Closed khoroshevskyi closed 2 years ago
Using sample table as input does not initialize all object variables, e.g.: _config. That leads to downsteem problems with reinitializing project. Example:
_config
peppy.Project("example/proj.csv")
Object variables:
{ "name": null, "_samples": [ { "time": "0", "organism": "frog", "protocol": "ATAC-seq", "file_path": "data/lab/project/frog_0h.fastq", "sample_name": "frog_0h" }, { "time": "1", "organism": "frog", "protocol": "ATAC-seq", "file_path": "data/lab/project/frog_1h.fastq", "sample_name": "frog_1h" }, { "time": "1", "organism": "human", "protocol": "ATAC-seq", "file_path": "data/lab/project/human_1h.fastq", "sample_name": "human_1h" }, { "time": "0", "organism": "human", "protocol": "ATAC-seq", "file_path": "data/lab/project/human_0h.fastq", "sample_name": "human_0h" }, { "time": "1", "organism": "mouse", "protocol": "ATAC-seq", "file_path": "data/lab/project/mouse_1h.fastq", "sample_name": "mouse_1h" }, { "time": "0", "organism": "mouse", "protocol": "ATAC-seq", "file_path": "data/lab/project/mouse_1h.fastq", "sample_name": "mouse_0h" } ], "st_index": "sample_name", "sst_index": [ "sample_name", "subsample_name" ], "_sample_df": { "time": { "frog_0h": "0", "frog_1h": "1", "human_0h": "0", "human_1h": "1", "mouse_0h": "0", "mouse_1h": "1" }, "organism": { "frog_0h": "frog", "frog_1h": "frog", "human_0h": "human", "human_1h": "human", "mouse_0h": "mouse", "mouse_1h": "mouse" }, "protocol": { "frog_0h": "ATAC-seq", "frog_1h": "ATAC-seq", "human_0h": "ATAC-seq", "human_1h": "ATAC-seq", "mouse_0h": "ATAC-seq", "mouse_1h": "ATAC-seq" }, "file_path": { "frog_0h": "data/lab/project/frog_0h.fastq", "frog_1h": "data/lab/project/frog_1h.fastq", "human_0h": "data/lab/project/human_0h.fastq", "human_1h": "data/lab/project/human_1h.fastq", "mouse_0h": "data/lab/project/mouse_1h.fastq", "mouse_1h": "data/lab/project/mouse_1h.fastq" }, "sample_name": { "frog_0h": "frog_0h", "frog_1h": "frog_1h", "human_0h": "human_0h", "human_1h": "human_1h", "mouse_0h": "mouse_0h", "mouse_1h": "mouse_1h" } }, "description": null, "_sample_table": { "time": { "frog_0h": "0", "frog_1h": "1", "human_0h": "0", "human_1h": "1", "mouse_0h": "0", "mouse_1h": "1" }, "organism": { "frog_0h": "frog", "frog_1h": "frog", "human_0h": "human", "human_1h": "human", "mouse_0h": "mouse", "mouse_1h": "mouse" }, "protocol": { "frog_0h": "ATAC-seq", "frog_1h": "ATAC-seq", "human_0h": "ATAC-seq", "human_1h": "ATAC-seq", "mouse_0h": "ATAC-seq", "mouse_1h": "ATAC-seq" }, "file_path": { "frog_0h": "data/lab/project/frog_0h.fastq", "frog_1h": "data/lab/project/frog_1h.fastq", "human_0h": "data/lab/project/human_0h.fastq", "human_1h": "data/lab/project/human_1h.fastq", "mouse_0h": "data/lab/project/mouse_1h.fastq", "mouse_1h": "data/lab/project/mouse_1h.fastq" }, "sample_name": { "frog_0h": "frog_0h", "frog_1h": "frog_1h", "human_0h": "human_0h", "human_1h": "human_1h", "mouse_0h": "mouse_0h", "mouse_1h": "mouse_1h" } }, "_subsample_df": null, "_large_sample_df": false, "_samples_touched": true, "_sample_table_path": "/home/bnt4me/Virginia/pephub_db/sample_pep/amendments2/sample_table.csv", "_subsample_tables_path": null }
Fixed!
Using sample table as input does not initialize all object variables, e.g.:
_config
. That leads to downsteem problems with reinitializing project. Example:peppy.Project("example/proj.csv")
Object variables: