dib-lab/dib-mmetsp

Code to generate re-assemblies of the Marine Microbial Eukaryote Transcriptome Sequencing Project (MMETSP)

dib-mmetsp's Issues

Is there a table mapping taxonomy to each of the protein sequences?

I'm looking for a table that maps the protein sequences to taxonomy lineage strings. Is this available?

Hard coded Paths

bash-4.1$ python main.py
Directory created: /work/databases/bio/mmetsp_new/mmetsp/
Traceback (most recent call last):
File "main.py", line 2, in
import getdata as data
File "/work/databases/bio/mmetsp_new/dib-MMETSP/getdata.py", line 149, in
for datafile in datafiles:
NameError: name 'datafiles' is not defined

Is there a way to extract the assembly sequence based on your annotation file?

Dear ljcohen,

I'm impressed by this work! So happy that I found it.
I'm mostly focus on the polyketide synthase of dinoflagellate, and I had also found ketosynthase gene in your annotation files.
However, the row name in the annotation is different from the header id inside each assembly file. Is there any way to find the connection between the row name and header id in the fasta file?
I will appreciate to hear your reply!

Best

Shaolin