miRTop / mirtop

command lines tool to annotate miRNAs with a standard mirna/isomir naming
https://mirtop.readthedocs.org
MIT License
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Integrate `join` sub-command to join multiple GFF files #31

Closed lpantano closed 6 years ago

lpantano commented 6 years ago

The main function that does this is already coded here:

https://github.com/miRTop/mirtop/blob/dev/mirtop/gff/merge.py#L3

dts is a dict where keys are sample name that could be the basename of the GFF file that are the input to the command, and values is nested dicts with the following structure:

dicts['colum0']['column4'] = [list1, list2, listn]

Each listn contains 4 elements: [IDU,NA,EXPRESSION, GFF_LINE]

Each value represent a variable inside attribute column as explained here:https://github.com/miRTop/incubator/blob/master/format/definition.md , except for the last one that is the entire GFF line.

Noted NA could be an empty value, that is not needed for this specific functionality.

Basically, it's needed a function to read each GFF to have the structure above explained, and the input that to the function merge.

Header needsto me modify to add the:

If this is unclear, just think a way to join two GFF, for instance from: https://github.com/miRTop/mirtop/blob/dev/data/examples/gff/correct_file.gff

Final function need to be tested and added as a unit test in https://github.com/miRTop/mirtop/blob/dev/test/test_functions.py

Thanks

lpantano commented 6 years ago

this was implemented in the in gff subcommand.