Delete the read-tide-index command and make generate-peptides capable of reading from either a FASTA file or a Tide index. Make sure it still outputs the peptide-to-protein mapping, like read-tide-index does.
Specifically, the following changes should be made to generate-peptides:
The required parameter can be either an index or a FASTA file.
All of the tide-index options related to peptide properties, amino acid modifications, decoy database generation and enzymatic digestion should be included.
The output file should contain the peptide sequence, its mass, and the list of protein IDs. Note that, if it makes the code more compact, this same file could be produced for the peptide-list=T option to tide-index. (Currently, that option doesn't include the protein IDs in the output.)
An optional decoy output file should also be created, based on whether decoys were requested.
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The attached patch adds the mass to the generate-peptides output. I tried to also add the protein IDs, but the different peptide data structures were confusing. There is some commented-out code in there from read-tide-index that is a start toward doing this. Kaipo, can you finish this up?
I don't think it's important that generate-peptides be able to read an existing index. It can just work from fasta (as it currently does). Thus, once we get the protein IDs in there, we can just delete the read-tide-index app and close this issue.
Specifically, the following changes should be made to generate-peptides:
The attached patch adds the mass to the generate-peptides output. I tried to also add the protein IDs, but the different peptide data structures were confusing. There is some commented-out code in there from read-tide-index that is a start toward doing this. Kaipo, can you finish this up?
I don't think it's important that generate-peptides be able to read an existing index. It can just work from fasta (as it currently does). Thus, once we get the protein IDs in there, we can just delete the read-tide-index app and close this issue.