Author: Witek Wolski
Date: 2021-12-07

# Creating Target Decoy Databases

#### Witek Wolski

#### 2021-12-07

Using the package prozor for creating standardized fasta. The package can be used to:

     * merge several fasta files into a single fasta file
     * add reverse sequences to the fasta file.
     * add contaminants to the fasta file

# Contaminants

This package provides two sets of typical contaminant proteins and peptides, one with and one without contaminants of human origin, which can be accessed by the functions `loadContaminantsFasta` and `loadContaminantsNoHumanFasta`. At the FGCZ we always are adding one of those two contaminant files to the database. To databases already containing human proteins, we will add the `ContaminantsNoHumanFasta`. The contaminants are easy to distinguish from other entries thanks to the `zz|FGCZCont` prefix.

    library(prozor)
    head(names(loadContaminantsFasta2021()))

    ## [1] "zz|fgczContaminants2021|" "zz|Y-FGCZCont00001|"
    ## [3] "zz|Y-FGCZCont00002|"      "zz|Y-FGCZCont00003|"
    ## [5] "zz|Y-FGCZCont00004|"      "zz|Y-FGCZCont00005|"

    length(loadContaminantsFasta2021())

    ## [1] 499

    length(loadContaminantsFasta2021(noHuman = TRUE))

    ## [1] 350

# Creating a fasta protein amino acid sequence database for searching.

To merge several fasta databases into a single file place them into a single folder and give the folder the name of the database. At the FGCZ the database name starts with the project number e.g. `p1000` a consecutive number e.g. `db1` and descriptive name `example,i.e.`p1000_db1_example`.

Add to the folder also an annotation.txt file. The annotation file should contain a single line formatted like a fasta entry header with the following conent: `aa|p<project_number>_<database_name>|<YYYYMMDD> <detailed_description>`.

Example : `AA|p1000_db1_example|20180119_Example https://github.com/protViz/prozor`

The package provides an example of such a folder with the fasta files. Based on this folder a database can be created.

    databasedirectory = system.file("p1000_db1_example",package = "prozor")
    #databasedirectory <- file.path(find.package("prozor"), "p1000_db1_example")
    dbname <- basename(databasedirectory)
    fasta <- grep("fasta", dir(databasedirectory),value = TRUE)
    files1 <- file.path(databasedirectory,fasta)
    annot <- grep("annotation",dir(databasedirectory), value = TRUE)
    annotation <- readLines(file.path(databasedirectory,annot))
    annotation

    ## [1] "AA|p2569_db1_mouse_phosPXS|20171029_UNIPROT http://www.uniprot.org/proteomes/UP000000589"

## Create non decoy database

    resDB <- createDecoyDB(files1, useContaminants = loadContaminantsFasta2021(),
                           annot = annotation, revLab = NULL)

    ## reading db :C:/Users/wolski/AppData/Local/Temp/RtmpMjltbO/Rinst9b83493886/prozor/p1000_db1_example/Annotation_allSeq.fasta.gz

    ## reading db :C:/Users/wolski/AppData/Local/Temp/RtmpMjltbO/Rinst9b83493886/prozor/p1000_db1_example/Annotation_canSeq.fasta.gz

    length(resDB)

    ## [1] 1954

Based on the directory name we build the name of the fasta file adding the current date.

    dirname(databasedirectory)

    ## [1] "C:/Users/wolski/AppData/Local/Temp/RtmpMjltbO/Rinst9b83493886/prozor"

    xx <- file.path(dirname(databasedirectory), paste(dbname,"_",format(Sys.time(), "%Y%m%d"),".fasta" ,sep = ""))
    print(xx)

    ## [1] "C:/Users/wolski/AppData/Local/Temp/RtmpMjltbO/Rinst9b83493886/prozor/p1000_db1_example_20211207.fasta"

    writeFasta(resDB, file=xx)

## Create decoy database

To add a decoy database, using reverse sequences specify the `revLab` parameter in the `createDecoyDB` function. The resulting database will be twice as long as the non-decoy database.

    resDBDecoy <- createDecoyDB(files1,
                                useContaminants = loadContaminantsFasta2021(),
                                annot = annotation,
                                revLab = "REV_")

    ## reading db :C:/Users/wolski/AppData/Local/Temp/RtmpMjltbO/Rinst9b83493886/prozor/p1000_db1_example/Annotation_allSeq.fasta.gz

    ## reading db :C:/Users/wolski/AppData/Local/Temp/RtmpMjltbO/Rinst9b83493886/prozor/p1000_db1_example/Annotation_canSeq.fasta.gz

    resDBDecoy[[length(resDBDecoy) - 1]]

    ## [1] "ADAFGLESLKQHAEAYDAFFADEDAAYKDVLPRFVPDSLLAKDSPLQLLGEKEGSLLETFYSNDFILPNSTWPGEFGSREKHAAGITHGGSLAVIDQDTLGMAKGFVDRLHDSGKTADPLRGEPPPEPKDERGPHFPVEPGGTVEVAVVGALQYFDAYSLIPFEAKLPELLRVAIDLGNNASHALEAPHKITGFPGGTKTGKDFTGASHWALRLMLPACRKEAIIGRLKKKAKEVAKQYDASVTPYSKGM"
    ## attr(,"name")
    ## [1] "REV_zz|Y-FGCZCont00497|"
    ## attr(,"Annot")
    ## [1] ">REV_zz|Y-FGCZCont00497|  tr|A0A445I1L0|A0A445I1L0_GLYSO L-ascorbate peroxidase OS=Glycine soja OX=3848 GN=D0Y65_029960 PE=3 SV=1"
    ## attr(,"class")
    ## [1] "SeqFastaAA"

    length(resDBDecoy)

    ## [1] 3907

    sum(duplicated(names(resDBDecoy)))

    ## [1] 764

    sum(duplicated(resDBDecoy))

    ## [1] 764

    dbname_decoy <- unlist(strsplit(dbname,"_"))
    dbname_decoy <- paste(c(dbname_decoy[1],"d",dbname_decoy[2:length(dbname_decoy)]),collapse = "_")
    dbname_decoy

    ## [1] "p1000_d_db1_example"

    xx <- file.path(dirname(databasedirectory), paste(dbname_decoy,"_",format(Sys.time(), "%Y%m%d"),".fasta" ,sep = ""))
    print(xx)

    ## [1] "C:/Users/wolski/AppData/Local/Temp/RtmpMjltbO/Rinst9b83493886/prozor/p1000_d_db1_example_20211207.fasta"

    writeFasta(resDBDecoy, file = xx)

# Session Info

    sessionInfo()

    ## R version 4.1.1 (2021-08-10)
    ## Platform: x86_64-w64-mingw32/x64 (64-bit)
    ## Running under: Windows 10 x64 (build 19044)
    ##
    ## Matrix products: default
    ##
    ## locale:
    ## [1] LC_COLLATE=C
    ## [2] LC_CTYPE=English_United States.1252
    ## [3] LC_MONETARY=English_United States.1252
    ## [4] LC_NUMERIC=C
    ## [5] LC_TIME=English_United States.1252
    ##
    ## attached base packages:
    ## [1] stats     graphics  grDevices utils     datasets  methods   base
    ##
    ## other attached packages:
    ## [1] prozor_0.3.1
    ##
    ## loaded via a namespace (and not attached):
    ##  [1] Rcpp_1.0.7            bslib_0.3.1           compiler_4.1.1
    ##  [4] pillar_1.6.4          jquerylib_0.1.4       tools_4.1.1
    ##  [7] digest_0.6.28         docopt_0.7.1          jsonlite_1.7.2
    ## [10] evaluate_0.14         lifecycle_1.0.1       tibble_3.1.4
    ## [13] lattice_0.20-44       AhoCorasickTrie_0.1.2 pkgconfig_2.0.3
    ## [16] rlang_0.4.11          Matrix_1.3-4          yaml_2.2.1
    ## [19] xfun_0.26             fastmap_1.1.0         stringr_1.4.0
    ## [22] knitr_1.36            sass_0.4.0            vctrs_0.3.8
    ## [25] hms_1.1.1             ade4_1.7-18           grid_4.1.1
    ## [28] R6_2.5.1              fansi_0.5.0           rmarkdown_2.11
    ## [31] tzdb_0.1.2            purrr_0.3.4           readr_2.0.1
    ## [34] seqinr_4.2-8          magrittr_2.0.1        htmltools_0.5.2
    ## [37] ellipsis_0.3.2        MASS_7.3-54           utf8_1.2.2
    ## [40] stringi_1.7.4         crayon_1.4.2