GSE parser used to parse the GSE soft file and generate expression table with phenotype headed.
parse_GSE_soft -l <GSE soft format file>
parse_GSE_soft -p <platform name or platform index> <GSE soft format file>
-l List the platforms in the GSE dataset.
-p Setting the platform index or platform id.
-h Print help message.
make
The GSE dataset may include several platforms, inorder to generate table like format data, the platform should be given first. So the first step is to investigate the platform list of the GSE dataset. The platforms information can be draw by:
# parse_GSE_soft -l <sotf format GSE file>
./parse_GSE_soft -l ./GSE41813_family.soft # list platform
> 0: Murine 15K long oligo array version 2.0 (3 samples)
Then generate the formated data table by assigning platform id.
# parse_GSE_soft -p <platform id> <sotf format GSE file>
./parse_GSE_soft -p 0 ./GSE41813_family.soft | head
Or
make test
Output format refer to output.tsv.