Version 0.1 of the KC7 crosscut metadata model, consisting of a
partial mapping of GTEx v7 metadata into DATS JSON. See the
releases/ subdirectory for the JSON files (in BDBag format) and
accompanying release notes.
To run the (preliminary) GTEx v7 to DATS converter (gtex_v7_to_dats.py)
download the two tab-delimited GTEx public metadata files from
https://www.gtexportal.org/home/datasets. The script expects to find
them in the current working directory:
- GTEx_v7_Annotations_SampleAttributesDS.txt
- GTEx_v7_Annotations_SubjectPhenotypesDS.txt
Running the conversion script with the --print_sample_histogram flag
will parse the two metadata files and display a histogram showing how
many subjects/patients (n_subjects, column 2) are linked to the
indicated number of samples (n_samples, column 1). For example:
bash-3.2$ ./bin/gtex_v7_to_dats.py --print_sample_histogram
INFO:root:Read 752 subject(s) from GTEx_v7_Annotations_SubjectPhenotypesDS.txt
INFO:root:Read 15598 sample(s) from GTEx_v7_Annotations_SampleAttributesDS.txt
Histogram of number of subjects that have a given number of samples
n_samples n_subjects
1 14
2 13
3 11
4 2
5 9
6 7
8 8
7 10
9 14
10 12
11 13
12 19
13 21
14 31
15 21
16 18
17 28
18 24
19 32
20 48
21 27
22 35
23 43
24 39
25 44
26 33
27 30
28 34
29 22
30 24
31 12
32 5
33 9
34 7
35 7
36 1
37 3
38 3
39 3
40 3
41 1
43 1
44 5
45 1
53 1
56 1
57 1
68 1
160 1
n_total_samples=15598
n_total_subjects=752
bash-3.2$
Running the conversion script as follows currently generates a single JSON file for each RNA-Seq sample in GTEx v7. In subsequent releases the samples will be linked directly to the DATS Datasets:
mkdir -p gtex_rnaseq_json
./bin/gtex_v7_to_dats.py --smafrze=RNASEQ --output_dir=gtex_rnaseq_json