clintval
Request - handling nonstandard tables
We have a sample sheet where we've added a custom section which is a headered table (along the lines of the [Data] section. It would be handy to be able to parse such a section using the sample-sheet library. (Currently, the library assumes that the custom section must be a dictionary of key-value pairs).
A made-up example of such a section follows: [Animals],, Name,Species,Status Benji,Dog,Good Sparky,Cat,Aloof Sparky,Bird,Sleeping
That's a good observation and should be supported! It may be a backwards incompatible feature request but I think an important one to better honor the specification:
Additional user-defined sections may be added to the Sample Sheet, as long as they adhere to the Sample Sheet formatting rules described above. They also cannot be named the same as sections defined by Illumina, and must be placed between the Header section and the Data section. These sections will be ignored by Illumina software, but can be used to store additional information for record keeping purposes or for processing in third-party software. Illumina may add to the standard Sample Sheet sections in the future without regard for naming conflicts with sections used by third-party software.
I'm a little slow in its release but have been developing a better API for this library and am taking all of these requests into consideration. Thank you!
