EricR86
commented
7 years ago Original comment by Eric Roberts (Bitbucket: ericr86, GitHub: ericr86).
This has been fixed on commit 793a5e054ad65bba8ec3dd79cb5cd618d16cee0e. This will be also fixed in an upcoming release along with a lot of other major improvements.
Unfortunately there's no good way of dealing with this issue immediately. If you're comfortable with editing code, you can try the code changes listed in that commit. Alternatively you can clone the respository from here and simply run "pip install . --upgrade" from the directory where you cloned genomedata archive. If you don't have mecurial you can also simply download a snapshot of the latest code from https://hoffmangroup.github.io/genomedata-bitbucket-backup/#!/hoffmanlab/genomedata/downloads/ and run "pip install . --upgrade" from that directory as well.
Hope that helps!
Original report (archived issue) by Anonymous.
Hello! I wanted to start by saying that I really like the API of this program, which is why I'm a little disappointed that I'm having trouble getting it working.
I'm attempting to run the genome-load-seq operation, as all I really need from this is the sequence retrieval. However, when I pass in the command genomedata-load-seq -d ./genomearchive ./TriTrypDB-32_LmajorFriedlin_Genome.fasta, I'm met with an error reporting an AssertionError on the statement assert seqfile_type in frozenset(["agp", "fasta"])
This is strange, as I looked in the file _load_seq.py and it seems that seqfile_type is actually an argument passed to the load_seq python method, and is set with a default argument. However, when I added the 'print(seqfile_type)' line just before the assert line and run the command again, I find that None is printed just before the error.
Nothing in the method before that changes the attribute so far as I can tell, so what's happening?
You can reach me at mullencr@miamioh.edu, I don't have an account here.