Re: migrate input file converter
Peter Beerli
thanks for your info, I am sure Migrate users love to see such a
converter (I cc the migrate support google group),
and I am sure you will get some feedback from microsatellite data
users. Concerning the loci names: I hope to rewrite parts of the data
reading
module thi summer so that migrate can take loci names and also can use
information about linkage among loci, currently I experiment with some
simple syntax
that allows mixture of dna and msat loci but there are still some
unsolved things, an example could be something like this:
(ldh=s1230 mpi_2=b1 str2=b1) str3=a1
[the loci ldh, mpi_2, and str2 are linked, the loci with s are
sequence, with b are brownian, and with a are infinite allele markers
etc.
thanks
Peter
On Mar 16, 2009, at 10:06 AM, Markus Riester wrote:
> Hi Peter,
>
> I wrote a small pedigree reconstruction tool and I chose as input
> format your
> migrate/phylip format with a few additional columns. I saw in your
> mailing
> list that your users have a similar hard time in generating input
> files as
> mine (had, I hope), so maybe you are interested in this tool here:
>
> http://www.bioinf.uni-leipzig.de/Software/FRANz/CSV_Import.html
>
> If you are interested, just let me know. You'd only have to remove
> the options
> for the new columns and the pedigree tab. I've also added optional
> locus names to the
> input format. Would be something like
>
> 1 3 / SIMPSONS
> L1
> L2
> L3
> 7 Springfield
> Grampa 1 1920 ? M 110/100 200/208 ?/?
> Homer 1 1950 ? M 110/170 200/210 300/302
> Bart 1 1982 ? M 110/120 200/212 302/304
> Lisa 1 1980 ? F 140/170 200/218 302/306
> Maggie 1 1988 ? F 110/140 210/212 300/304
> Marge 1 1952 ? F 120/140 212/218 ?/306
> Flanders 1 ? ? ? 150/160 214/220 300/?
>
> Best regards,
> Markus
>
>
> Markus Riester
> Bioinformatics email: mar...@bioinf.uni-leipzig.de
> University of Leipzig phone: +49 341 97 16685
> Haertelstrasse 16-18 fax : +49 341 97 16679
> D-04107 Leipzig, Germany www : http://www.bioinf.uni-leipzig.de/~markus