uc?export=download&id=1qsvMr_GkCSp1dyTJt1BZ6cElJwFFX2zO'
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14 MARKERS_LINK='https://drive.google.com/uc?export=download&id=18OmWNc7mF-4pzH6DQkPp1eKunN4BfvxD'
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16 LOOM_LINK='https://drive.google.com/uc?export=download&id=1qNk5cg8hJG3Nv1ljTKmUEnxTOf11EEZX'
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17 H5AD_LINK='https://drive.google.com/uc?export=download&id=1YpE0H_t_dkh17P-WBhPijKvRiGP0BlBz'
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19 H5AD_SC182_LINK='https://drive.google.com/uc?export=download&id=16PUJ2KAkXT8F1UkfqU-9LWoOJUkUG1rp'
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20 SCE_LINK='https://drive.google.com/uc?export=download&id=1UKdyf3M01uAt7oBg93JfmRvNVB_jlUKe'
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22 # Seurat v4 exclusives
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23 IFNB_BASE_FILE='ifnb_'
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25 IFNB_CTRL_INT_LINK='https://drive.google.com/uc?export=download&id=15E_MLz-UclJYInNaA7YKLhLo5W-qlykL'
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26 IFNB_STIM_INT_LINK='https://drive.google.com/uc?export=download&id=14iKgCJGPk16dEmpJJF-Gp_lBDcOdo-54'
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27
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28 ## Classify and UMAP mapping
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29 CLASSIFY_QUERY_LINK='https://oc.ebi.ac.uk/s/MlEDILFYRrvkS6E/download'
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30 CLASSIFY_RESULTS_ANCHORS_OBJECT_LINK='https://drive.google.com/uc?export=download&id=1Xtv4K_CxIU1cJ8RjJ7NTvzLQkLvc8a3i'
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31 # UMAP_RESULT_OBJECT_LINK='https://oc.ebi.ac.uk/s/k4MdM07y9DAnurp/download'
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32 UMAP_RESULT_OBJECT_LINK='https://oc.ebi.ac.uk/s/D1z4z2ef1e3dyc3/download'
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35 function get_data {
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36 local link=$1
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37 local fname=$2
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38
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39 if [ ! -f $fname ]; then
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40 echo "$fname not available locally, downloading.."
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41 wget -O $fname --retry-connrefused --waitretry=1 --read-timeout=20 --timeout=15 -t 3 $link
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42 fi
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43 }
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44
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45 # get matrix data
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46 mkdir -p test-data
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47 pushd test-data
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48 get_data $MTX_LINK mtx.zip
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49 unzip mtx.zip
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50 rm -f mtx.zip
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51
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52 get_data $RDS_LINK $BASENAME_FILE".rds"
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53 get_data $NORM_LINK $BASENAME_FILE"-normalised.rds"
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54 get_data $FVG_LINK $BASENAME_FILE"-fvg.rds"
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55 get_data $SCALED_LINK $BASENAME_FILE"-scaled.rds"
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56 get_data $PCA_LINK $BASENAME_FILE"-pca.rds"
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57 get_data $NEIGHBOURS_LINK $BASENAME_FILE"-neighbours.rds"
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58 get_data $CLUSTERS_LINK $BASENAME_FILE"-clusters.rds"
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59 get_data $TSNE_LINK $BASENAME_FILE"-tsne.rds"
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60 get_data $MARKERS_LINK $BASENAME_FILE"-markers.csv.zip"
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61
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62 unzip $BASENAME_FILE"-markers.csv.zip"
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63 rm -f $BASENAME_FILE"-markers.csv.zip"
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64
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65 get_data $LOOM_LINK $BASENAME_FILE"_loom.h5"
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66 get_data $SCE_LINK $BASENAME_FILE"_sce.rds"
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67 get_data $H5AD_LINK $BASENAME_FILE".h5ad"
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69 get_data $H5AD_SC182_LINK $BASENAME_FILE"_sc182.h5ad"
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70
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71 get_data $IFNB_CTRL_INT_LINK $IFNB_BASE_FILE"ctrl_norm_fvg.rds"
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72 get_data $IFNB_STIM_INT_LINK $IFNB_BASE_FILE"stim_norm_fvg.rds"
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73
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74 get_data $CLASSIFY_QUERY_LINK "Classify_query.rds"
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75 get_data $CLASSIFY_RESULTS_ANCHORS_OBJECT_LINK "Classify_anchors.rds"
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76 get_data $UMAP_RESULT_OBJECT_LINK "UMAP_result_integrated.rds"
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77