Commit 180823e3 authored by Etienne Rifa's avatar Etienne Rifa
Browse files

check DB file

parent f2d6e495
Pipeline #37422 passed with stage
in 12 seconds
...@@ -36,6 +36,8 @@ idtaxa_assign_fasta_fun <- function(fasta, id_db, output = "./assign_fasta/", co ...@@ -36,6 +36,8 @@ idtaxa_assign_fasta_fun <- function(fasta, id_db, output = "./assign_fasta/", co
dna <- RemoveGaps(dna) dna <- RemoveGaps(dna)
db_list <- unlist(strsplit(id_db,",")) db_list <- unlist(strsplit(id_db,","))
if(any(!file.exists(c(db_list)))){stop("One or more reference DB unreachable. Check path(s).")}
taxid_list=vector("list", length(db_list)+1) taxid_list=vector("list", length(db_list)+1)
for (i in 1:length(db_list)){ for (i in 1:length(db_list)){
db_file <- db_list[i] db_file <- db_list[i]
...@@ -53,7 +55,7 @@ idtaxa_assign_fasta_fun <- function(fasta, id_db, output = "./assign_fasta/", co ...@@ -53,7 +55,7 @@ idtaxa_assign_fasta_fun <- function(fasta, id_db, output = "./assign_fasta/", co
Fannot = list() Fannot = list()
for (seq_name in names(dna)){ for (seq_name in names(dna)){
flog.debug(seq_name) flog.debug(seq_name)
# create list # create list
L1=list(); L2=list() L1=list(); L2=list()
for (i in 1:length(db_list)){ for (i in 1:length(db_list)){
......
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