How To Convert Plink Ped(Or Bed) File Format In To Peas Software Format?

Question

[User 0422]

Hi All,

I need to convert my already existing plink ped file format in to PEAS format. Please help.

format of PEAS input should be following:

link text

Answer 1

[Martin A Hansen]

I don't really see how you can have the relevant information for that format in a BED file. Paste some line so I can have a look. But you can most likely do the conversion with Biopieces www.biopieces.org) either using read_bed or read_tab:

read_bed -i file.bed |
rename_keys -k Q_ID,SNPID |
rename_keys -k S_ID,Chrom |
rename_keys -k S_BEG,Position |
write_tab -ck SNPID,Chrom,Position,AlleleState,Strand,SampleID1,SampleID2,SampleID3 -x

or something down those lines ...

Cheers,

Martin

Answer 2

[User 0422]

Plink file also contains bed and bim file.

The thing is that one needs to recode the alleles from binary to additive and then convert it in to ABHU format, then transpose it taking binary markers name from bim file and sample id from fam file.

But then how to do it automatically? i mean by commands?

I hope this explains.

thanks

[Pierre Lindenbaum]

this should be a comment, not a new answer.

[User 0422]

Sorry! I didn't know that.

[Martin A Hansen]

The is not making much sense: Plink, bed, bim, and fam files... Show an example of the input data along with the requested output data - and with explanations of the different steps. Then I am prette sure someone will come up with an answer.