prozor

Determine minimal Protein set given list of peptide protein mappings. Various weights can be assigned to peptides (i.e. inverse peptide frequencies). Generate reverse decoy sequences

How to install:

For CRAN version (not the newest). Please use the github version.

install.packages("prozor")

This is how you install the github version.

install.packages("remotes")
remotes::install_github("protviz/prozor")

for Developers

downlod git repo. Use roxygenize2 to document new functions. Than run these 2 commands to update namespace and Rd files:

library(devtools)
document()

Example for creating a fasta file with the fgcz_create_fasta.R script

Go to fgcz-r-035.uzh.ch

ls ./fasta_db/p3071_Chlorella
more ./fasta_db/p3071_Chlorella/annotation.txt
more ./fasta_db/p3071_Chlorella/uniprot-taxonomy_3071.fasta
clear
/home/wolski/R/x86_64-pc-linux-gnu-library/3.5/prozor/script/fgcz_create_fasta.R -h
/home/wolski/R/x86_64-pc-linux-gnu-library/3.5/prozor/script/fgcz_create_fasta.R ./fasta_db/p3071_Chlorella -o /srv/www/htdocs/FASTA/

cat p3071_Chlorella_d.txt
cat p3071_Chlorella_d.txt | bfabric_save_fasta.py 3071  /srv/www/htdocs/FASTA/fgcz_3071_Chlorella_d_20200604.fasta
# 3071 is the bfabric project name