Open roushrsh opened 8 months ago
Hi @roushrsh 👋
Can you please provide the version of mokapot that you're using and please provide the full log? You should be able to find the version with:
import mokapot
print(mokapot.__version__)
To enable detailed logging within your python session, you can add:
import logging
logging.basicConfig(level=logging.INFO)
I'll do my best to answer your questions without this information for now though.
For protein-level confidence estimates, mokapot internally digests proteins from a FASTA file; the CSV files that you provided above are not supported. The protein grouping is performed based on all theoretical digested peptides for a protein sequence, so I would generally advise letting mokapot handle it. However, if you really want to provide your own sequences, you can do so by initializing the mokapot.proteins.Proteins
object directly:
However, you'll need to provide a mapping of target proteins to decoy proteins, a mapping of peptides to their generating proteins, and set of all shared peptides, in addition to other information. I strongly recommend using a FASTA file.
To my knowledge, the error you're seeing does not originate from the mokapot codebase, so I can't provide much insight without seeing the full log.
Edit/Update: Version is 0.10.0, but I had the same problem on the older version.
I made the protein structure and all the parts:
proteins = Proteins(peptide_map=dictionaryPepts, protein_map=dictionaryProts, shared_peptides= dict(zip([],[])), has_decoys=True, decoy_prefix='decoy_')
but when I use add_proteins
the Protein confidence estimates enabled
remains False
and nothing happens. How can I add them properly?
Even loading from fasta and replacing the parts with mine seems to do nothing.
I got the 'fasta' version to work though, thanks!
The approach you took should work with the Proteins
object should work. Can you create a tiny reproducible example to share?
Glad the fasta is working for you!
I'm trying to run mokapot on this file (TestAX.pin): https://drive.google.com/file/d/1T4447c9Y24hx3qHla_cW55HEg4A_XEuW/view?usp=sharing
Which works great to give peptide confidence:
I've then shuffled the peptides myself to make decoys which I would like to provide.
I've tried keeping them either their own row: https://drive.google.com/file/d/1mP-nsqDAER2JcxoUxHc1H6Ed5qx6SCH7/view?usp=sharing or grouped into one string so mokapot does the digesting (can I have this not done?) https://drive.google.com/file/d/1_A-q9rqytLr9-YYrW6UD69jrtf0APaXA/view?usp=sharing
I do :
then run
mokapot.brew(psms)
again.Regardless, in case 1)
and I get
and in case 2)
and I get the error:
Any suggestions?
Thanks