CRI-iAtlas / iatlas-data

MOVED TO GITLAB -> https://gitlab.com/cri-iatlas/iatlas-data.git
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`build_feature_tables` references file path that doesn't exist #22

Closed jaeddy closed 4 years ago

jaeddy commented 4 years ago

These lines in build_feature_tables.R seem to be outdated (on the feature/feather_file_structure branch here):

  cat(crayon::magenta("Importing feather file for features."), fill = TRUE)
  features <- read_iatlas_data_file(feather_file_folder, "/SQLite_data/features.feather") %>%
    dplyr::rename(name = feature) %>%
    dplyr::mutate(class = ifelse(is.na(class), default_class, class))
  cat(crayon::blue("Imported feather file for features."), fill = TRUE)

Neither the SQLite_data/ folder nor the features.feather file seem to exist under feather_files/:

feather_files/
├── driver_results
│   └── driver_results.feather
├── ecn_genes.feather
├── edges
│   ├── edges_TCGAImmune.feather
│   ├── edges_TCGAStudy.feather
│   ├── edges_TCGAStudy_Immune.feather
│   └── edges_TCGASubtype.feather
├── expr_matrix.feather
├── features
│   ├── immune_subtype_features.feather
│   ├── tcga_study_features.feather
│   └── tcga_subtype_features.feather
├── fmx_df.feather
├── gene_ids.feather
├── genes
│   ├── driver_mutation_genes.feather
│   ├── extra_cellular_network_genes.feather
│   ├── immunomodulator_genes.feather
│   └── io_target_genes.feather
├── network_node_label_friendly.feather
├── nodes
│   ├── nodes_TCGAImmune.feather
│   ├── nodes_TCGAStudy.feather
│   ├── nodes_TCGAStudy_Immune.feather
│   └── nodes_TCGASubtype.feather
├── relationships
│   ├── features_to_samples
│   │   ├── immune_subtype_features_to_samples.feather
│   │   ├── tcga_study_features_to_samples.feather
│   │   └── tcga_subtype_features_to_samples.feather
│   └── nodes_to_tags
│       ├── immune_subtype_nodes_to_tags.feather
│       ├── tcga_study_nodes_to_tags.feather
│       └── tcga_subtype_nodes_to_tags.feather
├── samples
│   ├── immune_subtype_samples.feather
│   ├── immune_subtype_samples_to_tags.feather
│   ├── tcga_study_samples.feather
│   ├── tcga_study_samples_to_tags.feather
│   ├── tcga_subtype_samples.feather
│   └── tcga_subtype_samples_to_tags.feather
└── tags
    ├── immune_subtype_tags.feather
    ├── tcga_study_tags.feather
    └── tcga_subtype_tags.feather
jonryser commented 4 years ago

Those files have been committed to the repo.