Pipeline for targeted functional metagenomic DNA capture probe design in R
Read in the database of sequences (in FASTA format) from dbCAN (http://csbl.bmb.uga.edu/dbCAN/download/CAZyDB.07202017.fa)
library(DECIPHER)Loading required package: RSQLitefas <- "http://csbl.bmb.uga.edu/dbCAN/download/CAZyDB.07202017.fa"
store_db <- "C:/Users/faysmith/OneDrive - University of Arkansas/R Code/New DB for probe/new"
seqs <- readAAStringSet(fas)trying URL 'http://csbl.bmb.uga.edu/dbCAN/download/CAZyDB.07202017.fa'
Content type 'text/plain; charset=UTF-8' length 463121677 bytes (441.7 MB)
downloaded 441.7 MBSeqs2DB("http://csbl.bmb.uga.edu/dbCAN/download/CAZyDB.07202017.fa", "FASTA", store_db, "CAZymes")
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Added 921174 new sequences to table Seqs.
1842348 total sequences in table Seqs.
Time difference of 113.09 secsPull out the GenBank numbers and then pull out familiy names as a string
#fam_names <- stri_extract(fam_names, regex='[.[A-Z][0-9]|?]')
fam_names
[1] "|AA0" "|AA0" "|AA0" "|AA0" "|AA0" "|AA0" "|AA0" "|AA0"
[9] "|AA0" "|AA0" "|AA0" "|AA0" "|AA0" "|AA0" "|AA0" "|AA0"
[17] "|AA0" "|AA0" "|AA0" "|AA0" "|AA0" "|AA0" "|AA0" "|AA0"
[25] "|AA0" "|AA0" "|AA0" "|AA0" "|AA0" "|AA0" "|AA0" "|AA0"
[33] "|AA0" "|AA0" "|AA0" "|AA0" "|AA0" "|AA0" "|AA0" "|AA0"
[41] "|AA0" "|AA0" "|AA0" "|AA0" "|AA0" "|AA0" "|AA0" "|AA0"
[49] "|AA0" "|AA0" "|AA0" "|AA0" "|AA0" "|AA0" "|AA0" "|AA0"
[57] "|AA0" "|AA0" "|AA0" "|AA0" "|AA0" "|AA0" "|AA0" "|AA0"
[65] "|AA0" "|AA0" "|AA0" "|AA0" "|AA0" "|AA0" "|AA0" "|AA0"
[73] "|AA0" "|AA0" "|AA0" "|AA0" "|AA0" "|AA0" "|AA0" "|AA0"
[81] "|AA0" "|AA0" "|AA0" "|AA0" "|AA0" "|AA0" "|AA0" "|AA0"
[89] "|AA0" "|AA0" "|AA0" "|AA0" "|AA0" "|AA0" "|AA0" "|AA0"
[97] "|AA0" "|AA10" "|AA10" "|AA10" "|AA10" "|AA10" "|AA10" "|AA10"
[105] "|AA10" "|AA10" "|AA10" "|AA10" "|AA10" "|AA10" "|AA10" "|AA10"
[113] "|AA10|3.2.1.78" "|AA10" "|AA10" "|AA10|1.-.-.-" "|AA10" "|AA10" "|AA10" "|AA10"
[121] "|AA10" "|AA10" "|AA10" "|AA10" "|AA10" "|AA10" "|AA10" "|AA10"
[129] "|AA10" "|AA10" "|AA10" "|AA10" "|AA10" "|AA10|1.-.-.-" "|AA10" "|AA10"
[137] "|AA10" "|AA10" "|AA10" "|AA10" "|AA10" "|AA10" "|AA10" "|AA10"
[145] "|AA10" "|AA10" "|AA10" "|AA10" "|AA10" "|AA10" "|AA10" "|AA10"
[153] "|AA10" "|AA10" "|AA10" "|AA10" "|AA10" "|AA10" "|AA10" "|AA10"
[161] "|AA10" "|AA10" "|AA10|1.-.-.-" "|AA10" "|AA10" "|AA10|1.-.-.-" "|AA10" "|AA10"
[169] "|AA10" "|AA10" "|AA10" "|AA10" "|AA10" "|AA10" "|AA10" "|AA10|1.-.-.-"
[177] "|AA10|1.-.-.-" "|AA10" "|AA10" "|AA10" "|AA10" "|AA10" "|AA10|1.-.-.-" "|AA10"
[185] "|AA10" "|AA10" "|AA10" "|AA10" "|AA10" "|AA10" "|AA10" "|AA10"
[193] "|AA10" "|AA10" "|AA10" "|AA10" "|AA10" "|AA10" "|AA10" "|AA10"
[201] "|AA10" "|AA10" "|AA10" "|AA10" "|AA10" "|AA10" "|AA10" "|AA10"
[209] "|AA10" "|AA10" "|AA10" "|AA10" "|AA10" "|AA10" "|AA10" "|AA10"
[217] "|AA10" "|AA10" "|AA10" "|AA10" "|AA10" "|AA10" "|AA10" "|AA10"
[225] "|AA10" "|AA10" "|AA10" "|AA10" "|AA10" "|AA10" "|AA10" "|AA10"
[233] "|AA10" "|AA10" "|AA10" "|AA10" "|AA10" "|AA10" "|AA10" "|AA10"
[241] "|AA10" "|AA10" "|AA10" "|AA10" "|AA10" "|AA10" "|AA10" "|AA10"
[249] "|AA10" "|AA10" "|AA10" "|AA10" "|AA10" "|AA10" "|AA10" "|AA10"
[257] "|AA10" "|AA10" "|AA10" "|AA10" "|AA10" "|AA10" "|AA10" "|AA10"
[265] "|AA10" "|AA10" "|AA10" "|AA10" "|AA10" "|AA10|1.-.-.-" "|AA10|1.-.-.-" "|AA10"
[273] "|AA10" "|AA10" "|AA10" "|AA10" "|AA10" "|AA10" "|AA10" "|AA10"
[281] "|AA10" "|AA10" "|AA10" "|AA10" "|AA10" "|AA10" "|AA10" "|AA10"
[289] "|AA10" "|AA10" "|AA10" "|AA10" "|AA10" "|AA10" "|AA10" "|AA10"
[297] "|AA10" "|AA10" "|AA10" "|AA10" "|AA10" "|AA10" "|AA10" "|AA10"
[305] "|AA10" "|AA10" "|AA10" "|AA10" "|AA10" "|AA10" "|AA10" "|AA10"
[313] "|AA10" "|AA10" "|AA10" "|AA10" "|AA10" "|AA10" "|AA10" "|AA10"
[321] "|AA10|1.-.-.-" "|AA10" "|AA10" "|AA10" "|AA10" "|AA10" "|AA10" "|AA10"
[329] "|AA10" "|AA10" "|AA10" "|AA10" "|AA10" "|AA10" "|AA10" "|AA10"
[337] "|AA10" "|AA10" "|AA10" "|AA10" "|AA10" "|AA10" "|AA10" "|AA10"
[345] "|AA10" "|AA10" "|AA10" "|AA10" "|AA10" "|AA10" "|AA10" "|AA10"
[353] "|AA10" "|AA10" "|AA10" "|AA10" "|AA10" "|AA10" "|AA10" "|AA10"
[361] "|AA10" "|AA10" "|AA10" "|AA10" "|AA10" "|AA10" "|AA10" "|AA10"
[369] "|AA10" "|AA10" "|AA10" "|AA10" "|AA10" "|AA10" "|AA10" "|AA10"
[377] "|AA10" "|AA10" "|AA10" "|AA10" "|AA10" "|AA10" "|AA10" "|AA10"
[385] "|AA10" "|AA10" "|AA10" "|AA10" "|AA10" "|AA10" "|AA10" "|AA10"
[393] "|AA10" "|AA10" "|AA10" "|AA10" "|AA10" "|AA10" "|AA10" "|AA10"
[401] "|AA10" "|AA10" "|AA10" "|AA10" "|AA10" "|AA10" "|AA10" "|AA10"
[409] "|AA10" "|AA10" "|AA10" "|AA10" "|AA10" "|AA10" "|AA10" "|AA10"
[417] "|AA10" "|AA10" "|AA10" "|AA10" "|AA10" "|AA10" "|AA10" "|AA10"
[425] "|AA10" "|AA10" "|AA10" "|AA10" "|AA10" "|AA10" "|AA10" "|AA10"
[433] "|AA10" "|AA10" "|AA10" "|AA10" "|AA10" "|AA10" "|AA10" "|AA10"
[441] "|AA10" "|AA10" "|AA10" "|AA10" "|AA10" "|AA10" "|AA10" "|AA10"
[449] "|AA10" "|AA10" "|AA10" "|AA10" "|AA10" "|AA10" "|AA10" "|AA10"
[457] "|AA10" "|AA10" "|AA10" "|AA10" "|AA10" "|AA10" "|AA10" "|AA10"
[465] "|AA10" "|AA10" "|AA10" "|AA10" "|AA10" "|AA10" "|AA10" "|AA10"
[473] "|AA10" "|AA10" "|AA10" "|AA10" "|AA10" "|AA10" "|AA10" "|AA10"
[481] "|AA10" "|AA10" "|AA10" "|AA10" "|AA10" "|AA10" "|AA10" "|AA10"
[489] "|AA10" "|AA10" "|AA10" "|AA10" "|AA10" "|AA10" "|AA10" "|AA10"
[497] "|AA10" "|AA10" "|AA10" "|AA10" "|AA10" "|AA10" "|AA10" "|AA10"
[505] "|AA10" "|AA10" "|AA10" "|AA10" "|AA10" "|AA10" "|AA10" "|AA10"
[513] "|AA10" "|AA10" "|AA10" "|AA10" "|AA10" "|AA10" "|AA10" "|AA10"
[521] "|AA10" "|AA10" "|AA10" "|AA10" "|AA10" "|AA10" "|AA10" "|AA10"
[529] "|AA10" "|AA10" "|AA10" "|AA10" "|AA10" "|AA10" "|AA10" "|AA10"
[537] "|AA10" "|AA10" "|AA10" "|AA10" "|AA10" "|AA10" "|AA10" "|AA10"
[545] "|AA10" "|AA10" "|AA10" "|AA10" "|AA10" "|AA10" "|AA10" "|AA10"
[553] "|AA10" "|AA10" "|AA10" "|AA10" "|AA10" "|AA10" "|AA10" "|AA10"
[561] "|AA10" "|AA10" "|AA10" "|AA10" "|AA10" "|AA10" "|AA10" "|AA10"
[569] "|AA10" "|AA10" "|AA10" "|AA10" "|AA10" "|AA10" "|AA10" "|AA10"
[577] "|AA10" "|AA10" "|AA10" "|AA10" "|AA10" "|AA10" "|AA10" "|AA10"
[585] "|AA10" "|AA10" "|AA10" "|AA10" "|AA10" "|AA10" "|AA10" "|AA10"
[593] "|AA10" "|AA10" "|AA10" "|AA10" "|AA10" "|AA10" "|AA10" "|AA10"
[601] "|AA10" "|AA10" "|AA10" "|AA10" "|AA10" "|AA10" "|AA10" "|AA10"
[609] "|AA10" "|AA10" "|AA10" "|AA10" "|AA10" "|AA10" "|AA10" "|AA10"
[617] "|AA10" "|AA10" "|AA10" "|AA10" "|AA10" "|AA10" "|AA10" "|AA10"
[625] "|AA10" "|AA10" "|AA10" "|AA10" "|AA10" "|AA10" "|AA10" "|AA10"
[633] "|AA10" "|AA10" "|AA10" "|AA10" "|AA10" "|AA10" "|AA10" "|AA10"
[641] "|AA10" "|AA10" "|AA10" "|AA10" "|AA10" "|AA10" "|AA10" "|AA10"
[649] "|AA10" "|AA10" "|AA10" "|AA10" "|AA10" "|AA10" "|AA10" "|AA10"
[657] "|AA10" "|AA10" "|AA10" "|AA10" "|AA10" "|AA10" "|AA10" "|AA10"
[665] "|AA10" "|AA10" "|AA10" "|AA10" "|AA10" "|AA10" "|AA10" "|AA10"
[673] "|AA10" "|AA10" "|AA10" "|AA10" "|AA10" "|AA10" "|AA10" "|AA10"
[681] "|AA10" "|AA10" "|AA10" "|AA10" "|AA10" "|AA10" "|AA10" "|AA10"
[689] "|AA10" "|AA10" "|AA10" "|AA10" "|AA10" "|AA10" "|AA10" "|AA10"
[697] "|AA10" "|AA10" "|AA10" "|AA10" "|AA10" "|AA10" "|AA10" "|AA10"
[705] "|AA10" "|AA10" "|AA10" "|AA10" "|AA10" "|AA10" "|AA10" "|AA10"
[713] "|AA10" "|AA10" "|AA10" "|AA10" "|AA10" "|AA10" "|AA10" "|AA10"
[721] "|AA10" "|AA10" "|AA10" "|AA10" "|AA10" "|AA10" "|AA10" "|AA10"
[729] "|AA10" "|AA10" "|AA10" "|AA10" "|AA10" "|AA10" "|AA10" "|AA10"
[737] "|AA10" "|AA10" "|AA10" "|AA10" "|AA10" "|AA10" "|AA10" "|AA10"
[745] "|AA10" "|AA10" "|AA10" "|AA10" "|AA10" "|AA10" "|AA10" "|AA10"
[753] "|AA10" "|AA10" "|AA10" "|AA10" "|AA10" "|AA10" "|AA10" "|AA10"
[761] "|AA10" "|AA10" "|AA10" "|AA10" "|AA10" "|AA10" "|AA10" "|AA10"
[769] "|AA10" "|AA10" "|AA10" "|AA10" "|AA10" "|AA10" "|AA10" "|AA10"
[777] "|AA10" "|AA10" "|AA10" "|AA10" "|AA10" "|AA10" "|AA10" "|AA10"
[785] "|AA10" "|AA10" "|AA10" "|AA10" "|AA10" "|AA10" "|AA10" "|AA10"
[793] "|AA10" "|AA10" "|AA10" "|AA10" "|AA10" "|AA10" "|AA10" "|AA10"
[801] "|AA10" "|AA10" "|AA10" "|AA10" "|AA10" "|AA10" "|AA10" "|AA10"
[809] "|AA10" "|AA10" "|AA10" "|AA10" "|AA10" "|AA10" "|AA10" "|AA10"
[817] "|AA10" "|AA10" "|AA10" "|AA10" "|AA10" "|AA10" "|AA10" "|AA10"
[825] "|AA10" "|AA10" "|AA10" "|AA10" "|AA10" "|AA10" "|AA10" "|AA10"
[833] "|AA10" "|AA10" "|AA10" "|AA10" "|AA10" "|AA10" "|AA10" "|AA10"
[841] "|AA10" "|AA10" "|AA10" "|AA10" "|AA10" "|AA10" "|AA10" "|AA10"
[849] "|AA10" "|AA10" "|AA10" "|AA10" "|AA10" "|AA10" "|AA10" "|AA10"
[857] "|AA10" "|AA10" "|AA10" "|AA10" "|AA10" "|AA10" "|AA10" "|AA10"
[865] "|AA10" "|AA10" "|AA10" "|AA10" "|AA10" "|AA10" "|AA10" "|AA10"
[873] "|AA10" "|AA10" "|AA10" "|AA10" "|AA10" "|AA10" "|AA10" "|AA10"
[881] "|AA10" "|AA10" "|AA10" "|AA10" "|AA10" "|AA10" "|AA10" "|AA10"
[889] "|AA10" "|AA10" "|AA10" "|AA10" "|AA10" "|AA10" "|AA10" "|AA10"
[897] "|AA10" "|AA10" "|AA10" "|AA10" "|AA10" "|AA10" "|AA10" "|AA10"
[905] "|AA10" "|AA10" "|AA10" "|AA10" "|AA10" "|AA10" "|AA10" "|AA10"
[913] "|AA10" "|AA10" "|AA10" "|AA10" "|AA10" "|AA10" "|AA10" "|AA10"
[921] "|AA10" "|AA10" "|AA10" "|AA10" "|AA10" "|AA10" "|AA10" "|AA10"
[929] "|AA10" "|AA10" "|AA10" "|AA10" "|AA10" "|AA10" "|AA10" "|AA10"
[937] "|AA10" "|AA10" "|AA10" "|AA10" "|AA10" "|AA10" "|AA10" "|AA10"
[945] "|AA10" "|AA10" "|AA10" "|AA10" "|AA10" "|AA10" "|AA10" "|AA10"
[953] "|AA10" "|AA10" "|AA10" "|AA10" "|AA10" "|AA10" "|AA10" "|AA10"
[961] "|AA10" "|AA10" "|AA10" "|AA10" "|AA10" "|AA10" "|AA10" "|AA10"
[969] "|AA10" "|AA10" "|AA10" "|AA10" "|AA10" "|AA10" "|AA10" "|AA10"
[977] "|AA10" "|AA10" "|AA10" "|AA10" "|AA10" "|AA10" "|AA10" "|AA10"
[985] "|AA10" "|AA10" "|AA10" "|AA10" "|AA10" "|AA10" "|AA10" "|AA10"
[993] "|AA10" "|AA10" "|AA10" "|AA10" "|AA10" "|AA10" "|AA10" "|AA10"
[ reached getOption("max.print") -- omitted 918938 entries ]Seperating sequences by subfamily
AA <- SearchDB(AA0_db, type = "AAStringSet", nameBy = "row_names")
Search Expression:
select row_names, sequence from _Seqs where row_names in (select row_names from Seqs)
AAStringSet of length: 100
Time difference of 0.21 secs**Note: Need to write in code to extract the subfamily names from the inital file, then use that list to automate this process
Add2DB(clus, AA0_db)
Expression:
update Seqs set cluster = :cluster where row_names = :row_names
Added to table Seqs: "cluster".
Time difference of 0.21 secsconSeqs <- IdConsensus(path_cazy_nuc, type = "AAStringSet", colName = "cluster", verbose = TRUE)
Couldn't set synchronous mode: file is not a database
Use `synchronous` = NULL to turn off this warning.Error in result_create(conn@ptr, statement) : file is not a databaseNow for the array design and validation steps
probes <- DesignArray(conSeqs, maxPermutations=2, numProbes = 20,verbose = TRUE)
Error in DesignArray(conSeqs, maxPermutations = 2, numProbes = 20, verbose = TRUE) :
myDNAStringSet must be a DNAStringSet.Try to use the GenBank numbers to call NCBI nucleotide sequences:
Seqs2DB(cazy_nuc, "DNAStringSet", "C:/Users/faysmith/OneDrive - University of Arkansas/R Code/New DB for probe/nuc_cazy", "Nuc_Cazymes")
Couldn't set synchronous mode: file is not a database
Use `synchronous` = NULL to turn off this warning.Error in result_create(conn@ptr, statement) : file is not a database