I am having trouble figuring out
GFF3Writer tool from
I have a regular ensembl
gff3 file and want to extract only certain types of features.
I get an empty gff output with only one header line. What am I doing wrong?
Here is my code below.:
``` in_file = "test.gff" in_handle = open(in_file) out_file = "test.parse.gff3" out_handle = open(out_file, "w") limit_info = dict( gff_id = ["1"], # chromosome 1 gff_type = ["ncRNA"]) # get non coding RNA reader = GFFParser() writer = GFF3Writer() writer.write(reader.parse_simple(in_handle, limit_info=limit_info), out_handle) in_handle.close() out_handle.close() ```
If I try to get features using GFF.parse, the following code works with no problems:
``` for rec in GFF.parse(in_handle, limit_info=limit_info): print rec.features ```