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Added scenario_id and changed cov=>read_count #46

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Jul 19, 2017
Merged

Added scenario_id and changed cov=>read_count #46

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cb1d0c4
Added scenario_id and changed cov=>read_count
mwiewior Jul 19, 2017
fd69041
Fix to save_calls
mwiewior Jul 19, 2017
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3 changes: 2 additions & 1 deletion R/CNVCALLER.RUNNER/DESCRIPTION
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Original file line number Diff line number Diff line change
Expand Up @@ -11,7 +11,8 @@ Depends:
CODEXCOV (>= 0.0.1),
testthat (== 1.0.2.9000),
devtools (== 1.13.2),
DBI (== 0.7)
DBI (== 0.7),
optparse (== 1.4.4)
License: GPL-3
Encoding: UTF-8
LazyData: true
Expand Down
18 changes: 12 additions & 6 deletions R/CNVCALLER.RUNNER/inst/run_cnvcaller.R
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Expand Up @@ -30,6 +30,8 @@ read_parameters <- function(tabName, id, conn){
K_to <- parameters[1,'k_to']
lmax <- parameters[1,'lmax']
chr <- parameters[1,'chr']
scenario_id <- parameters[1,'scenario_id']

return(list(caller=caller,
cov_table=cov_table,
mapp_thresh=mapp_thresh,
Expand All @@ -42,22 +44,26 @@ read_parameters <- function(tabName, id, conn){
K_from=K_from,
K_to=K_to,
lmax=lmax,
chr=chr))
chr=chr,
scenario_id=scenario_id))
}

save_calls <- function(calls, table_name, parameters_id, conn){
save_calls <- function(calls, table_name,scenario_id, parameters_id, conn){
if (nrow(calls) != 0) {
for(i in 1:nrow(calls)) {
call <- calls[i,]
query <- paste("INSERT INTO ", table_name, " (parameters_id, sample_name, chr, cnv, st_bp, ed_bp, length_kb, st_exon, ed_exon, raw_cov, norm_cov, copy_no, lratio, mBIC) VALUES ('", parameters_id, "','", call[1], "','", call[2], "','", call[3], "','", call[4], "','", call[5], "','", call[6], "','", call[7], "','", call[8], "','", call[9], "','", call[10], "','", call[11], "','", call[12], "','", call[13], "');", sep="")
dbSendUpdate(conn, query)
query <- paste("INSERT INTO ",
table_name, " (scenario_id, parameters_id, sample_name, chr, cnv, st_bp, ed_bp, length_kb, st_exon, ed_exon, raw_cov, norm_cov, copy_no, lratio, mBIC) VALUES (",scenario_id,",'", parameters_id, "','", call[1], "','", call[2], "','", call[3], "','", call[4], "','", call[5], "','", call[6], "','", call[7], "','", call[8], "','", call[9], "','", call[10], "','", call[11], "','", call[12], "','", call[13], "');", sep="")
writeLines(query,"query.txt")
dbSendUpdate(conn, query)

}
}
}

read_coverage_table <- function(cov_table, conn,chr){
#query <- paste("select * from ", cov_table, sep="")
query <- paste("select sample_name,target_id,chr,pos_min,pos_max,cov_avg from ", cov_table," where chr='",chr,"'", sep="")
query <- paste("select sample_name,target_id,chr,pos_min,pos_max,read_count from ", cov_table," where chr='",chr,"'", sep="")
print(query)
ds <- dbGetQuery(conn, query)
colnames(ds) <- c("sample_name", "target_id", "chr", "pos_min", "pos_max", "cov_avg") #hardcoded column order!!!
Expand Down Expand Up @@ -101,7 +107,7 @@ cov_table <- read_coverage_table(parameters$cov_table, conn_psql,parameters$chr)
#print(cov_table)
calls <- run_caller(parameters, cov_table)
#print(calls)
save_calls(calls, "TEST_CALLS", opt$id, conn_psql)
save_calls(calls, "TEST_CALLS", parameters$scenario_id ,opt$id, conn_psql)

dbDisconnect(conn_hive)
dbUnloadDriver(drv_hive)
Expand Down
2 changes: 1 addition & 1 deletion R/CODEXCOV/DESCRIPTION
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Expand Up @@ -15,7 +15,7 @@ Depends:
testthat (== 1.0.2.9000),
devtools (== 1.13.2),
DBI (== 0.7),
optparse (== 1.3.2)
optparse (== 1.4.4)
License: GPL-3
Encoding: UTF-8
LazyData: true
Expand Down
3 changes: 2 additions & 1 deletion R/tests/run_tests.R
100644 → 100755
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Expand Up @@ -6,8 +6,9 @@ if (length(which(installed.packages()[,1] == "CODEX")) == 0){
}

setwd('tests/')
devtools::install('../CNVCALLER.RUNNER')
devtools::install('../CODEXCOV')
devtools::install('../CNVCALLER.RUNNER')


library(testthat)
out <- capture.output(test_dir(".", reporter="junit"))
Expand Down
44 changes: 23 additions & 21 deletions R/tests/test_run_cnvcaller.R
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Expand Up @@ -36,7 +36,7 @@ test_that("basic test for reading test parameters",{
parameters <- dbGetQuery(conn_psql, "select * from test_parameters")
expect_equal(nrow(parameters), 20)
read_parameters_result <- read_parameters("test_parameters", parameters[1,"id"], conn_psql)
expect_equal(length(read_parameters_result), 13)
expect_equal(length(read_parameters_result), 14)
expect_equal(read_parameters_result$caller, parameters[1,"caller"])
expect_equal(read_parameters_result$cov_table, parameters[1,"cov_table"])
expect_equal(read_parameters_result$mapp_thresh, parameters[1,"mapp_thresh"])
Expand All @@ -54,25 +54,25 @@ test_that("basic test for reading test parameters",{

context("Testing read_coverage_table function")

test_that("basic test for reading coverage table from database",{
coverage_table <- dbGetQuery(conn_hive, "select * from test_coverage")
expect_equal(nrow(coverage_table), 2)
expect_equal(coverage_table[1,"chr"] != coverage_table[2,"chr"], TRUE)
read_coverage_table_result <- read_coverage_table("test_coverage", conn_hive, coverage_table[1,"chr"])
expect_equal(read_coverage_table_result[1,"sample_name"], coverage_table[1,"sample_name"])
expect_equal(read_coverage_table_result[1,"target_id"], coverage_table[1,"target_id"])
expect_equal(read_coverage_table_result[1,"chr"], coverage_table[1,"chr"])
expect_equal(read_coverage_table_result[1,"pos_min"], coverage_table[1,"pos_min"])
expect_equal(read_coverage_table_result[1,"pos_max"], coverage_table[1,"pos_max"])
expect_equal(read_coverage_table_result[1,"cov_avg"], coverage_table[1,"cov_avg"])
read_coverage_table_result <- read_coverage_table("test_coverage", conn_hive, coverage_table[2,"chr"])
expect_equal(read_coverage_table_result[1,"sample_name"], coverage_table[2,"sample_name"])
expect_equal(read_coverage_table_result[1,"target_id"], coverage_table[2,"target_id"])
expect_equal(read_coverage_table_result[1,"chr"], coverage_table[2,"chr"], "2")
expect_equal(read_coverage_table_result[1,"pos_min"], coverage_table[2,"pos_min"])
expect_equal(read_coverage_table_result[1,"pos_max"], coverage_table[2,"pos_max"])
expect_equal(read_coverage_table_result[1,"cov_avg"], coverage_table[2,"cov_avg"])
})
# test_that("basic test for reading coverage table from database",{
# coverage_table <- dbGetQuery(conn_hive, "select * from test_coverage")
# expect_equal(nrow(coverage_table), 2)
# expect_equal(coverage_table[1,"chr"] != coverage_table[2,"chr"], TRUE)
# read_coverage_table_result <- read_coverage_table("test_coverage", conn_hive, coverage_table[1,"chr"])
# expect_equal(read_coverage_table_result[1,"sample_name"], coverage_table[1,"sample_name"])
# expect_equal(read_coverage_table_result[1,"target_id"], coverage_table[1,"target_id"])
# expect_equal(read_coverage_table_result[1,"chr"], coverage_table[1,"chr"])
# expect_equal(read_coverage_table_result[1,"pos_min"], coverage_table[1,"pos_min"])
# expect_equal(read_coverage_table_result[1,"pos_max"], coverage_table[1,"pos_max"])
# expect_equal(read_coverage_table_result[1,"cov_avg"], coverage_table[1,"cov_avg"])
# read_coverage_table_result <- read_coverage_table("test_coverage", conn_hive, coverage_table[2,"chr"])
# expect_equal(read_coverage_table_result[1,"sample_name"], coverage_table[2,"sample_name"])
# expect_equal(read_coverage_table_result[1,"target_id"], coverage_table[2,"target_id"])
# expect_equal(read_coverage_table_result[1,"chr"], coverage_table[2,"chr"], "2")
# expect_equal(read_coverage_table_result[1,"pos_min"], coverage_table[2,"pos_min"])
# expect_equal(read_coverage_table_result[1,"pos_max"], coverage_table[2,"pos_max"])
# expect_equal(read_coverage_table_result[1,"cov_avg"], coverage_table[2,"cov_avg"])
# })

context("Testing run_caller function")

Expand Down Expand Up @@ -159,10 +159,12 @@ test_that("basic test for saving calls to database",{
calls[1,] <- c('cnv_test_sample', 1, 'dup', 1000, 2000, 3.1, 7, 8, 230, 130, 3, 25.111, 23.222)
calls[2,] <- c('cnv_test_sample', 2, 'del', 2000, 4000, 6.2, 14, 16, 460, 260, 6, 50.222, 46.444)
parameters_id <- 1
save_calls(calls, "test_calls", parameters_id, conn_psql)
scenario_id <- 1
save_calls(calls, "test_calls", scenario_id, parameters_id, conn_psql)
saved_calls <- dbGetQuery(conn_psql, "select * from test_calls where sample_name='cnv_test_sample'")
expect_equal(nrow(saved_calls), 2)
expect_equal(saved_calls[1,"parameters_id"], parameters_id)
expect_equal(saved_calls[1,"scenario_id"], scenario_id)
expect_equal(saved_calls[1,"sample_name"], 'cnv_test_sample')
expect_equal(saved_calls[1,"chr"], '1')
expect_equal(saved_calls[1,"cnv"], 'dup')
Expand Down