Closed zhuchcn closed 1 year ago
lydiayliu
commented
1 year ago Why splitFiltered but not split_filtered to match the rest of the formats?
Can you also try with a sample where split_fasta = true; filter_fasta = true but no expression table is provided? there should be nothing outputted if in split_filtered. I also don't think there should be anything outputted in split?
zhuchcn
commented
1 year ago Why splitFiltered but not split_filtered to match the rest of the formats?
Done! Here is what looks like right now with merge_variant_noncoding = both, split_fasta = true, and filter_fasta = true
test/output/test-integration-merge/call-NonCanonicalPeptide-1.0.0/UCLA0001/moPepGen-0.11.3/output/
├── decoy
│ ├── UCLA0001_merged_peptides_filtered_encode_decoy.fasta
│ ├── UCLA0001_merged_peptides_filtered_encode_decoy.fasta.dict
│ ├── UCLA0001_split_circRNA_encode_decoy.fasta
│ ├── UCLA0001_split_circRNA_encode_decoy.fasta.dict
│ ├── UCLA0001_split_circRNA-RNAEditingSite_encode_decoy.fasta
│ ├── UCLA0001_split_circRNA-RNAEditingSite_encode_decoy.fasta.dict
│ ├── UCLA0001_split_Fusion_encode_decoy.fasta
│ ├── UCLA0001_split_Fusion_encode_decoy.fasta.dict
│ ├── UCLA0001_split_Fusion-Noncoding_encode_decoy.fasta
│ ├── UCLA0001_split_Fusion-Noncoding_encode_decoy.fasta.dict
│ ├── UCLA0001_split_gINDEL-circRNA_encode_decoy.fasta
│ ├── UCLA0001_split_gINDEL-circRNA_encode_decoy.fasta.dict
│ ├── UCLA0001_split_gINDEL_encode_decoy.fasta
│ ├── UCLA0001_split_gINDEL_encode_decoy.fasta.dict
│ ├── UCLA0001_split_gSNP_encode_decoy.fasta
│ ├── UCLA0001_split_gSNP_encode_decoy.fasta.dict
│ ├── UCLA0001_split_Noncoding_encode_decoy.fasta
│ ├── UCLA0001_split_Noncoding_encode_decoy.fasta.dict
│ ├── UCLA0001_split_RNAEditingSite_encode_decoy.fasta
│ └── UCLA0001_split_RNAEditingSite_encode_decoy.fasta.dict
├── encode
│ ├── UCLA0001_merged_peptides_filtered_encode.fasta
│ ├── UCLA0001_merged_peptides_filtered_encode.fasta.dict
│ ├── UCLA0001_split_circRNA_encode.fasta
│ ├── UCLA0001_split_circRNA_encode.fasta.dict
│ ├── UCLA0001_split_circRNA-RNAEditingSite_encode.fasta
│ ├── UCLA0001_split_circRNA-RNAEditingSite_encode.fasta.dict
│ ├── UCLA0001_split_Fusion_encode.fasta
│ ├── UCLA0001_split_Fusion_encode.fasta.dict
│ ├── UCLA0001_split_Fusion-Noncoding_encode.fasta
│ ├── UCLA0001_split_Fusion-Noncoding_encode.fasta.dict
│ ├── UCLA0001_split_gINDEL-circRNA_encode.fasta
│ ├── UCLA0001_split_gINDEL-circRNA_encode.fasta.dict
│ ├── UCLA0001_split_gINDEL_encode.fasta
│ ├── UCLA0001_split_gINDEL_encode.fasta.dict
│ ├── UCLA0001_split_gSNP_encode.fasta
│ ├── UCLA0001_split_gSNP_encode.fasta.dict
│ ├── UCLA0001_split_Noncoding_encode.fasta
│ ├── UCLA0001_split_Noncoding_encode.fasta.dict
│ ├── UCLA0001_split_RNAEditingSite_encode.fasta
│ └── UCLA0001_split_RNAEditingSite_encode.fasta.dict
├── split_filtered
│ ├── UCLA0001_split_circRNA.fasta
│ ├── UCLA0001_split_circRNA-RNAEditingSite.fasta
│ ├── UCLA0001_split_Fusion.fasta
│ ├── UCLA0001_split_Fusion-Noncoding.fasta
│ ├── UCLA0001_split_gINDEL-circRNA.fasta
│ ├── UCLA0001_split_gINDEL.fasta
│ ├── UCLA0001_split_gSNP.fasta
│ ├── UCLA0001_split_Noncoding.fasta
│ └── UCLA0001_split_RNAEditingSite.fasta
├── UCLA0001_merged_peptides.fasta
├── UCLA0001_merged_peptides_filtered.fasta
├── UCLA0001_merged_peptides_filtered_summary.txt
├── UCLA0001_merged_peptides_summary.txt
├── UCLA0001_noncoding_peptides_filtered.fasta
├── UCLA0001_variant_peptides.fasta
├── UCLA0001_variant_peptides_filtered.fasta
├── UCLA0001_variant_peptides_filtered_summary.txt
└── UCLA0001_variant_peptides_summary.txtAs discussed, we want:
lydiayliu
commented
1 year ago filter_fasta = TRUE), in decoy / encode directories have split and split_filtered subdirectoriesfilter_fasta = TRUE)filter_fasta = TRUE)zhuchcn
commented
1 year ago We want to call encodeFasta and decoyFasta on both the unfiltered and filtered fasta. And we currently allow uses to turn of the encode/decoy functions. Should we get ride of params.encode_fasta and params.decoy_fasta? So they will always be called. This just makes the logic simple a little bit.
lydiayliu
commented
1 year ago No for CCLE I specifically turn off encode_fasta and decoy_fasta because I literally don't need all the encode and decoy fastas flotting around... they can't be used as input to merge
zhuchcn
commented
1 year ago I think I implemented the way you want. There are too many output files so the complete tree output probably won't fit here. I put the directory structure for fasta, gvf and parser entrypoint to the file below on the cluster so you can take a look.
/hot/user/czhu/pipeline-call-NoncanonicalPeptide/tree_output.txt
I also changed the parameter from merge_variant_noncoding to database_processing_modes which I think is more reasonable.
lydiayliu
commented
1 year ago We are almost there!! Commenting on the output file
For fasta entry point or process_unfiltered_fasta = FALSE, we also don't need to output the unfiltered merged.fasta
├── UCLA0001_merged_peptides.fasta
├── UCLA0001_merged_peptides_filtered.fasta
├── UCLA0001_merged_peptides_filtered_summary.txt
├── UCLA0001_noncoding_peptides_filtered.fasta
├── UCLA0001_variant_peptides_filtered.fasta
├── UCLA0001_variant_peptides_filtered_summary.txt
└── variant_summary.txt Although I suspect that it is easier to output it than not output it... It doesn't hurt but is a bit of waste as a duplicated file.
Otherwise, now noncoding_peptides_filtered.fasta would only be outputted as part of split right?
zhuchcn
commented
1 year ago In the last commit, I added a tag of 'variant_only' to the summarizeFasta output from the 'plain' workflow. Also updated the 'tree_output.txt'. Let me know what you think!
lydiayliu
commented
1 year ago It is a bit long winded but I think it works.
├── UCLA0001_variant_peptides.fasta
├── UCLA0001_variant_peptides_filtered.fasta
├── UCLA0001_variant_peptides_filtered_summary.txt
├── UCLA0001_variant_peptides_filtered_variant_only_summary.txt
└── UCLA0001_variant_peptides_summary.txtI don't like how the unfiltered summary is just called _variant_peptides_summary.txt but it matches with the fasta. Let's just keep it like this!
zhuchcn
commented
1 year ago I don't like how the unfiltered summary is just called _variant_peptides_summary.txt but it matches with the fasta. Let's just keep it like this!
That's what I was thinking, too, so they can match up.
splitFastaoutput dir is changed to splitFiltered if 'filterFasta' is used, otherwise still 'filter'.Example output below with
merge_variant_noncodingset to 'both'.Closes #80
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