meuGenoma v1.3
Antonio C B Oliveira
September 2008
meuGenoma is a Python program to match genomes sequenced by 23andMe and/or deCODEme with the
information in SNPedia.
The following files are used:
meugenoma.txt
A one line text file with two
strings: <name> <pop>.
<name>
is a string that identifies a person. <pop> is
the population identifier used in SNPedia {CEU,HCB,JPT,YRI}
<name>_23andme.txt
The tab-delimited file
downloaded from 23andme including all
genotype calls
<name>_decodeme.csv
The comma separated file
downloaded from deCODEme
including all genotype calls
meuGenoma read SNPedia and generate auxiliary files in subdirectory meuGenomaTemp. This
process might take a few hours depending on the speed of the internet
connection and might fail due to time out. If this happens, the program should
be executed again and it will automatically restart from where it was
stopped. In order to use the latest
information from SNPedia the subdirectory meuGenomaTemp should be deleted. Storing a local copy of
the information from SNPedia saves time when running meuGenoma for more than one person. The program
works with files from both 23andMe and deCODEme or with a single file from one of them.
Two output files are produced:
<name>_<yyyy-mm-dd>.csv
One line for each SNP containing the
information obtained from SNPedia plus the genotypes
from 23andMe and deCODEme.
The SNP name is a hyperlink to the corresponding entry in SNPedia. Using the macro in this
spreadsheet, convenient genome reports (e.g.
xls pdf) can be produced. The report includes useful
information as follows:
[>]
indicates a new SNP or modified SNPedia
information as compared to the previous run of the program.
[<>] genotypes
provided by 23andMe and deCODEme
differ
[?] difficult
to interpret genotypes because we do not know the strand orientation of SNPedia alleles.
[??] alleles
in SNPedia are incompatible with genotypes provided
by 23andMe or deCODEme
[>>]
genotype is not the most common variant according to frequency data in SNPedia
<name>_dump.txt
Contains
all relevant information, saved to enable the program to detect differences in
a subsequent run.
meuGenoma is
available as a Windows executable, Python source code and demo input files
in meuGenoma.zip .
www.barbosadeoliveira.com/meuGenoma
2008/09/21