Skip to content

datatagsuite/ETL-Public

Folders and files

NameName
Last commit message
Last commit date

Latest commit

 

History

4 Commits
 
 
 
 
 
 
 
 
 
 

Repository files navigation

ETL-Public v0.1

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

About

No description, website, or topics provided.

Resources

Stars

Watchers

Forks

Packages

No packages published