Closed lpantano closed 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:
dts
sample name
dicts['colum0']['column4'] = [list1, list2, listn]
Each listn contains 4 elements: [IDU,NA,EXPRESSION, GFF_LINE]
listn
[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.
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
this was implemented in the in gff subcommand.
gff
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 aresample 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