Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Names are not exported #58

Open
cswrd opened this issue Aug 7, 2022 · 3 comments
Open

Names are not exported #58

cswrd opened this issue Aug 7, 2022 · 3 comments

Comments

@cswrd
Copy link

cswrd commented Aug 7, 2022

Hi, I've just created the first draft of my pedigree. I entered only the persons' names as meta information, exported the file (standard settings) and reimported the file. The graph was still there with all edges but all other meta information was missing, especially the names.

The *.ped doesn't contain much information:

OPENPED 1 15 14 1 -9
OPENPED 2 5 4 2 -9
OPENPED 3 1 2 3 -9
OPENPED 4 7 6 2 -9
OPENPED 5 9 8 1 -9
OPENPED 6 0 0 2 -9
OPENPED 7 0 0 1 -9
OPENPED 8 0 0 2 -9
OPENPED 9 0 0 1 -9
OPENPED 10 0 0 2 -9
OPENPED 11 5 10 2 -9
OPENPED 12 0 0 2 -9
OPENPED 13 5 12 2 -9
OPENPED 14 0 0 2 -9
OPENPED 15 0 0 1 -9
OPENPED 16 0 0 1 -9
OPENPED 17 16 13 1 -9
OPENPED 18 16 13 2 -9
OPENPED 19 16 13 2 -9
OPENPED 20 0 0 1 -9
OPENPED 21 20 11 2 -9
OPENPED 22 20 11 2 -9
OPENPED 23 15 14 2 -9
OPENPED 24 0 0 1 -9
OPENPED 25 24 23 3 -9

@dconlan
Copy link
Collaborator

dconlan commented Aug 8, 2022

The code says the PED format is from something called plink
http://pngu.mgh.harvard.edu/~purcell/plink/data.shtml#ped

The PED file is a white-space (space or tab) delimited file: the first six columns are mandatory:

 Family ID
 Individual ID
 Paternal ID
 Maternal ID
 Sex (1=male; 2=female; other=unknown)
 Phenotype

The IDs are alphanumeric: the combination of family and individual ID should uniquely identify a person. A PED file must have 1 and only 1 phenotype in the sixth column. The phenotype can be either a quantitative trait or an affection status column: PLINK will automatically detect which type (i.e. based on whether a value other than 0, 1, 2 or the missing genotype code is observed).

So perhaps not the format you are after. There is no option to export the data in native format (json data used internally). This could be added, or you could try the fairly complicated GA4GH FHIR format which includes almost all the internal data.

@cswrd
Copy link
Author

cswrd commented Aug 8, 2022

thx, I just wanted to persist the diagram with all information I've drawn. It doesn't matter which format it is atm. I understand like there no option to persist the entire diagram/all entered data, right now?

@dconlan
Copy link
Collaborator

dconlan commented Aug 9, 2022

The GA4GH FHIR format does save the majority of the data, there are some fringe cases it doesn't cover. For instance a single node can represent multiple people but this would save the node as a single person

Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Labels
None yet
Development

No branches or pull requests

2 participants