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callers wrapper (#33)
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* first, not tested, not working version

* run_CODEXCOV.R file removed

* CODEXCOV_wrapper.R file done

* bugfix in CODEXCOV_wrapper.R

* run_cnvcaller.R divided into functions

* bugfix

* changed parameters tables

* bugfixes in run_cnvcaller.R

* proper driver managment

* coverage table name from paramaters

* option for only Y chr

* bugfix
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@wkusmirek @mwiewior
wkusmirek authored and mwiewior committed Jul 14, 2017
1 parent e3c7a7e commit dbc5cdd
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45 changes: 45 additions & 0 deletions R/CNVCALLER.RUNNER/R/CODEXCOV_wrapper.R
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library('CODEXCOV')

#' Function Description
#'
#' Function description.
#' @param mapp_thresh
#' @param cov_thresh_from
#' @param cov_thresh_to
#' @param length_thresh_from
#' @param length_thresh_to
#' @param gc_thresh_from
#' @param gc_thresh_to
#' @param K_from
#' @param K_to
#' @param ds
#' @param lmax
#' @keywords
#' @export
#' @examples
#' run_wrapper_CODEXCOV
run_wrapper_CODEXCOV <- function(mapp_thresh,
cov_thresh_from,
cov_thresh_to,
length_thresh_from,
length_thresh_to,
gc_thresh_from,
gc_thresh_to,
K_from,
K_to,
lmax,
cov_table){
calls <- run_CODEXCOV(as.double(mapp_thresh),
strtoi(cov_thresh_from),
strtoi(cov_thresh_to),
strtoi(length_thresh_from),
strtoi(length_thresh_to),
strtoi(gc_thresh_from),
strtoi(gc_thresh_to),
strtoi(K_from),
strtoi(K_to),
strtoi(lmax),
cov_table
)
calls
}
139 changes: 99 additions & 40 deletions R/CNVCALLER.RUNNER/inst/run_cnvcaller.R
100644 → 100755
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@@ -1,48 +1,107 @@
#!/usr/bin/env Rscript
library(devtools)
#install('CODEXCOV')
library('CODEXCOV')
install('CNVCALLER.RUNNER') ### zakomentować!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
library('CNVCALLER.RUNNER')
library(optparse)

#install.packages("RJDBC",dep=TRUE)
library(RJDBC)

option_list <- list(
make_option("--id", default=1,
help="Id of parameters [default %default]"),
make_option("--mapp_thresh", default=0.9,
help="Mapping threshold for quality checking. [default %default]"),
make_option("--cov_thresh_from", default=20,
help="Coverage threshold (begin of interval) for quality checking. [default %default]"),
make_option("--cov_thresh_to", default=4000,
help="Coverage threshold (end of interval) for quality checking. [default %default]"),
make_option("--length_thresh_from", default=20,
help="Length threshold (begin of interval) for quality checking. [default %default]"),
make_option("--length_thresh_to", default=2000,
help="Length threshold (end of interval) for quality checking. [default %default]"),
make_option("--gc_thresh_from", default=20,
help="GC threshold (begin of interval) for quality checking. [default %default]"),
make_option("--gc_thresh_to", default=80,
help="GC threshold (end of interval) for quality checking. [default %default]"),
make_option("--K_from", default=1,
help="K value (begin of interval). [default %default]"),
make_option("--K_to", default=9,
help="K value (end of interval). [default %default]"),
make_option("--lmax", default=200,
help="Maximum CNV length in number of exons returned. [default %default]"),
make_option("--cov_table", default="ds",
help="Coverage table. [default %default]")
make_option("--tabName", default="public.test_parameters",
help="Parameters table. [default %default]"),
make_option("--id", default="1",
help="Parameters id. [default %default]")
)

opt <- parse_args(OptionParser(option_list=option_list))

calls <- run_CODEXCOV(opt$mapp_thresh,
opt$cov_thresh_from,
opt$cov_thresh_to,
opt$length_thresh_from,
opt$length_thresh_to,
opt$gc_thresh_from,
opt$gc_thresh_to,
opt$K_from,
opt$K_to,
opt$lmax,
opt$cov_table
)
read_parameters <- function(tabName, id, conn){
query <- paste("Select * from ", tabName, " where id = ", id, ";", sep="")
parameters <- dbGetQuery(conn, query)
caller <- parameters[1,'caller']
cov_table <- parameters[1,'cov_table']
mapp_thresh <- parameters[1,'mapp_thresh']
cov_thresh_from <- parameters[1,'cov_thresh_from']
cov_thresh_to <- parameters[1,'cov_thresh_to']
length_thresh_from <- parameters[1,'length_thresh_from']
length_thresh_to <- parameters[1,'length_thresh_to']
gc_thresh_from <- parameters[1,'gc_thresh_from']
gc_thresh_to <- parameters[1,'gc_thresh_to']
K_from <- parameters[1,'k_from']
K_to <- parameters[1,'k_to']
lmax <- parameters[1,'lmax']
return(list(caller=caller,
cov_table=cov_table,
mapp_thresh=mapp_thresh,
cov_thresh_from=cov_thresh_from,
cov_thresh_to=cov_thresh_to,
length_thresh_from=length_thresh_from,
length_thresh_to=length_thresh_to,
gc_thresh_from=gc_thresh_from,
gc_thresh_to=gc_thresh_to,
K_from=K_from,
K_to=K_to,
lmax=lmax))
}

save_calls <- function(calls, conn){
if (nrow(calls) != 0) {
for(i in 1:nrow(calls)) {
call <- calls[i,]
query <- paste("INSERT INTO TEST_CALLS (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 ('", opt$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)
}
}
}

read_coverage_table <- function(cov_table, conn){
#query <- paste("select * from ", cov_table, sep="")
query <- paste("select * from ", cov_table, " where chr='Y'", sep="")
ds <- dbGetQuery(conn, query)
colnames(ds) <- c("sample_name", "target_id", "chr", "pos_min", "pos_max", "cov_avg")
ds
}

run_caller <- function(parameters, cov_table){
if (parameters$caller == "codex"){
calls <- run_wrapper_CODEXCOV(parameters$mapp_thresh,
parameters$cov_thresh_from,
parameters$cov_thresh_to,
parameters$length_thresh_from,
parameters$length_thresh_to,
parameters$gc_thresh_from,
parameters$gc_thresh_to,
parameters$K_from,
parameters$K_to,
parameters$lmax,
cov_table
)
calls
} else if(parameters$caller == "xhmm") {
}
}

if (!file.exists("zsi-bio-cdh-hive-jdbc_2.11-0.1-assembly.jar")) {
download.file("http://zsibio.ii.pw.edu.pl:50007/repository/maven-releases/pl/edu/pw/ii/zsibio/zsi-bio-cdh-hive-jdbc_2.11/0.1/zsi-bio-cdh-hive-jdbc_2.11-0.1-assembly.jar",destfile="zsi-bio-cdh-hive-jdbc_2.11-0.1-assembly.jar")
}
drv_hive <- JDBC("com.cloudera.hiveserver2.hive.core.Hive2JDBCDriver", "./zsi-bio-cdh-hive-jdbc_2.11-0.1-assembly.jar",identifier.quote="`")
conn_hive <- dbConnect(drv_hive, "jdbc:hive2://cdh01.ii.pw.edu.pl:10000", "mwiewior", "")

if (!file.exists("postgresql-42.1.1.jar")) {
download.file("http://zsibio.ii.pw.edu.pl:50007/repository/zsi-bio-raw/common/jdbc/postgresql-42.1.1.jar",destfile="postgresql-42.1.1.jar")
}
drv_psql <- JDBC("org.postgresql.Driver", "./postgresql-42.1.1.jar",identifier.quote="`")
conn_psql <- dbConnect(drv_psql, "jdbc:postgresql://cdh00.ii.pw.edu.pl:15432/cnv-opt", "cnv-opt", "zsibio321")

parameters <- read_parameters(opt$tabName, opt$id, conn_psql)
#print(parameters)
cov_table <- read_coverage_table(parameters$cov_table, conn_hive)
#print(cov_table)
calls <- run_caller(parameters, cov_table)
#print(calls)
save_calls(calls, conn_psql)

dbDisconnect(conn_hive)
dbUnloadDriver(drv_hive)

dbDisconnect(conn_psql)
dbUnloadDriver(drv_psql)
83 changes: 0 additions & 83 deletions R/CODEXCOV/inst/run_CODEXCOV.R
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2 changes: 2 additions & 0 deletions sql/parameters_calls_model.sql
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Expand Up @@ -4,6 +4,8 @@ CREATE SCHEMA IF NOT EXISTS CNV;

CREATE TABLE IF NOT EXISTS CNV.PARAMETERS (
id SERIAL PRIMARY KEY,
caller TEXT,
cov_table TEXT,
mapp_thresh TEXT,
cov_thresh_from TEXT,
cov_thresh_to TEXT,
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42 changes: 22 additions & 20 deletions sql/parameters_calls_test_model.sql
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@@ -1,5 +1,7 @@
CREATE TABLE IF NOT EXISTS TEST_PARAMETERS (
id SERIAL PRIMARY KEY,
caller TEXT,
cov_table TEXT,
mapp_thresh TEXT,
cov_thresh_from TEXT,
cov_thresh_to TEXT,
Expand All @@ -12,26 +14,26 @@ CREATE TABLE IF NOT EXISTS TEST_PARAMETERS (
lmax TEXT
);

INSERT INTO TEST_PARAMETERS VALUES (1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11);
INSERT INTO TEST_PARAMETERS VALUES (2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12);
INSERT INTO TEST_PARAMETERS VALUES (3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13);
INSERT INTO TEST_PARAMETERS VALUES (4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14);
INSERT INTO TEST_PARAMETERS VALUES (5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15);
INSERT INTO TEST_PARAMETERS VALUES (6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16);
INSERT INTO TEST_PARAMETERS VALUES (7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17);
INSERT INTO TEST_PARAMETERS VALUES (8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18);
INSERT INTO TEST_PARAMETERS VALUES (9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19);
INSERT INTO TEST_PARAMETERS VALUES (10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20);
INSERT INTO TEST_PARAMETERS VALUES (11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21);
INSERT INTO TEST_PARAMETERS VALUES (12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22);
INSERT INTO TEST_PARAMETERS VALUES (13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23);
INSERT INTO TEST_PARAMETERS VALUES (14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24);
INSERT INTO TEST_PARAMETERS VALUES (15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25);
INSERT INTO TEST_PARAMETERS VALUES (16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26);
INSERT INTO TEST_PARAMETERS VALUES (17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27);
INSERT INTO TEST_PARAMETERS VALUES (18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28);
INSERT INTO TEST_PARAMETERS VALUES (19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29);
INSERT INTO TEST_PARAMETERS VALUES (20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30);
INSERT INTO TEST_PARAMETERS VALUES (1, 'codex', 'cnv.coverage_target', 2, 3, 4, 5, 6, 7, 8, 9, 10, 11);
INSERT INTO TEST_PARAMETERS VALUES (2, 'codex', 'cnv.coverage_target', 3, 4, 5, 6, 7, 8, 9, 10, 11, 12);
INSERT INTO TEST_PARAMETERS VALUES (3, 'codex', 'cnv.coverage_target', 4, 5, 6, 7, 8, 9, 10, 11, 12, 13);
INSERT INTO TEST_PARAMETERS VALUES (4, 'codex', 'cnv.coverage_target', 5, 6, 7, 8, 9, 10, 11, 12, 13, 14);
INSERT INTO TEST_PARAMETERS VALUES (5, 'codex', 'cnv.coverage_target', 6, 7, 8, 9, 10, 11, 12, 13, 14, 15);
INSERT INTO TEST_PARAMETERS VALUES (6, 'codex', 'cnv.coverage_target', 7, 8, 9, 10, 11, 12, 13, 14, 15, 16);
INSERT INTO TEST_PARAMETERS VALUES (7, 'codex', 'cnv.coverage_target', 8, 9, 10, 11, 12, 13, 14, 15, 16, 17);
INSERT INTO TEST_PARAMETERS VALUES (8, 'codex', 'cnv.coverage_target', 9, 10, 11, 12, 13, 14, 15, 16, 17, 18);
INSERT INTO TEST_PARAMETERS VALUES (9, 'codex', 'cnv.coverage_target', 10, 11, 12, 13, 14, 15, 16, 17, 18, 19);
INSERT INTO TEST_PARAMETERS VALUES (10, 'xhmm', 'cnv.coverage_target', 11, 12, 13, 14, 15, 16, 17, 18, 19, 20);
INSERT INTO TEST_PARAMETERS VALUES (11, 'xhmm', 'cnv.coverage_target', 12, 13, 14, 15, 16, 17, 18, 19, 20, 21);
INSERT INTO TEST_PARAMETERS VALUES (12, 'xhmm', 'cnv.coverage_target', 13, 14, 15, 16, 17, 18, 19, 20, 21, 22);
INSERT INTO TEST_PARAMETERS VALUES (13, 'xhmm', 'cnv.coverage_target', 14, 15, 16, 17, 18, 19, 20, 21, 22, 23);
INSERT INTO TEST_PARAMETERS VALUES (14, 'xhmm', 'cnv.coverage_target', 15, 16, 17, 18, 19, 20, 21, 22, 23, 24);
INSERT INTO TEST_PARAMETERS VALUES (15, 'xhmm', 'cnv.coverage_target', 16, 17, 18, 19, 20, 21, 22, 23, 24, 25);
INSERT INTO TEST_PARAMETERS VALUES (16, 'xhmm', 'cnv.coverage_target', 17, 18, 19, 20, 21, 22, 23, 24, 25, 26);
INSERT INTO TEST_PARAMETERS VALUES (17, 'xhmm', 'cnv.coverage_target', 18, 19, 20, 21, 22, 23, 24, 25, 26, 27);
INSERT INTO TEST_PARAMETERS VALUES (18, 'xhmm', 'cnv.coverage_target', 19, 20, 21, 22, 23, 24, 25, 26, 27, 28);
INSERT INTO TEST_PARAMETERS VALUES (19, 'xhmm', 'cnv.coverage_target', 20, 21, 22, 23, 24, 25, 26, 27, 28, 29);
INSERT INTO TEST_PARAMETERS VALUES (20, 'xhmm', 'cnv.coverage_target', 21, 22, 23, 24, 25, 26, 27, 28, 29, 30);

CREATE TABLE IF NOT EXISTS TEST_CALLS (
id SERIAL PRIMARY KEY,
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