Open johnomics opened 7 years ago
Hey! I have just seen your post because I had the same problem. The key is that the script does not produces the file itself. You have to run it in this way:
python hisat2_extract_splice_sites.py path/annotation.gtf > path/splicingsites.txt
@infphilo I think this can be closed.
I am running HISAT 2.0.5 and working with the Arabidopsis thaliana annotation Araport11, specifically the GTF. This file is not processed by
hisat2_extract_splice_sites.py
. It produces no output:And running verbosely produces an error:
The GTF records look like this:
So
hisat2_extract_splice_sites.py
is failing because it ignores the last attribute (line 52):Strictly speaking, the Araport11 GTF is malformed, as every attribute should end with a semicolon, even the last (GTF format definition), so technically the script is correct.
But as the script is only interested in the
gene_id
andtranscript_id
attributes, perhapsattr
in the loop above could be checked for one of these values before it is added tovalues_dict
, rather than after the completevalues_dict
has been created, and the[:-1]
could be removed?